electrostatics

Summary

Summary: The branch of physics dealing with electric phenomena not associated with electricity in motion, electric charges at rest, their electric fields, and potentials. (Random House Unabridged Dictionary, 2d ed; McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)

Top Publications

  1. pmc PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 32:W665-7. 2004
  2. pmc H++: a server for estimating pKas and adding missing hydrogens to macromolecules
    John C Gordon
    Department of Computer Science, Virginia Tech Blacksburg, VA 24061, USA
    Nucleic Acids Res 33:W368-71. 2005
  3. 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
  4. pmc Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
    Roxana E Georgescu
    Department of Physics, City College of New York, New York 10031, USA
    Biophys J 83:1731-48. 2002
  5. 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
  6. ncbi GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences
    Donald Petrey
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Methods Enzymol 374:492-509. 2003
  7. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
  8. ncbi Plasma membrane phosphoinositide organization by protein electrostatics
    Stuart McLaughlin
    Department of Physiology and Biophysics, Health Sciences Center, Stony Brook University, Stony Brook, New York 11794, USA
    Nature 438:605-11. 2005
  9. pmc Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme
    Jim Warwicker
    Department of Biomolecular Sciences, UMIST, P O Box 88, Manchester M60 1QD, UK jim
    Protein Sci 13:2793-805. 2004
  10. ncbi Molecular shape and electrostatics in the encoding of relevant chemical information
    Anthony Nicholls
    OpenEye Scientific Software, Inc, 3600 Cerrillos Rd Suite 1107, Santa Fe, NM 87507, USA
    J Comput Aided Mol Des 19:661-86. 2005

Detail Information

Publications330 found, 100 shown here

  1. pmc PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    Todd J Dolinsky
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA
    Nucleic Acids Res 32:W665-7. 2004
    ..and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics...
  2. pmc H++: a server for estimating pKas and adding missing hydrogens to macromolecules
    John C Gordon
    Department of Computer Science, Virginia Tech Blacksburg, VA 24061, USA
    Nucleic Acids Res 33:W368-71. 2005
    ..Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model...
  3. 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...
  4. pmc Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
    Roxana E Georgescu
    Department of Physics, City College of New York, New York 10031, USA
    Biophys J 83:1731-48. 2002
    ..Multiconformation continuum electrostatics (MCCE) combines continuum electrostatics and molecular mechanics force fields in Monte Carlo sampling to ..
  5. 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...
  6. ncbi GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences
    Donald Petrey
    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
    Methods Enzymol 374:492-509. 2003
    ..An on-line manual, details on obtaining the software, and technical notes about the program and the Troll software library can be found at the Honig laboratory Web site (http://trantor.bioc.columbia.edu)...
  7. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    ..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
  8. ncbi Plasma membrane phosphoinositide organization by protein electrostatics
    Stuart McLaughlin
    Department of Physiology and Biophysics, Health Sciences Center, Stony Brook University, Stony Brook, New York 11794, USA
    Nature 438:605-11. 2005
    ..Recent studies suggest that membrane proteins concentrate PIP2 and, in response to local increases in intracellular calcium concentration, release it to interact with other biologically important molecules...
  9. pmc Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme
    Jim Warwicker
    Department of Biomolecular Sciences, UMIST, P O Box 88, Manchester M60 1QD, UK jim
    Protein Sci 13:2793-805. 2004
    ....
  10. ncbi Molecular shape and electrostatics in the encoding of relevant chemical information
    Anthony Nicholls
    OpenEye Scientific Software, Inc, 3600 Cerrillos Rd Suite 1107, Santa Fe, NM 87507, USA
    J Comput Aided Mol Des 19:661-86. 2005
    ..Necessary, but not sufficient, to this proposition are the importance of shape and electrostatics to activity, the facility to easily represent, store and compare field properties, and knowledge of the ..
  11. pmc Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex
    Valeria Menchise
    Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 6, I 80134 Naples, Italy
    Proc Natl Acad Sci U S A 100:12021-6. 2003
    ..The conformational rigidity of PNAs is enhanced by the presence of the chiral centers, limiting the ability of PNA strands to adopt other conformations and, ultimately, increasing the selectivity in molecular recognition...
