hydrophobicity

Summary

Summary: The property of substances of reduced affinity for or repulsion of water.

Top Publications

  1. ncbi Recognition of transmembrane helices by the endoplasmic reticulum translocon
    Tara Hessa
    Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 433:377-81. 2005
  2. ncbi Bilayer thickness and membrane protein function: an energetic perspective
    Olaf S Andersen
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA
    Annu Rev Biophys Biomol Struct 36:107-30. 2007
  3. ncbi Interfaces and the driving force of hydrophobic assembly
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 437:640-7. 2005
  4. ncbi Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases
    Amol P Pawar
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Mol Biol 350:379-92. 2005
  5. ncbi The principle of gating charge movement in a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:42-8. 2003
  6. pmc YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
    Xue Song Zhang
    Artie McFerrin Department of Chemical Engineering, Texas A and M University, College Station, TX 77843 3122, USA
    J Bacteriol 189:3051-62. 2007
  7. ncbi Hydrophobicity: an ancient damage-associated molecular pattern that initiates innate immune responses
    Seung Yong Seong
    Ghost Lab, Laboratory of Cellular and Molecular Immunology, National Insstitute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Nat Rev Immunol 4:469-78. 2004
  8. ncbi X-ray structure of a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:33-41. 2003
  9. pmc Relationship between expression of the family of M proteins and lipoteichoic acid to hydrophobicity and biofilm formation in Streptococcus pyogenes
    Harry S Courtney
    Department of Medicine, University of Tennessee, Memphis, Tennessee, United States of America
    PLoS ONE 4:e4166. 2009
  10. pmc Role of peptide hydrophobicity in the mechanism of action of alpha-helical antimicrobial peptides
    Yuxin Chen
    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Biomolecular Structure MS 8101, P O Box 6511, Aurora, CO 80045, USA
    Antimicrob Agents Chemother 51:1398-406. 2007

Detail Information

Publications339 found, 100 shown here

  1. ncbi Recognition of transmembrane helices by the endoplasmic reticulum translocon
    Tara Hessa
    Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
    Nature 433:377-81. 2005
    ..of designed polypeptide segments, we have determined the basic features of this code, including a 'biological' hydrophobicity scale...
  2. ncbi Bilayer thickness and membrane protein function: an energetic perspective
    Olaf S Andersen
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA
    Annu Rev Biophys Biomol Struct 36:107-30. 2007
    ..The lipid bilayer thus becomes an allosteric regulator of membrane function...
  3. ncbi Interfaces and the driving force of hydrophobic assembly
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 437:640-7. 2005
    ..Despite the basic principles underlying the hydrophobic effect being qualitatively well understood, only recently have theoretical developments begun to explain and quantify many features of this ubiquitous phenomenon...
  4. ncbi Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases
    Amol P Pawar
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    J Mol Biol 350:379-92. 2005
    ....
  5. ncbi The principle of gating charge movement in a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:42-8. 2003
    ..Our findings lead us to conclude that the voltage-sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore...
  6. pmc YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
    Xue Song Zhang
    Artie McFerrin Department of Chemical Engineering, Texas A and M University, College Station, TX 77843 3122, USA
    J Bacteriol 189:3051-62. 2007
    ..Based on our findings, we propose that this locus be named bhsA, for influencing biofilm through hydrophobicity and stress response.
  7. ncbi Hydrophobicity: an ancient damage-associated molecular pattern that initiates innate immune responses
    Seung Yong Seong
    Ghost Lab, Laboratory of Cellular and Molecular Immunology, National Insstitute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Nat Rev Immunol 4:469-78. 2004
  8. ncbi X-ray structure of a voltage-dependent K+ channel
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 423:33-41. 2003
    ..Flexible hinges suggest that the voltage-sensor paddles move in response to membrane voltage changes, carrying their positive charge across the membrane...
  9. pmc Relationship between expression of the family of M proteins and lipoteichoic acid to hydrophobicity and biofilm formation in Streptococcus pyogenes
    Harry S Courtney
    Department of Medicine, University of Tennessee, Memphis, Tennessee, United States of America
    PLoS ONE 4:e4166. 2009
    b>Hydrophobicity is an important attribute of bacteria that contributes to adhesion and biofilm formation...
  10. pmc Role of peptide hydrophobicity in the mechanism of action of alpha-helical antimicrobial peptides
    Yuxin Chen
    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Biomolecular Structure MS 8101, P O Box 6511, Aurora, CO 80045, USA
    Antimicrob Agents Chemother 51:1398-406. 2007
    ..J. Biol. Chem. 2005, 280:12316-12329, 2005) was used as the framework to study the effects of peptide hydrophobicity on the mechanism of action of antimicrobial peptides...
  11. ncbi Membrane-protein topology
    Gunnar von Heijne
    Center for Biomembrane Research and Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, SE 10691 Stockholm
    Nat Rev Mol Cell Biol 7:909-18. 2006
    ....
  12. ncbi Factors associated with adherence to and biofilm formation on polystyrene by Stenotrophomonas maltophilia: the role of cell surface hydrophobicity and motility
    Arianna Pompilio
    Laboratory of Clinical Microbiology, Department of Biomedical Sciences, G D Annunzio University of Chieti Pescara, Chieti, Italy
    FEMS Microbiol Lett 287:41-7. 2008
    ..correlation between adherence to and formation of biofilm on polystyrene, and cell surface properties such as hydrophobicity and motility...
  13. pmc Positioning of proteins in membranes: a computational approach
    Andrei L Lomize
    College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109 1065, USA
    Protein Sci 15:1318-33. 2006
    ..Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/...
  14. pmc Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region
    Gilad Ofek
    Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Virol 84:2955-62. 2010
    ..0001) were found between virus neutralization and CDR H3 hydrophobicity, as defined by predicted free energies of transfer from water to a lipid bilayer interface or to octanol...
  15. ncbi Effects of drug hydrophobicity on liposomal stability
    David R Khan
    Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA
    Chem Biol Drug Des 71:3-7. 2008
    ....
  16. ncbi Structure, stability, and chaperone function of alphaA-crystallin: role of N-terminal region
    Madhuchhanda Kundu
    Protein Chemistry Laboratory, Department of Chemistry, Bose Institute, 93 1 A P C Road, Kolkata 700 009, India
    Biopolymers 86:177-92. 2007
    ..The role of thermodynamic stability, oligomeric size, and surface hydrophobicity in chaperone function is discussed...
  17. pmc Probing the mechanisms of fibril formation using lattice models
    Mai Suan Li
    Institute of Physics, Polish Academy of Sciences, Al Lotnikow 32 46, 02 668 Warsaw, Poland
    J Chem Phys 129:175101. 2008
    ..The detailed analysis shows that elements of the three popular models, namely, nucleation and growth, templated assembly, and nucleated conformational conversion are present at various stages of fibril assembly...
  18. ncbi Effects of subinhibitory concentrations of amikacin and ciprofloxacin on the hydrophobicity and adherence to epithelial cells of uropathogenic Escherichia coli strains
    Dorota Wojnicz
    Department of Biology and Medical Parasitology, Medical University of Wroclaw, Mikulicza Radeckiego 9, 50 367 Wroclaw, Poland
    Int J Antimicrob Agents 29:700-4. 2007
    The effect of subinhibitory concentrations of amikacin and ciprofloxacin on the hydrophobicity and adherence to uroepithelial cells of Escherichia coli strains was investigated...