  12. pmc Gating charges in the activation and inactivation processes of the HERG channel
    Mei Zhang
    Department of Physiology, Virginia Commonwealth University, 1101 E Marshall St, Richmond, VA 23298, USA
    J Gen Physiol 124:703-18. 2004
    ..Furthermore, channel domain other than S4 contributes to gating charge involved in hERG's inactivation process...
  13. ncbi Next generation, sequentially assembled ultrathin films: beyond electrostatics
    John F Quinn
    Centre for Nanoscience and Nanotechnology, Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria, Australia 3010
    Chem Soc Rev 36:707-18. 2007
    ..We discuss the assembly of films via a number of different methodologies, with particular emphasis on those that provide enhanced orientational control, stimuli-responsive behaviour, and improved film stability...
  14. pmc Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding
    Alain Laederach
    Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 104:7045-50. 2007
    ..This study showcases a robust approach for the development of kinetic models from collections of local structural probes...
  15. ncbi Electrostatics dominate quadruplex stability
    Ivan V Smirnov
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143 0446, USA
    Biopolymers 85:91-101. 2007
    Stabilization of nucleic acid structures results from a balance of multiple interactions, including electrostatics, base stacking, hydrophobic interactions, hydrogen bonding, van der Waals forces, etc...
  16. pmc Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
    Yu Bai
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:1035-40. 2005
    ..An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated...
  17. pmc Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
    Noriko Handa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 12:1621-32. 2003
    ..TT1542 is a homohexamer in the crystal and in solution, the six monomers forming a cylindrical structure. Putative active sites are suggested by the structure and conserved amino acid residues...
  18. ncbi Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    Michael Feig
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Comput Chem 25:265-84. 2004
    ..25% between each other for both native and nonnative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations...
  19. pmc PI(3,4,5)P3 and PI(4,5)P2 lipids target proteins with polybasic clusters to the plasma membrane
    Won Do Heo
    Department of Molecular Pharmacology, 318 Campus Drive, Clark Building, Stanford University Medical School, Stanford, CA 94305, USA
    Science 314:1458-61. 2006
    ....
  20. ncbi Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology
    Maria Teresa Neves-Petersen
    Department of Physics and Nanotechnology, University of Aalborg, Biostructure and Protein Engineering Group, Sohngaardsholmsvej 49, DK 9000 Aalborg, Denmark
    Biotechnol Annu Rev 9:315-95. 2003
    ..g., its substrate, a surface or an inhibitor is essentially an understanding of the role of electrostatics in intermolecular interactions...
  21. pmc Multiconformation continuum electrostatics analysis of the NhaA Na+/H+ antiporter of Escherichia coli with functional implications
    Elena Olkhova
    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max von Laue Strasse 3, D 60438 Frankfurt am Main, Germany
    Proc Natl Acad Sci U S A 103:2629-34. 2006
    ..We have used multiconformation continuum electrostatics method to investigate the protonation states of residues in the sodium proton exchanger NhaA from Escherichia ..
  22. pmc Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V
    M A Miteva
    French National Institute of Health and Medical Research INSERM U428, University Paris V, 75006 Paris, France
    Biophys J 86:488-98. 2004
    ..This substitution causes electrostatic destabilization of the domain by approximately 3 kcal/mol. Together these effects likely explain the lowered expression levels in R2-FV carriers...
  23. ncbi Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle
    Alexey Onufriev
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 332:1183-93. 2003
    ..When combined with state-to-state transition rules based on accessibility considerations, a model for non-equilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems...
  24. ncbi Exploring protein native states and large-scale conformational changes with a modified generalized born model
    Alexey Onufriev
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
    Proteins 55:383-94. 2004
    ..models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation...
  25. ncbi Electrostatics in protein binding and function
    Neeti Sinha
    Basic Research Laboratory, Center for Cancer Research, Bldg 469 National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
    Curr Protein Pept Sci 3:601-14. 2002
    ..b>Electrostatics play a major role in defining the mechanisms of protein-protein complex formation, molecular recognitions, ..
  26. pmc Electrostatic and steric contributions to block of the skeletal muscle sodium channel by mu-conotoxin
    Kwokyin Hui
    Department of Physiology and Biophysics, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1
    J Gen Physiol 119:45-54. 2002
    ....