  19. ncbi An analysis of protein domain linkers: their classification and role in protein folding
    Richard A George
    Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill NW7 1AA, UK
    Protein Eng 15:871-9. 2002
    ..Based on these results we have constructed a linker database intended for the rational design of linkers for domain fusion, which can be accessed via the Internet at http://mathbio.nimr.mrc.ac.uk...
  20. ncbi Modifications of hydrophobicity, in vitro adherence and cellular aggregation of Streptococcus mutans by Helichrysum italicum extract
    A Nostro
    Dipartimento Farmaco Biologico, Sezione Microbiologia, Facoltà di Farmacia Università di Messina, Villaggio Annunziata, Italy
    Lett Appl Microbiol 38:423-7. 2004
    ..The purpose of the present study was to examine whether sublethal concentrations of Helichrysum italicum extract could affect some of the cariogenic properties of Streptococcus mutans...
  21. ncbi Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity?
    Aubrey D N J de Grey
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Bioessays 27:436-46. 2005
    ..of these cases reveals that they are in fact wholly consistent with the hypothesis that code disparity and hydrophobicity are much more powerful barriers to functional gene transfer than any other...
  22. ncbi Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    Buyong Ma
    Basic Research Program, SAIC Frederick Inc, Center for Cancer Research, Nanobiology Program, NCI Frederick, Frederick MD 21702, USA
    Curr Opin Chem Biol 10:445-52. 2006
    ..Under kinetic control, the final protein aggregations are the outcome of maximizing the van der Waals interactions between side chains and backbone hydrogen bonds...
  23. ncbi Influence of curli expression by Escherichia coli 0157:H7 on the cell's overall hydrophobicity, charge, and ability to attach to lettuce
    Renee R Boyer
    Department of Food Science and Technology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    J Food Prot 70:1339-45. 2007
    ..In this study, the effect of curli expression on the cell's overall hydrophobicity, charge, and ability to attach to cut and whole iceberg lettuce surfaces was examined...
  24. ncbi Surface hydrophobicity of Aspergillus nidulans conidiospores and its role in pellet formation
    Jens Dynesen
    Center for Process Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, 2800 Lyngby, Denmark
    Biotechnol Prog 19:1049-52. 2003
    ..To study the influence of the fungal conidiospore wall hydrophobicity on conidiospore agglomeration, pellet formation of an A...
  25. ncbi Structure and mechanism of the lactose permease of Escherichia coli
    Jeff Abramson
    Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK
    Science 301:610-5. 2003
    ..We propose a possible mechanism for lactose/proton symport (co-transport) consistent with both the structure and a large body of experimental data...
  26. pmc Regulation of sodium channel function by bilayer elasticity: the importance of hydrophobic coupling. Effects of Micelle-forming amphiphiles and cholesterol
    Jens A Lundbaek
    Novo Nordisk A S, Måløv, Denmark
    J Gen Physiol 123:599-621. 2004
    ..These results provide strong support for the notion that bilayer-protein hydrophobic coupling allows the bilayer elastic properties to regulate membrane protein function...
  27. ncbi Structures of the toll-like receptor family and its ligand complexes
    Mi Sun Jin
    Department of Chemistry and Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 373 1 Kusong Dong, Yusong gu, Daejeon, 305 701, Korea
    Immunity 29:182-91. 2008
    ..This observation suggests the hypothesis that dimerization of the extracellular domains forces the intracellular TIR domains to dimerize, and this initiates signaling by recruiting intracellular adaptor proteins...
  28. ncbi Position-dependent hydrophobicity of the antimicrobial magainin peptide affects the mode of peptide-lipid interactions and selective toxicity
    Tomoya Tachi
    Graduate School of Biostudies, Kyoto University, Sakyo ku, Kyoto 606 8501, Japan
    Biochemistry 41:10723-31. 2002
    ..to zwitterionic phospholipids constituting the outer leaflets of mammalian cell membranes because of the low hydrophobicity of the peptide [Matsuzaki, K. (1999) Biochim. Biophys. Acta 1462, 1-10]...
  29. ncbi Yeast and bacteria cell hydrophobicity and hydrocarbon biodegradation in the presence of natural surfactants: rhamnolipides and saponins
    E Kaczorek
    Institute of Chemical Technology and Engineering, Poznan University of Technology, Pl M Skłodowskiej Curie 2, 60 965 Poznan, Poland
    Bioresour Technol 99:4285-91. 2008
    ..study concerns the relation between hydrocarbon biodegradation in the presence of natural surfactants and cell hydrophobicity resulting from the use of these surfactants...
  30. ncbi Rationalization of the effects of mutations on peptide and protein aggregation rates
    Fabrizio Chiti
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 424:805-8. 2003
    ..chains can be correlated to a remarkable extent with changes in simple physicochemical properties such as hydrophobicity, secondary structure propensity and charge...
  31. ncbi Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle
    Zakhar O Shenkarev
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
    FEBS J 273:2658-72. 2006
    ..The antimicrobial and hemolytic properties of cyclotides, along with the relative hydrophobicity of the peptides, point to the biological membrane as a target for cyclotides...
  32. ncbi Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern
    Tong Liang Zhang
    College of Information Sciences and Technology, Donghua University, China
    J Theor Biol 250:186-93. 2008
    ..In this study, based on the concept of PseAA composition, the approximate entropy and hydrophobicity pattern of a protein sequence are used to characterize the PseAA components...
  33. pmc The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity
    Michelle A Emrick
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 103:18101-6. 2006
    ..Thus, an N-terminal hydrophobic cluster that includes the gatekeeper forms a novel structural unit, which functions to maintain the "off" state of ERK2 before cell signal activation...
  34. ncbi The effect of Piper betle and Psidium guajava extracts on the cell-surface hydrophobicity of selected early settlers of dental plaque
    Fathilah Abdul Razak
    Department of Oral Biology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
    J Oral Sci 48:71-5. 2006
    ..that treatment of the early plaque settlers with 1 mg/ml extract of Psidium guajava reduced the cell-surface hydrophobicity of Strep. sanguinis, Strep. mitis and Actinomyces sp. by 54.1%, 49.9% and 40.6%, respectively...
  35. ncbi Cell surface hydrophobicity of Candida albicans isolated from elder patients undergoing denture-related candidosis
    Roberta Diavana de Souza
    Laboratory of Stomatology, Centre of Biological and Health Sciences, Pontifical Catholic University of Parana, Curitiba, Brazil
    Gerodontology 26:157-61. 2009
    ..Candida albicans cells with higher cell surface hydrophobicity (CSH) rates, so-called hydrophobic, present higher adhesion success in different host tissues than cells with ..
  36. ncbi Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications
    P Fickers
    Centre Wallon de Biologie Industrielle, Service de Technologie Microbienne, Universite de Liege, Boulevard du Rectorat, Batiment 40, B 4000 Liege, Belgium
    FEMS Yeast Res 5:527-43. 2005
    ..These examples demonstrate distinct advantages of Y. lipolytica for their use in bioconversion reactions of biotechnologically interesting hydrophobic substrates...
  37. pmc Characterization of signal that directs C-tail-anchored proteins to mammalian mitochondrial outer membrane
    Chika Horie
    Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812 8582, Japan
    Mol Biol Cell 13:1615-25. 2002
    ..The structural characteristics of the signal thus defined were also confirmed with mammalian C-tail-anchored protein OMP25...
  38. ncbi Keeping G proteins at bay: a complex between G protein-coupled receptor kinase 2 and Gbetagamma
    David T Lodowski
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Science 300:1256-62. 2003
    ....
  39. ncbi Modulating the therapeutic activity of nanoparticle delivered paclitaxel by manipulating the hydrophobicity of prodrug conjugates
    Steven M Ansell
    Celator Pharmaceuticals Corporation, Vancouver, BC, Canada
    J Med Chem 51:3288-96. 2008
    A series of paclitaxel prodrugs designed for formulation in lipophilic nanoparticles are described. The hydrophobicity of paclitaxel was increased by conjugating a succession of increasingly hydrophobic lipid anchors to the drug using ..
  40. ncbi Hydrophobicity of mucosal surface and its relationship to gut barrier function
    Xiaofa Qin
    Department of Surgery, UMDNJ New Jersey Medical School, Newark, New Jersey 07103, USA
    Shock 29:372-6. 2008
    ..Thus, the goal of this study was to establish a reproducible method of measuring mucosal hydrophobicity and test the hypothesis that conditions that decrease mucosal hydrophobicity are associated with increased gut ..
  41. ncbi Mode of heavy meromyosin adsorption and motor function correlated with surface hydrophobicity and charge
    Nuria Albet-Torres
    Department of Chemistry and Biomedical Sciences, University of Kalmar, SE 391 82 Kalmar, Sweden
    Langmuir 23:11147-56. 2007
    ..The results are compared to previous studies of the microtubule-kinesin system and are also discussed in relation to fundamental studies of actomyosin and nanotechnological developments and applications...
  42. pmc Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism
    Alexandr P Kornev
    San Diego Supercomputer Center, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 103:17783-8. 2006
    ..It spans the molecule and plays a coordinating role in activated kinases. The spine is disordered in the inactive kinases and can explain how stabilization of the whole molecule is achieved upon phosphorylation...
  43. pmc Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins
    S Selvaraj
    Computational Biology Research Center CBRC, Institute of Advanced Industrial Science and Technology AIST 2 41 6 Aomi, Koto ku, Tokyo 135 0064, Japan
    Biophys J 84:1919-25. 2003
    ..The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (alpha/beta)(8) barrel proteins are proposed...
  44. pmc Dynamic cell surface hydrophobicity of Lactobacillus strains with and without surface layer proteins
    Virginia Vadillo-Rodriguez
    Department of Biomedical Engineering, University of Groningen, Groningen, The Netherlands
    J Bacteriol 186:6647-50. 2004
    Variations in surface hydrophobicity of six Lactobacillus strains with and without an S-layer upon changes in ionic strength are derived from contact angle measurements with low- and high-ionic-strength aqueous solutions...
  45. pmc Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins
    Richard Wolfenden
    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
    J Gen Physiol 129:357-62. 2007
  46. ncbi Identification of novel membrane proteins by searching for patterns in hydropathy profiles
    John D Clements
    School of Biochemistry and Molecular Biology, Australian National University, Canberra, Australia
    Eur J Biochem 269:2101-7. 2002
    ..This approach should prove a useful adjunct to sequence-based retrieval tools when searching for novel membrane proteins...
  47. pmc Scooby-domain: prediction of globular domains in protein sequence
    Richard A George
    Inpharmatica Ltd, 60 Charlotte Street, London W1T 2NU, UK
    Nucleic Acids Res 33:W160-3. 2005
    Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary ..
  48. pmc Folding amphipathic helices into membranes: amphiphilicity trumps hydrophobicity
    Mónica Fernández-Vidal
    Department of Physiology and Biophysics, University of California at Irvine, Irvine, CA 92697 4560, USA
    J Mol Biol 370:459-70. 2007
    ..is important for membrane-interface binding, an unanswered question is its importance relative to simple hydrophobicity-driven partitioning...
  49. ncbi Effects on adhesiveness and hydrophobicity of sub-inhibitory concentrations of netilmicin
    Pio Maria Furneri
    Dipartimento di Scienze Microbiologiche e Scienze Ginecologiche, Universita di Catania, sez di Microbiologia, Via Androne 81, Catania 95124, Italy
    Int J Antimicrob Agents 22:164-7. 2003
    The effect of sub-inhibitory concentrations (SICs) of netilmicin on bacterial hydrophobicity and adhesiveness to conjunctival cells was investigated. One strain each of Pseudomonas aeruginosa, Pseudomonas spp., Staphylococcus aureus and S...
  50. pmc An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity
    Gang Zhao
    Department of Biochemistry and Cell Biology, Stony Brook University, New York 11794 5215, USA
    Protein Sci 15:1987-2001. 2006
    b>Hydrophobicity analyses applied to databases of soluble and transmembrane (TM) proteins of known structure were used to resolve total genomic hydrophobicity profiles into (helical) TM sequences and mainly "subhydrophobic" ..
  51. ncbi Visualization of an unstable coiled coil from the scallop myosin rod
    Yu Li
    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454 9110, USA
    Nature 424:341-5. 2003
    ..The N-terminal 14 residues are poorly ordered; the rest of the S2 segment forms a flexible coiled coil with poorly packed core residues. The unusual absence of interhelical salt bridges here exposes apolar core atoms to solvent...
  52. ncbi Intrinsically unstructured proteins
    Peter Tompa
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518, PO Box 7, Budapest, Hungary
    Trends Biochem Sci 27:527-33. 2002
    ..In this review, recent findings are surveyed to illustrate that this novel but rapidly advancing field has reached a point where these proteins can be comprehensively classified on the basis of structure and function...
  53. pmc Cholesterol-induced protein sorting: an analysis of energetic feasibility
    J A Lundbaek
    Institute of Biological Psychiatry, Sct Hans Hospital, Roskilde, DK 4000, Denmark
    Biophys J 84:2080-9. 2003
    ..We conclude that cholesterol-induced changes in the bilayer physical properties allow for effective and accurate sorting which will be important generally for protein partitioning between different membrane domains...
  54. ncbi The polar hydrophobicity of fluorinated compounds
    Justin C Biffinger
    Department of Chemistry, University of Nebraska, Lincoln, NE 68588 0304, USA
    Chembiochem 5:622-7. 2004
  55. ncbi Gauss-function-Based model of hydrophobicity density in proteins
    Leszek Konieczny
    Institute of Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31 034 Cracow, Poland
    In Silico Biol 6:15-22. 2006
    The model adopting the three-dimensional Gauss function to express the hydrophobicity distribution in proteins is presented in this paper...
  56. ncbi The excised heat-shock domain of alphaB crystallin is a folded, proteolytically susceptible trimer with significant surface hydrophobicity and a tendency to self-aggregate upon heating
    Bishwajit Kundu
    Institute of Microbial Technology, Sector 39 A, Chandigarh 160 036, India
    Protein Expr Purif 36:263-71. 2004
    ..sheet) domain thus obtained is found to be (a) predominantly trimeric, and to display (b) significant surface hydrophobicity, (c) a marked tendency to undergo degradation, and (d) a tendency to aggregate upon heating, and on exposure ..