  27. pmc Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation
    Navin Pokala
    Department of Molecular and Cell Biology, University of California, Berkeley, 237 Hilde brand Hall, Berkeley, CA 94720 3206, USA
    Protein Sci 13:925-36. 2004
    b>Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition...
  28. ncbi Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications
    Paweł Grochowski
    Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 02 106 Warsaw, Poland
    Biopolymers 89:93-113. 2008
    This work is a review of the Poisson-Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding...
  29. pmc Calculating pKa values in enzyme active sites
    Jens Erik Nielsen
    Departments of Pharmacology, Chemistry, and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
    Protein Sci 12:1894-901. 2003
    ..The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts...
  30. ncbi Annotating nucleic acid-binding function based on protein structure
    Eric W Stawiski
    Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    J Mol Biol 326:1065-79. 2003
    ..Our method can also distinguish NA-binding proteins from other proteins that have similar, large positive electrostatic patches on their surfaces, but that do not bind nucleic acids...
  31. pmc Tuning magnesium sensitivity of BK channels by mutations
    Huanghe Yang
    Department of Biomedical Engineering and Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, Missouri 63130, USA
    Biophys J 91:2892-900. 2006
    ....
  32. ncbi The role of electrostatics in colicin nuclease domain translocation into bacterial cells
    Daniel Walker
    Department of Biology, University of York, York YO10 5YW, United Kingdom
    J Biol Chem 282:31389-97. 2007
    ....
  33. ncbi Moment-based prediction of DNA-binding proteins
    Shandar Ahmad
    Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 4 Kawazu, Iizuka 820 8502, Fukuoka, Japan
    J Mol Biol 341:65-71. 2004
    ..The speed and accuracy of this method, in combination with homology-based methods of structure prediction, should enhance genome-wide recognition of DNA-binding proteins...
  34. ncbi Different roles of electrostatics in heat and in cold: adaptation by citrate synthase
    Sandeep Kumar
    Basic Research Program, SAIC Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI Frederick, Building 469, Room 151, Frederick, MD 21702, USA
    Chembiochem 5:280-90. 2004
    b>Electrostatics plays a major role in heat adaptation by thermophilic proteins. Here we ask whether electrostatics similarly contributes to cold adaptation in psychrophilic proteins...
  35. pmc Adaptation mechanism of the aspartate receptor: electrostatics of the adaptation subdomain play a key role in modulating kinase activity
    Diane J Starrett
    Molecular Biophysics Program and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309 0215, USA
    Biochemistry 44:1550-60. 2005
    ..site-directed mutagenesis to neutralize each acidic residue within the subdomain to probe the hypothesis that electrostatics in this region play a significant role in the mechanism of kinase activation and modulation...
  36. ncbi Protein dynamics and electrostatics in the function of p-hydroxybenzoate hydroxylase
    Barrie Entsch
    Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 0606, USA
    Arch Biochem Biophys 433:297-311. 2005
    ..This network serves to protonate and deprotonate the substrate and product in the active site to promote catalysis and regulate the coordination of conformational states for efficient catalysis...
  37. pmc Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix
    Bosco K Ho
    Centre de Biophysique Moléculaire Numérique CBMN, B 5030 Gembloux, Belgium
    Protein Sci 12:2508-22. 2003
    ..However, steric clashes alone do not account for the diagonal regions. Using electrostatics to analyze the conformational dependence of specific interatomic interactions, we find that the diagonal shape ..
  38. pmc Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics
    Li Zhang
    Department of Chemistry, University of California, Riverside, California 92521, USA
    Biophys J 90:3106-19. 2006
    ..This work is expected to be useful for understanding the function of native CCP-containing regulators of complement activation and receptors and for the design of antiviral therapeutics and complement inhibitors...
  39. ncbi Ribosome motions modulate electrostatic properties
    Joanna Trylska
    Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
    Biopolymers 74:423-31. 2004
    ..Functional rearrangement of the ribosome leads to electrostatic changes which may help the translocation of the tRNAs during the elongation stage...