  57. ncbi The correlation between surface hydrophobicity and adherence of Bifidobacterium strains from centenarians' faeces
    Wei Hao Pan
    College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Dong Road, Haidian District, Beijing 100083, China
    Anaerobe 12:148-52. 2006
    ..Surface hydrophobicity and adherence capability to intestinal epithelial cells in vitro of bifidobacteria were simultaneously ..
  58. pmc Cargo surface hydrophobicity is sufficient to overcome the nuclear pore complex selectivity barrier
    Bracha Naim
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    EMBO J 28:2697-705. 2009
    ..to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and plant interaction network between cargo and FG ..
  59. ncbi Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation
    M Michael Gromiha
    Computational Biology Research Center CBRC, Institute of Advanced Industrial Science and Technology AIST, Tokyo, Japan
    Proteins 55:316-29. 2004
    ..we propose a new consensus approach for locating these stabilizing residues based on long-range interactions, hydrophobicity, and conservation of amino acid residues...
  60. ncbi Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity
    Mikołaj Owsianiak
    Institute of Chemical Technology and Engineering, Department of Biotechnology and Food Microbiology, Poznan University of Technology, Pl M Skłodowskiej Curie 2, 60 965, Poznan, Poland
    Appl Microbiol Biotechnol 84:545-53. 2009
    In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing ..
  61. ncbi Evaluation of adherence, hydrophobicity, aggregation, and biofilm development of Flavobacterium johnsoniae-like isolates
    A Basson
    Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
    Microb Ecol 55:1-14. 2008
    ..of conventional biofilm-associated structures such as fimbriae, pili, and flagella suggest that surface hydrophobicity, and/or autoaggregation and coaggregation may play an important role in adherence and biofilm formation...
  62. ncbi Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific
    Jie Zheng
    Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
    Biochemistry 47:2497-509. 2008
    ....
  63. pmc Flexibility in HIV-1 assembly subunits: solution structure of the monomeric C-terminal domain of the capsid protein
    Luis A Alcaraz
    Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, Elche Alicante, Spain
    Biophys J 93:1264-76. 2007
    ..This extraordinary ability of CAC to change its structure may contribute to the different modes of association of CA during HIV assembly, and should be taken into account in the design of new drugs against this virus...
  64. ncbi Hydrophobicity and biofilm formation of lipophilic skin corynebacteria
    Anna K Kwaszewska
    Department of Pharmaceutical Microbiology, Medical University of Lodz, Pomorska 137, 90 235 Lódź, Poland
    Pol J Microbiol 55:189-93. 2006
    ..These two groups are the most common coryneform bacteria isolated from nosocomial infections and these attributes most likely promote them to cause opportunistic infections...
  65. ncbi Acidosis regulates the stability, hydrophobicity, and activity of the BH3-only protein Bnip3
    Donna P Frazier
    Department of Pharmacology and the Vascular Biology Institute, University of Miami Medical Center, Florida 33136, USA
    Antioxid Redox Signal 8:1625-34. 2006
    ..These results demonstrate a pH-sensitive shift in the stability and apparent hydrophobicity of Bnip3 monomers that correlates closely with membrane binding and function.
  66. ncbi Effects of rugged nanoprotrusions on the surface hydrophobicity and water adhesion of anisotropic micropatterns
    Xuefeng Gao
    Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, PR China
    Langmuir 23:4886-91. 2007
    ....
  67. ncbi (Meth)acrylate monomer-induced cytotoxicity and intracellular Ca(2+) mobilization in human salivary gland carcinoma cells and human gingival fibroblast cells related to monomer hydrophobicity
    Toshiko Atsumi
    Department of Oral Physiology, Meikai University, School of Dentistry, 1 1, Keyakidai, Sakado, Saitama 350 0283, Japan
    Biomaterials 27:5794-800. 2006
    ..For both HSG and HGF cells, the cytotoxicity of the monomers was approximately proportional to their hydrophobicity (logP). No increase in [Ca(2+)](i) was found with hydrophilic monomers, even with 10mm stimulation...
  68. ncbi Solvent accessible surface area of amino acid residues in globular proteins: correlation of apparent transfer free energies with experimental hydrophobicity scales
    Alexey K Shaytan
    Physics Department, Moscow State University, Moscow 119991, Russia
    Biomacromolecules 10:1224-37. 2009
    ..The correlation of these statistical energies with several experimental hydrophobicity scales is discussed...
  69. ncbi Characterization of disinfection byproduct precursors based on hydrophobicity and molecular size
    Guanghui Hua
    Department of Civil and Environmental Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
    Environ Sci Technol 41:3309-15. 2007
    ..water sources was fractionated using XAD resins and ultrafiltration membranes into different groups based on hydrophobicity and molecular weight (MW), respectively...
  70. ncbi Effect of the hydrophobicity to net positive charge ratio on antibacterial and anti-endotoxin activities of structurally similar antimicrobial peptides
    Yosef Rosenfeld
    Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
    Biochemistry 49:853-61. 2010
    ..The positions of the D-amino acids were preserved. These peptides differ in their net positive charge and hydrophobicity. However, their overall structure in the membrane is similar, as determined by Fourier transform infrared ..
  71. ncbi Heating and reduction affect the reaction with tannins of wine protein fractions differing in hydrophobicity
    Matteo Marangon
    Dipartimento di Biotecnologie agrarie and Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia C I R V E Università di Padova, via dell Università 16, 35020 Legnaro PD, Italy
    Anal Chim Acta 660:110-8. 2010
    ..A significant correlation between hydrophobicity of the wine protein fractions and the haze formed after reacting with wine tannins was found, with the most ..
  72. pmc Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis
    Ashutosh Tiwari
    Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
    J Biol Chem 284:27746-58. 2009
    ..status of purified wild-type (WT) and mutant SOD1 proteins to changes in electrophoretic mobility and surface hydrophobicity as detected by 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence...
  73. ncbi Relationship between expression of cell surface hydrophobicity protein 1 (CSH1p) and surface hydrophobicity properties of Candida dubliniensis
    Kevin C Hazen
    Departments of Pathology and Microbiology, University of Virginia Health System, P O Box 800904, 3129 MR5, Charlottesville, VA 22908 0904, USA
    Curr Microbiol 48:447-51. 2004
    ..Unlike C. albicans, which variably expresses cell surface hydrophobicity (CSH) depending on environmental conditions, C. dubliniensis is hydrophobic under all environmental conditions...
  74. ncbi Hydrophobicity density profiles to predict thermal stability enhancement in proteins
    Angel Mozo-Villarias
    Departament de Ciencies Mediques Basiques, Universitat de Lleida, 25198, Lleida, Spain
    Protein J 25:529-35. 2006
    A hydrophobicity density is defined for a protein through its hydrophobicity tensor (similar to the inertia tensor), by using the Eisenberg hydrophobicity scale of the hydrophobic amino acids of a protein...
  75. ncbi Bile acid induces hydrophobicity-dependent membrane alterations
    Sandeep Akare
    Arizona Cancer Center, Department of Cell Biology and Anatomy, University of Arizona, 1515 N Campbell Avenue, Tucson, Arizona 85724, United States
    Biochim Biophys Acta 1735:59-67. 2005
    ..In colonic cells, where bile acid uptake is minimal, the hydrophobicity-induced membrane perturbation and alterations have been proposed, but these membrane alterations are largely ..
  76. ncbi A thermodynamic interpretation of cell hydrophobicity in aerobic granulation
    Y Liu
    Environmental Engineering Research Centre, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore
    Appl Microbiol Biotechnol 64:410-5. 2004
    ..granulation can be regarded as a microorganism-to-microorganism self-immobilization process, in which cell hydrophobicity could be a decisive parameter in determining the microorganism-to-microorganism interaction and structural ..
  77. ncbi A hydrophobicity-dependent motif responsible for surface expression of cardiac potassium channel
    Na Pan
    Key laboratory of Molecular Biophysics Huazhong University of Science and Technology of the Ministry of Education, Wuhan 430074, PR China
    Cell Signal 21:349-55. 2009
    ..the mutation did not affect the channel kinetics, whereas the surface expression increased with increasing hydrophobicity of the middle residue 'X' of the RXR motif...
  78. ncbi In vitro effects of bovine lactoferrin on autoaggregation ability and surface hydrophobicity of bifidobacteria
    Morshedur Rahman
    Laboratory of Dairy Food Science, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
    Anaerobe 14:73-7. 2008
    Changes in autoaggregation ability and surface hydrophobicity of bifidobacteria with addition of bovine lactoferrin in liquid media were investigated...
  79. pmc Conformational transition of Sec machinery inferred from bacterial SecYE structures
    Tomoya Tsukazaki
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Nature 455:988-91. 2008
    ....
  80. pmc Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects
    James M Kovacs
    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, 80045, USA
    Biopolymers 84:283-97. 2006
    Understanding the hydrophilicity/hydrophobicity of amino acid side chains in peptides/proteins is one the most important aspects of biology...
  81. ncbi Use of water to evaluate hydrophobicity of organically-modified xerogel enzyme supports
    Joseph S Clifford
    Department of Chemical Engineering, University of Waterloo, Ontario, Canada
    Biotechnol Bioeng 92:231-7. 2005
    ..The physicochemical properties of xerogels, such as hydrophobicity, can be manipulated by the introduction of organically-modified silicates...
  82. pmc Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
    Susanne Moelbert
    NEC Laboratories America, Princeton, NJ 08540, USA
    Protein Sci 13:752-62. 2004
    b>Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tend to occur at the surface of a folded protein...
  83. ncbi Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin
    Sergei E Permyakov
    Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
    Proteins 53:855-62. 2003
    ..4 +/- 0.2 microM) leads only to a very moderate folding of this protein and CaD136 remains substantially unfolded within its tight complex with calmodulin. The biological significance of these observations is discussed...
  84. ncbi P-glycoprotein efflux inhibition by amphiphilic diblock copolymers: relationship between copolymer concentration and substrate hydrophobicity
    Jason A Zastre
    Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, R C Wilson Pharmacy Building, Athens, Georgia 30602, USA
    Mol Pharm 5:643-53. 2008
    ..Therefore, the objectives of these studies were to assess if association of P-gp substrates differing in hydrophobicity will impact the effective concentration range for P-gp inhibition by amphiphilic diblock copolymers based on ..
  85. pmc Enhanced surface hydrophobicity by coupling of surface polarity and topography
    Nicolas Giovambattista
    Department of Physics, Brooklyn College of the City University of New York, Brooklyn, NY 11210 2889
    Proc Natl Acad Sci U S A 106:15181-5. 2009
    ..topography and polarity of the surface act in concert with the asymmetric charge distribution of water, the hydrophobicity varies substantially and, further, can be maximal for a surface with significant polarity...
  86. pmc Differential hydrophobicity drives self-assembly in Huntington's disease
    Martin G Burke
    Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 100:13928-33. 2003
    ..Our results reveal that the relative hydrophobicity of the poly(glutamine) block as compared with the rest of the (proline-based) exon1 fragment, ignored to date, ..
  87. ncbi Hydrophobicity, shape, and pi-electron contributions during translesion DNA synthesis
    Xuemei Zhang
    Departments of Pharmacology and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    J Am Chem Soc 128:143-9. 2006
    ....
  88. ncbi Strong correlation between statistical transmembrane tendency and experimental hydrophobicity scales for identification of transmembrane helices
    Gang Zhao
    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794 5215, USA
    J Membr Biol 229:165-8. 2009
    Direct physical chemistry measurements of the hydrophobicity of amino acids or their derivatives have often been used to estimate the propensity of amino acids to participate in transmembrane helices...
  89. pmc The role of hydrophobicity in the antimicrobial and hemolytic activities of polymethacrylate derivatives
    Kenichi Kuroda
    Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, 1011 N University Ave, Ann Arbor, MI 48109, USA
    Chemistry 15:1123-33. 2009
    ..The study on the membrane binding of dye-labeled polymers to large, unilamellar vesicles showed that the hydrophobicity of polymers enhances their binding to lipid bilayers and induces collapse of the polymer chain in solution, ..
  90. ncbi Influence of temperature on biofilm formation by Listeria monocytogenes on various food-contact surfaces: relationship with motility and cell surface hydrophobicity
    G Di Bonaventura
    Center of Excellence for Aging, G d Annunzio University Foundation, Chieti, Italy
    J Appl Microbiol 104:1552-61. 2008
    To assess the ability of Listeria monocytogenes to form biofilm on different food-contact surfaces with regard to different temperatures, cellular hydrophobicity and motility.
  91. ncbi Salmonella Sofia differs from other poultry-associated Salmonella serovars with respect to cell surface hydrophobicity
    T W R Chia
    Food Science Australia, Brisbane, P O Box 3312, Tingalpa DC, Queensland 4173, Australia
    J Food Prot 71:2421-8. 2008
    ..It has been suggested that physicochemical properties such as surface charge and hydrophobicity may affect bacterial attachment to surfaces and their ability to persist in food systems...
  92. ncbi Altered hydrophobicity and membrane composition in stress-adapted Listeria innocua
    Mark A Moorman
    Kellogg Company, Battle Creek, Michigan 49014, USA
    J Food Prot 71:182-5. 2008
    ..The present study included an assessment of the effects of acid, starvation, cold, and heat stress on net cell hydrophobicity and fatty acid composition in L. innocua...
  93. ncbi Removal of BTEX vapours from waste gas streams using silica aerogels of different hydrophobicity
    Suzana Standeker
    Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
    J Hazard Mater 165:1114-8. 2009
    ..By increasing the degree of hydrophobicity, aerogels become less effective, but they do not adsorb water vapour from gas stream...
  94. ncbi Insights into DNA recombination from the structure of a RAD51-BRCA2 complex
    Luca Pellegrini
    University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1GA, UK
    Nature 420:287-93. 2002
    ..Cancer-associated mutations that affect the BRC repeat disrupt its predicted interaction with RAD51, yielding structural insight into mechanisms for cancer susceptibility...
  95. ncbi Chemical hydrophobicity and uptake by plant roots
    Erik M Dettenmaier
    Utah Water Research Laboratory, Utah State University, 8200 Old Main Hill, Logan, Utah 84322, USA
    Environ Sci Technol 43:324-9. 2009
    ..root uptake and transfer into shoot tissues occurs only for compounds falling within an intermediate hydrophobicity range...