  40. pmc Incomplete ion dissociation underlies the weakened attraction between DNA helices at high spermidine concentrations
    Jie Yang
    Department of Physics, University of Vermont, Burlington, Vermont, USA
    Biophys J 89:1932-40. 2005
    ..This is contrary to the suggestion that the binding of spermidine at higher concentrations causes DNA overcharging and consequent electrostatic repulsion...
  41. ncbi Structure of B-DNA with cations tethered in the major groove
    Tinoush Moulaei
    Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332 0400, USA
    Biochemistry 44:7458-68. 2005
    ..In addition, these interactions appear to be associated with displacement of counterions from the major groove of the DNA...
  42. pmc The contribution of phosphate-phosphate repulsions to the free energy of DNA bending
    Kevin Range
    Department of Chemistry, University of Minnesota 207 Pleasant Street SE, Minneapolis, MN 55455 0431, USA
    Nucleic Acids Res 33:1257-68. 2005
    ..The calculations predict that the phosphate-phosphate repulsions account for approximately 30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle...
  43. ncbi Is a small number of charge neutralizations sufficient to bend nucleosome core DNA onto its superhelical ramp?
    Gerald S Manning
    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854 8087, USA
    J Am Chem Soc 125:15087-92. 2003
    ....
  44. ncbi Gate electrostatics and quantum capacitance of graphene nanoribbons
    Jing Guo
    Department of Electrical and Computer Engineering, University of Florida, Gainesville, Florida 32611, USA
    Nano Lett 7:1935-40. 2007
    ..Magnetic field results in pronounced oscillations on C-V characteristics...
  45. pmc Computational protein design is a challenge for implicit solvation models
    Alfonso Jaramillo
    Service de Conformation de Macromolécules Biologiques et Bioinformatique, CP263 Université Libre de Bruxelles, Brussels, Belgium
    Biophys J 88:156-71. 2005
    ..This contrasts with native recognition, which depends less on solvation and more on other nonbonded contributions...
  46. pmc Ion-mediated nucleic acid helix-helix interactions
    Zhi Jie Tan
    Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA
    Biophys J 91:518-36. 2006
    ..The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations...
  47. ncbi Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis
    Eric Alsop
    Department of Chemistry, California State Polytechnic University at Pomona, Pomona, CA 91768, USA
    Protein Eng 16:871-4. 2003
    ..Therefore, we believe that our results, in addition to being theoretically interesting, will facilitate identification of charge-altering mutations likely to increase the stability of a particular protein structure...
  48. ncbi Role of protein-water interactions and electrostatics in alpha-synuclein fibril formation
    Larissa A Munishkina
    Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
    Biochemistry 43:3289-300. 2004
    ..Moderate concentrations of anions affected both the rates of nucleation and the elongation of alpha-synuclein fibrillation, primarily via their effect on the interaction of the protein with water...
  49. pmc Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: distributions of phi
    Franc Avbelj
    National Institute of Chemistry, Hajdrihova 19, Ljubljana Sl 1115, Slovenia
    Proc Natl Acad Sci U S A 100:5742-7. 2003
    ..ii) The ESM is partly successful in predicting the g(phi) distributions. Electrostatic solvation is primarily responsible, and steric clash between pairs of atoms connected by torsion angles is not responsible...
  50. ncbi Empirical relationships between protein structure and carboxyl pKa values in proteins
    William R Forsyth
    Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA
    Proteins 48:388-403. 2002
    ..Aspartates and glutamates at the N-termini of helices have mean pK(a) values of 2.8 (+/-0.5) and 3.4 (+/-0.6), respectively, about 0.6 units less than the overall mean values...
  51. ncbi Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations
    Pavel Hobza
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Center for Complex Molecular Systems and Biomolecules, Dolejskova 3, 182 23 Prague 8, Czech Republic
    J Am Chem Soc 124:11802-8. 2002
    ..1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases...
  52. pmc Computational methods for biomolecular electrostatics
    Feng Dong
    Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, Missouri 63110, USA
    Methods Cell Biol 84:843-70. 2008
    ..contributions from linear, angular, and torsional forces in covalent bonds, van der waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of ..
  53. ncbi Computational studies of CXCR1, the receptor of IL-8/CXCL8, using molecular dynamics and electrostatics
    Nicholas Huynh
    Department of Biochemistry, University of California, Riverside, CA 92521, USA
    Biopolymers 89:52-61. 2008
    ....
  54. ncbi Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials
    Sergei Izvekov
    Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 0850, USA
    J Phys Chem B 112:4711-24. 2008
    ..With continued development, such effective potentials may provide an accurate and highly efficient alternative to Ewald-based long-range electrostatics methods.
  55. pmc Phosphatidic acid domains in membranes: effect of divalent counterions
    Jordi Faraudo
    Departament de Fisica, Universitat Autonoma de Barcelona, Bellaterra, Spain
    Biophys J 92:2806-18. 2007
    ..We conclude with a discussion of the implications of our results in the context of recent experimental studies in model systems and in real cells...
  56. ncbi Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel
    Ramzi Kutteh
    School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia
    J Phys Chem B 111:1090-8. 2007
    ..perform molecular dynamics simulations on the HERG model, followed by free energy, structural, and continuum electrostatics calculations...
  57. pmc Electrostatics in the cytoplasmic pore produce intrinsic inward rectification in kir2.1 channels
    Shih Hao Yeh
    Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
    J Gen Physiol 126:551-62. 2005
    ..We propose that neutral and positively charged residues at site 224 increase a local energy barrier, which reduces K+ efflux more than K+ influx, thereby producing inward rectification...
  58. pmc Relating microscopic charge movement to macroscopic currents: the Ramo-Shockley theorem applied to ion channels
    Wolfgang Nonner
    Department of Physiology and Biophysics, University of Miami School of Medicine, Miami, Florida, 33101 6430, USA
    Biophys J 87:3716-22. 2004
    ..Even without calculation or simulation, the Ramo-Shockley theorem eliminates a class of interpretations of experimental results. The theorem may also be used at each time step of simulations to compute external current...
  59. ncbi Role of electrostatics in the interaction between cytochrome f and plastocyanin of the cyanobacterium Phormidium laminosum
    Beatrix G Schlarb-Ridley
    Department of Biochemistry and Cambridge Centre for Molecular Recognition, University of Cambridge, Cambridge CB2 1QW, U K
    Biochemistry 41:3279-85. 2002
    ..The study shows that the electrostatics of the interaction between plastocyanin and cytochrome f of P. laminosum in vitro are not optimized for k(2)...
  60. ncbi Immunophysical exploration of C3d-CR2(CCP1-2) interaction using molecular dynamics and electrostatics
    Li Zhang
    Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
    J Mol Biol 369:567-83. 2007
    ....
  61. ncbi Effect of "helper lipid" on lipoplex electrostatics
    Danielle Hirsch-Lerner
    Laboratory of Membrane and Liposome Research, Department of Biochemistry, Hebrew University Hadassah Medical School, PO Box 12272, Jerusalem 91120, Israel
    Biochim Biophys Acta 1714:71-84. 2005
    ..This study aimed to better characterize cationic liposome and lipoplex electrostatics, which seems to play a major role in the formation and the performance of lipoplexes in vitro and in vivo...
  62. ncbi Electrostatics and the assembly of an RNA virus
    Paul van der Schoot
    Department of Physics and Astronomy, UCLA, Box 951547, Los Angeles, California 90095 1547, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 71:061928. 2005
    ..We compare our results with studies on the self-assembly of both synthetic and natural viruses...
  63. pmc Continuum electrostatics fails to describe ion permeation in the gramicidin channel
    Scott Edwards
    Protein Dynamics Unit, Department of Physics, Faculty of Science, Australian National University, Canberra, A C T 0200, Australia
    Biophys J 83:1348-60. 2002
    We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure...
  64. ncbi Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase
    Jason Quenneville
    Department of Chemistry, University of California, Davis, CA 95616, USA
    Biochim Biophys Acta 1757:1035-46. 2006
    ..In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton ..
  65. ncbi Identification and in silico analysis of a new group of double-histone fold-containing proteins
    Claudio Greco
    Dipartimento di Biotecnologie e Bioscienze, Universita degli Studi Milano Bicocca, P zza della Scienza 2, 20126 Milano, Italy
    J Mol Model 12:76-84. 2005
    ....