  96. ncbi Adsorption induced enzyme denaturation: the role of polymer hydrophobicity in adsorption and denaturation of alpha-chymotrypsin on allyl glycidyl ether (AGE)-ethylene glycol dimethacrylate (EGDM) copolymers
    Challa Lahari
    Biotransformations Laboratory, Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India
    Langmuir 26:1096-106. 2010
    Effects of changes in hydrophobicity of polymeric support on structure and activity of alpha-chymotrypsin (E.C. 3.4.21...
  97. ncbi How does shear affect aggregation in granular sludge sequencing batch reactors? Relations between shear, hydrophobicity, and extracellular polymeric substances
    E Dulekgurgen
    Environmental Engineering Department, Pamukkale University, Denizli, Turkey
    Water Sci Technol 58:267-76. 2008
    ..Aggregative physiology-related parameters, being cell surface hydrophobicity and extracellular polymeric substances (EPS), followed increasing trends parallel to the progress of ..
  98. ncbi Insight into heterogeneity in cell-surface hydrophobicity and ability to degrade hydrocarbons among cells of two hydrocarbon-degrading bacterial populations
    Christian O Obuekwe
    Division of Microbiology, Department of Biological Sciences, Faculty of Science, Kuwait University, P O Box 5969, Safat 13060, Kuwait
    Can J Microbiol 53:252-60. 2007
    ..R0032A and Burkholderia cepacia gave rise to bacterial populations of increasing cell-surface hydrophobicity. Thus, hydrophobicity of the first generation (H1) was less than that of the second generation (H2), which was ..
  99. ncbi Cytotoxicity, hydrophobicity, uptake, and distribution of osmium(II) anticancer complexes in ovarian cancer cells
    Sabine H van Rijt
    Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
    J Med Chem 53:840-9. 2010
    The cytotoxicity, hydrophobicity (log P), cellular uptake, aqueous reactivity, and extent of DNA adduct formation in the A2780 ovarian carcinoma cells for four osmium(II) arene complexes [(eta(6)-arene)Os(4-methyl-picolinate)Cl] that ..
  100. pmc Cell wall mannan and cell surface hydrophobicity in Candida albicans serotype A and B strains
    James Masuoka
    Department of Pathology, University of Virginia Health System, Charlottesville 22908 0904, USA
    Infect Immun 72:6230-6. 2004
    Cell surface hydrophobicity contributes to the pathogenesis of the opportunistic fungal pathogen Candida albicans...
  101. pmc A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA
    Keith T Gagnon
    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
    Nucleic Acids Res 37:3074-82. 2009
    ..These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism...

Research Grants68

  1. Targeting superbugs: discovery and development of new broad-spectrum lipopeptides
    Jian Li; Fiscal Year: 2013
    ..aeruginosa, A. baumannii and K. pneumoniae. Overall, this project targets the urgent global unmet medical need and responds in a timely manner to the recent global call for discovery of new antibiotics: The 10 x '20 Initiative. ..
  2. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    ..limited detection of low abundance proteins and proteins with extreme isoelectric point, molecular weight, and hydrophobicity, especially membrane proteins...
  3. Detection of engineered nanomaterials in drinking water, food, commercial product
    Paul K Westerhoff; Fiscal Year: 2010
    ..a similar fashion as organic chemicals, by pre-treating and analyzing (LC/MS) them based upon solubility and hydrophobicity characteristics...
  4. Cytoskeletal Keratins in Epithelial Immunity to Bacterial Keratitis
    K P CONNIE TAM; Fiscal Year: 2013
    ..and their killing action is independent of peptide/bacterial membrane electrostatic attraction, peptide hydrophobicity and defined secondary structure, suggesting they differ from other AMPs in how they interact with bacterial ..
  5. Tumor drug delivery systems based on polymalic acid
    Julia Y Ljubimova; Fiscal Year: 2010
    ..This includes (a) improvement of endosomal disruption activity through enhanced hydrophobicity by exchange of valine in the present carrier with leucine ethylester thereby increasing membrane permeation;(b)..
  6. Targeting of alpha7 nAChR for therapeutic effects
    Roger L Papke; Fiscal Year: 2013
    ..We will use our new discoveries about how these drugs work to help make alpha7-stimulating drugs optimally designed to treat specific diseases. ..
  7. CD36 and Intestinal Fat Absorption
    Nada A Abumrad; Fiscal Year: 2013
    ..our novel preliminary data demonstrating that CD36 deletion increases the bile acid pool, decreases bile hydrophobicity and effectively protects against gallstone formation...
  8. Engineering DNA Delivery Polymers using Combinatorial and Cheminformatics Methods
    Kaushal Rege; Fiscal Year: 2013
    ..g. molecular weight, hydrophobicity, zeta potential, etc...
  9. Design of New Antimicrobials
    Robert S Hodges; Fiscal Year: 2012
    ..We have taken an approach of systematic alteration in the amphipathicity, hydrophobicity and structure of two different classes of antimicrobial peptides by single L- and D- amino acid substitutions...
  10. Proteomic Evaluation of the Blood-Brain Barrier Receptor-Mediated Transportome
    Eric V Shusta; Fiscal Year: 2013
    ..RMT receptors are membrane proteins that because of their low abundance and hydrophobicity are not well profiled using traditional two dimensional gel or tandem mass spectrometry methods...
  11. Membrane Protein Folding and Assembly
    Stephen H White; Fiscal Year: 2013
    ..of this project is to tighten the connection between the physical and biological principles as represented by hydrophobicity scales for predicting TM helices...
  12. Novel Polymer Coatings to Prevent Biofilms on Urinary Stents and Catheters
    JEFFREY LAWRENCE DALSIN; Fiscal Year: 2011
    ..adhesion, such as silver-coated surfaces, control-release antibiotics, and surface modification to change hydrophobicity. These approaches have enjoyed varying degrees of success, but all suffer from numerous limitations...
  13. Structure-Activity Relationship in Host Defense Peptides
    GREGORY ALEXANDER CAPUTO; Fiscal Year: 2010
    ..modifications focusing on the cationic amino acids in the sequence as well as modification of net charge/hydrophobicity of the HDPs will be the central experiments...
  14. STRUCTURAL DYNAMICS OF VINCULIN IN ADHESION JUNCTIONS
    Tina Izard; Fiscal Year: 2012
    ..Finally, we will also define the structure and function of metavinculin, an isoform of vinculin that plays essential roles in the formation and function of muscle tissue. ..
  15. Glycoproteins and Glycan-Binding IgGs: Biomarkers for Cancer and Inflammatory Di
    Hyesook Kim; Fiscal Year: 2013
    ..glycan microarrays using glycan linkers selected among 9 in-house synthesized linkers of various lengths and hydrophobicity and (c) detect glycan-binding profiles of IgGs or IgMs to obtain prostate cancer-specific biomakers by the ..
  16. Dual Mode Nanoemulsions for 19F MRI and Fluorescence Detection
    Jelena M Janjic; Fiscal Year: 2009
    ..Unusual physicochemical properties of PFPE oils, high hydrophobicity and significant lipophobicity, make the synthetic modifications and formulations of these oils more difficult ..
  17. Structural Contexts and Functional Consequences of Protein S-nitrosylation
    Eric R Schreiter; Fiscal Year: 2010
    ..To accomplish this we will use computational methods to search for similarities in the charge distribution, hydrophobicity, secondary structure, etc...
  18. Mycolate-specific T cell function in human immunity to Mycobacterium tuberculosis
    Anne Kasmar; Fiscal Year: 2013
    ..to Mycobacterium tuberculosis Mycolic acids are abundant constituents of the mycobacterial cell wall whose hydrophobicity leads to the clinically-useful acid-fast smear...
  19. Celecoxib Derivative: Host Cell-Directed Inhibitors of Intracellular Pathogens
    Kristy M Ainslie; Fiscal Year: 2013
    ..AR-12 concentrations were limited with in vivo application because the of the drug's hydrophobicity. To overcome solubility issues, we propose encapsulating AR-12 in acetalated dextran (Ac-DEX) particles that ..
  20. Rational Design of Viral-Mimetic Lipid Gene Vectors
    Francis C Szoka; Fiscal Year: 2013
    ..Specific aim 1: To design, synthesize and characterize novel lipids that alter their charge, interfacial hydrophobicity and phase preference at low pH...
  21. Interactions of engineered nanomaterials with lung alveolar epithelium
    EDWARD DAVID CRANDALL; Fiscal Year: 2010
    ..g., charge and hydrophobicity). With this knowledge, improved nanomedical and biological applications (e.g...
  22. Molecular Mechanisms of L. monocytogenes Adhesion Through Surface Biopolymers
    NEHAL IBRAHIM ABU LAIL; Fiscal Year: 2010
    ..monocytogenes charge, hydrophobicity, and elasticity and thus their attachment to surfaces. I further hypothesize that epidemic strains of L...
  23. FABPs Mediate Activation of PPAR Alpha Receptors by N-Acylethanolamines
    Martin Kaczocha; Fiscal Year: 2012
    ..Due to their hydrophobicity, NAEs are unable to traverse the aqueous cytosol unassisted...
  24. Myosin structural and kinetic mechanisms that differentiate fast and slow muscle
    Douglas M Swank; Fiscal Year: 2012
    ..4) Test our MECHANISTIC HYPOTHESIS that the degree of hydrophobicity in the converter is critical to its function by substituting amino acids that decrease the IFM myosin isoform&..
  25. RHIZOBIAL LIPOPOLYSACCHARIDES ESSENTIAL FOR INFECTION
    Russell W Carlson; Fiscal Year: 2010
    ..Methylation and acetylation changes to the O-chain polysaccharide and an overall change in the hydrophobicity of the LPS and the whole rhizobial cell occur during symbiosis. Our Specific Aims are: (1...
  26. Understanding Beta-Sheet Structure in Aqueous Solution
    Jeffery W Kelly; Fiscal Year: 2013
    ..alter the electronic properties of the aromatic ring, the amphiphilicity of the N-linked carbohydrate, and the hydrophobicity and hydrogen bonding potential of the Thr residue to understand the stabilizing aspects of this tripartite ..
  27. Nanospheres as Delivery Vehicles for Psoriasis Therapeutics
    LARISA contact SHEIHET; Fiscal Year: 2010
    ..The choice of oligo(DTR-diacid) for the middle block was based on its tunable hydrophobicity and degradability under physiological conditions...
  28. Antigen stability as a parameter in rational T(CD8+)-targeting vaccine design
    LAURENCE CRANE EISENLOHR; Fiscal Year: 2013
    ..Furthermore, unshielded hydrophobicity (such as an untethered transmembrane domain) constitutes one driver of sufficiently rapid protein catabolism...
  29. Development of a Novel Atmospheric Pressure Glow Discharge for Ambient Mass Spect
    JUSTIN MICHAEL WISEMAN; Fiscal Year: 2011
    ..We believe it is important to show our customers a range of molecules in size and hydrophobicity to make it easier for them to assess the likelihood their proposed application will be successful...
  30. Self-Cleaning Sensor Membranes to Improve Glucose Monitoring In Vivo
    MELISSA GRUNLAN; Fiscal Year: 2010
    ..mechanical properties as well as thermally-modulated swelling/dewelling behavior, surface hydrophilicity/- hydrophobicity, glucose diffusion and cell-release behavior, (2) iteratively evaluate the efficacy of selected ..
  31. Mode of action of the salivary antimicrobial peptide histatin-5
    ALBERT MOCHON; Fiscal Year: 2009
    ..We will investigate the functional domain of Hst-5 to determine which characteristic of the peptides (i.e. hydrophobicity, amphipathicit, etc.) allow for the nove cytoplasmic translocation of Hst-5 into C. albicans...
  32. Therapeutic intervention for Brucella
    AMY RAMBOW LARSEN; Fiscal Year: 2009
    ..The small peptide size coupled with its hydrophobicity and cationic charge suggests rapid penetration of eukaryotic cells...
  33. Electrostatically triggered hydrophobic self-assembly of protein hydrogels
    Kevin Baler; Fiscal Year: 2013
    ..The techniques developed in this proposal lay the foundation for the design of additional functional protein hydrogel scaffolds for applications in areas such as wound healing and dialysis. ..
  34. Mechanistic analysis of transport through the mucus barrier
    Katharina Ribbeck; Fiscal Year: 2013
    ..While the relevance of particle size, net charge, and hydrophobicity for mucus transport has been studied in isolation, the effect of combining these properties and the role of ..
  35. Development of a Novel Atmospheric Pressure Glow Discharge for Ambient Mass Spect
    JUSTIN MICHAEL WISEMAN; Fiscal Year: 2012
    ..We believe it is important to show our customers a range of molecules in size and hydrophobicity to make it easier for them to assess the likelihood their proposed application will be successful...
  36. Capillary Electrophoresis and Protein Biophysics
    George M Whitesides; Fiscal Year: 2010
    This research is focused on the development of new techniques, based on the hydrophobicity of their surfaces, for separating, characterizing, and manipulating proteins...
  37. Nanoporous Drug Delivery Systems
    Sergei N Smirnov; Fiscal Year: 2013
    ..modified inside and with multifunctional exterior modification will be investigated for employing the hydrophobicity switching mechanism to intracellular transfection of small drug molecules and nucleic acids...
  38. pH-Triggered Membrane Insertion of Proteins
    DOUGLAS TOBIAS; Fiscal Year: 2013
    ....
  39. A Silicate Prodrug Strategy for Enhancing Nanoparticle Delivery of Taxanes
    CHRIS MACOSKO; Fiscal Year: 2011
    ..provided by applicant): Hypothesis: Silicate prodrugs of taxane antitumor agents, customized to have proper hydrophobicity and hydrolytic lability, can be formulated with amphiphilic block copolymers into nanoparticles that are ..
  40. FUNCTIONAL ELEMENTS IN ALPHA CRYSTALLIN CHAPERONE
    Krishna K Sharma; Fiscal Year: 2010
    ..Determine the amino acid sequences (binding site) in aB-crystallin that contribute to the enhanced hydrophobicity and chaperone function at 37C following deletion of 54-61 sequence...
  41. Spectroscopic markers for blue-fluorescing tryptophan in proteins
    LAURA JEANNE JUSZCZAK; Fiscal Year: 2012
    ..this proposal is to understand how the disparate factors of pH, in the case of short tryptophan peptides, and hydrophobicity and steric hindrance, in the case of proteinaceous tryptophans, both result in blue-shifted fluorescence ..