  66. ncbi The alpha7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics
    Shiva Amiri
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Mol Membr Biol 22:151-62. 2005
    ..These studies illustrate how molecular models of members of the nicotinic receptor superfamily of channels may be used to study structure-function relationships...
  67. pmc Structural origins of efficient proton abstraction from carbon by a catalytic antibody
    Erik W Debler
    Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:4984-9. 2005
    ....
  68. ncbi Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions
    George I Makhatadze
    Department of Biochemistry and Molecular Biology, Penn State University, College of Medicine, Hershey, PA 17033, USA
    J Mol Biol 336:929-42. 2004
    ..Such a mechanism of thermostabilization, although predicted from the basic thermodynamic considerations, has never been identified experimentally...
  69. pmc Solution pH alters mechanical and electrical properties of phosphatidylcholine membranes: relation between interfacial electrostatics, intramembrane potential, and bending elasticity
    Yong Zhou
    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA
    Biophys J 92:2451-62. 2007
    ..These mechanical and electrical studies lead to the conclusion that the effect of pH on membrane bending stiffness results from alterations in interfacial, as opposed to intramembrane, electrostatics.
  70. ncbi The open pore conformation of potassium channels
    Youxing Jiang
    Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 417:523-6. 2002
    ..The open conformation favours high conduction by compressing the membrane field to the selectivity filter, and also permits large organic cations and inactivation peptides to enter the pore from the intracellular solution...
  71. ncbi Analytical electrostatics for biomolecules: beyond the generalized Born approximation
    Grigori Sigalov
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
    J Chem Phys 124:124902. 2006
    ..At the same time, ALPB is equally computationally efficient. The new model is incorporated into the AMBER molecular modeling package and tested on small proteins...
  72. ncbi eF-site and PDBjViewer: database and viewer for protein functional sites
    Kengo Kinoshita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    Bioinformatics 20:1329-30. 2004
    ..To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program...
  73. pmc Quantitative membrane electrostatics with the atomic force microscope
    Yi Yang
    Department of Physics and Astronomy, Rice University, Houston, Texas, USA
    Biophys J 92:1966-74. 2007
    ..double layer interactions in electrolyte solutions, but provides only a qualitative view of interfacial electrostatics. We have fully characterized silicon nitride probe tips and other experimental parameters to allow a ..
  74. ncbi A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: structure, function and electrostatics
    Katia D'Ambrosio
    Istituto di Biostrutture e Bioimmagini, C N R, Napoli, Italy
    J Mol Biol 362:743-52. 2006
    ....
  75. ncbi Fluorescent polymeric transducer for the rapid, simple, and specific detection of nucleic acids at the zeptomole level
    Kim Doré
    Centre de Recherche en Sciences et Ingénierie des Macromolécules, Departement de Chimie, Universite Laval, Quebec City, Quebec, Canada G1K 7P4
    J Am Chem Soc 126:4240-4. 2004
    ..This simple system is versatile enough to detect nucleic acids of various lengths, including a segment from the RNA genome of the Influenza virus...
  76. ncbi Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations
    Celeste Sagui
    Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
    J Chem Phys 120:73-87. 2004
    ..simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields...
  77. ncbi Influence of electric charge variation at residues 209 and 159 on the interaction of eIF4E with the mRNA 5' terminus
    Joanna Zuberek
    Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki i Wigury Street, 02 089 Warsaw, Poland
    Biochemistry 43:5370-9. 2004
    ..e., equal to the sum of the individual destabilizing changes of DeltaG degrees. The possible implication of these results for the mechanism of control of eIF4E by phosphorylation, especially for the "clamping model", is discussed...
  78. ncbi Electrostatics of PEGylated micelles and liposomes containing charged and neutral lipopolymers
    Olga Garbuzenko
    Laboratory of Membrane and Liposome Research, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
    Langmuir 21:2560-8. 2005
    The electrostatics of large unilamellar vesicles (LUVs) of various lipid compositions were determined and correlated with steric stabilization...
  79. ncbi Efficient evaluation of binding free energy using continuum electrostatics solvation
    Danzhi Huang
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Med Chem 47:5791-7. 2004
    ..The present approach is about 2 orders of magnitude faster than previous LIE methods and can be used for ranking large libraries of structurally diverse compounds docked by automatic computational tools...