  42. Endoplasmic Reticulum (ER) Associated Degradation of Membrane Proteins in Yeast
    Jeffrey L Brodsky; Fiscal Year: 2013
    ..factors? How is a cytoplasmic, misfolded domain recognized, retro-translocated, and destroyed when the hydrophobicity of the membrane anchor is altered, or when the domain is linked to the membrane by a lipid? Do different ..
  43. Oxarane-Acrylate System to Double the Clinical Service Life of Restorative Resins
    H Ralph Rawls; Fiscal Year: 2013
    ..Five specific aims are proposed: 1. To determine the effect of using oxiranes, increased hydrophobicity, and IPNs on resin mechanical properties, physical properties and in vitro biocompatibility...
  44. Biochemistry and Biophysics of the Preocular Tear Film
    Igor A Butovich; Fiscal Year: 2013
    ....
  45. Mimicry of Amyloid Oligomers
    James S Nowick; Fiscal Year: 2013
    ..The effect of promising amyloid oligomer mimics on long-term potentiation, long-term synaptic depression, and dendritic spine density at synapses will be studied in mouse hipocampal slices and rat organotypic slices. ..
  46. Hydrophobic Effects in Biophysical Systems and Protein-Protein Interactions
    David Chandler; Fiscal Year: 2010
    ..The hydrophobic effect is arguably the most fundamental of physical forces orchestrating the structure of proteins and protein complexes. It is therefore central to health and life. ..
  47. Linking the physical and chemical characteristics of Qdots to their toxicity
    TERRANCE JAMES KAVANAGH; Fiscal Year: 2013
    ..known to be determinants for the interaction of nanoparticles with cells and tissues, including shape, size, hydrophobicity, and surface charge...
  48. Role of carrier plasma protein corona in their vascular wall localization
    LOLA ENIOLA-ADEFESO; Fiscal Year: 2013
    ..margination of spherical carriers from human blood flow;(2) the coupled effect of material type and material hydrophobicity, surface coating, and particle size and shape in prescribing carrier margination;and (3) the role of cell-..
  49. Pathogen-host Interactions that Remodel the Cytoskeleton
    Tina Izard; Fiscal Year: 2010
    ..abstract_text> ..
  50. Tools to Connect Protein Conformations, Dynamics, and Associations
    Daniel Schwartz; Fiscal Year: 2013
    ..The surfac is expected to indirectly influence film formation through the mobility of proteins on the surface and their propensity for cluster formation, properties that likely depend on Fn conformation. ..
  51. Synthesis and Study of Minimal Protein Folding Models: Molecular Torsion Balance
    Craig S Wilcox; Fiscal Year: 2010
    ..The Lum-Chandler-Weeks (LCW) theory of hydrophobicity makes intriguing predictions on how hydrophobicity changes with the sizes of alkyl surfaces...
  52. Level-Set Variational Implicit-Solvent Approach to Biomolecular Interactions
    Bo Li; Fiscal Year: 2013
    ..The project also provides material for an urgently needed course on mathematical and computational molecular biology. ..
  53. Understanding, Predicting, and Engineering Membrane Permeability
    Matthew P Jacobson; Fiscal Year: 2012
    ..developing series of compounds that differ in well-defined ways, such as stereochemistry, rigidity, size, hydrophobicity, etc...
  54. ELECTRON TRANSFER WITHIN PROTEIN COMPLEXES
    Brian M Hoffman; Fiscal Year: 2013
    ..We also propose to 'translate'the understanding derived from these studies to the problem of nucleotide-regulated, conformationally-linked ET in catalysis by nitrogenase. ..
  55. Protein misfolding and aggregation
    NIKOLAY DOKHOLYAN; Fiscal Year: 2013
    ..we will use proven biophysical and biochemical techniques to assess changes in oligomeric state and surface hydrophobicity as wild type and mutant SOD1 aggregate...
  56. UNDERSTANDING THE INTERACTION OF ANKYRINS AND NANOMATERIALS
    CARLOS DIEGO GARCIA; Fiscal Year: 2013
    ..The proposed project will also develop a novel surface-based method to study real-time binding of proteins in the presence of pharmaceutical compounds that would otherwise interfere with the association of other proteins in cells. ..
  57. Immunoglobulin CDR-H3 and neutralizing antibodies to HIV
    Harry Schroeder; Fiscal Year: 2009
    ..will be cloned and sequenced to further correlate the relationship between neutralization and CDR-H3 length or hydrophobicity. The creation of vaccines capable of eliciting neutralizing antibodies to HIV has proven more difficult than ..
  58. Computational design of beta-barrel membrane proteins
    JAMES ALAN STAPLETON; Fiscal Year: 2013
    ..The study proposed here is a systematic exploration of the extent to which the hydrophobicity of the surface amino acid residues determines whether a 2-barrel protein will remain soluble or insert into a ..
  59. Fluorous mediated J aggregation as a bright NIR target specific imaging agent
    ELLEN MAY SLETTEN; Fiscal Year: 2013
    ....
  60. Predicting protein flexibility and stability
    Donald Jacobs; Fiscal Year: 2010
    ..abstract_text> ..
  61. Simulation and Prediction of Protein Folding
    Michael Levitt; Fiscal Year: 2012
    ..We propose new methods involving homologous sequences, non-linear mapping of conformation space and robust clustering. ..
  62. The Energetic Cost of Protein Retrotranslocation during ER-associated Degradation
    CHRISTOPHER JAMES GUERRIERO; Fiscal Year: 2012
    ..Second, since little is known about how integral membrane hydrophobicity influences ERAD efficiency, I propose to generate chimeric constructs including the Ste6p* degron with varied ..
  63. Mitochondrial RNA transport as a novel therapy
    MICHAEL JOHN PALLADINO; Fiscal Year: 2013
    ..The extreme hydrophobicity of mitochondrial-encoded proteins remains a technical hurdle to such therapies...
  64. CYCLIC PRODRUGS OF OPIOID PEPTIDES
    RONALD BORCHARDT; Fiscal Year: 2007
    ..esterase-sensitive cyclic prodrugs of a model opioid peptide (DADLE) that exhibit physicochemical properties (hydrophobicity, low hydrogen bonding potential, no charge) favorable for high transcellular permeation...
  65. Local Anesthetic Interactions with Membranes
    Gary Strichartz; Fiscal Year: 2005
    ..4. Correlate the the measures in Aims 1-3 in order to determine the relative contributions of LA hydrophobicity, charge, dipole moment and intramolecular bonding to membrane partitioning and to permeation, and the relative ..
  66. MOLECULAR BASIS OF VIRULENCE FACTORS OF ORAL FUNGAL SP.
    Mary Ann Jabra Rizk; Fiscal Year: 2006
    ..dubliniensis is a species that exhibits constant cell surface hydrophobicity, possessing a homologue to the C...
  67. SINGLE-STRANDED NUCLEIC ACID BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1992
    ..These proposed studies are basic to our understanding of those physiological processes such as DNA replication, transcription and translation that require a single-stranded nucleic acid template...
  68. REGULATORY DOMAINS OF G PROTEIN COUPLED RECEPTORS
    Ellen Weiss; Fiscal Year: 2002
    ..Additional mutations will be made at these sites to determine the requirement for charge, hydrophobicity, size or specific secondary structure...