  80. ncbi Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure
    Diane Lejeune
    Centre de Biophysique Moleculaire Numerique, Faculté universitaire des Sciences agronomiques, Gembloux, Belgium
    Proteins 61:258-71. 2005
    ..These pairs were analyzed individually. Finally, we studied the conformation of DNA in the interaction sites. Despite the prevalence of B-DNA in the database, our results suggest that A-DNA is favored in the interaction sites...
  81. ncbi Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    Rong Chen
    Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
    Proteins 47:281-94. 2002
    ..Our method optimizes desolvation, shape complementarity, and electrostatics using a Fast Fourier Transform algorithm...
  82. pmc Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein
    Philip R Hardwidge
    Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, MN 55905, USA
    Nucleic Acids Res 30:1879-85. 2002
    ..We suggest that asymmetric phosphate neutralization contributes favorably to DNA bending by CAP, but cannot account for the full DNA deformation...
  83. ncbi pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    Tammy Man Kuang Cheng
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 68:503-15. 2007
    ..The scheme is based on Coulombic electrostatics with distance dependent dielectric constant, and implicit desolvation energy with atomic solvation parameters ..
  84. pmc Water in protein structure prediction
    Garegin A Papoian
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0371, USA
    Proc Natl Acad Sci U S A 101:3352-7. 2004
    ..Long-range pairing of hydrophilic groups is an integral part of protein architecture. Specific water-mediated interactions are a universal feature of biomolecular recognition landscapes in both folding and binding...
  85. ncbi Lateral sequestration of phosphatidylinositol 4,5-bisphosphate by the basic effector domain of myristoylated alanine-rich C kinase substrate is due to nonspecific electrostatic interactions
    Jiyao Wang
    Department of Physiology and Biophysics, State University of New York, Stony Brook, New York 11794 8661, USA
    J Biol Chem 277:34401-12. 2002
    ..This electrostatic sequestration was observed experimentally using a phospholipase C assay. Our results are consistent with the hypothesis that MARCKS could reversibly sequester much of the PIP(2) in the plasma membrane...
  86. ncbi The catalytic power of ketosteroid isomerase investigated by computer simulation
    Isabella Feierberg
    Department of Cell and Molecular Biology, Uppsala University Biomedical Center, Box 596, SE 751 24 Uppsala, Sweden
    Biochemistry 41:15728-35. 2002
    ..The existence of such a water molecule could explain how the enzyme manages to maintain a low pK(a) for the general base residue...
  87. ncbi Ions and RNA folding
    David E Draper
    Department of Chemistry and 2Program in Molecular and Computational Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
    Annu Rev Biophys Biomol Struct 34:221-43. 2005
    ....
  88. ncbi Tuning bulk electrostatics to regulate protein function
    Zach Serber
    Department of Chemical and Systems Biology, Stanford University School of Medicine, MC 5174, Stanford, CA 94305, USA
    Cell 128:441-4. 2007
    ..This provides a beautiful example of how phosphorylation can produce decisive changes in protein function through bulk electrostatics, without the necessity of intricate conformational changes.
  89. ncbi Electrostatic fasteners hold the T cell receptor-CD3 complex together
    Donald M Engelman
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
    Mol Cell 11:5-6. 2003
    ..2003). Such interactions can strongly stabilize subunit associations while permitting conformation changes during signaling...
  90. pmc Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies
    Donald Hamelberg
    Department of Chemistry, Georgia State University, 50 Decatur Street, Atlanta, GA 30303, USA
    Nucleic Acids Res 30:3615-23. 2002
    ....
  91. ncbi Continuum electrostatic analysis of irregular ionization and proton allocation in proteins
    Assen Koumanov
    Karolinska Institutet, Department of Biosciences, Huddinge, Sweden
    Proteins 46:85-96. 2002
    ..This finding provides a new interpretation of the experimentally observed chemical shift of this residue...
  92. ncbi Bacterial osmosensing: roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology and Materials Science Center plus, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochim Biophys Acta 1666:88-104. 2004
    ..7 mV for monovalent ions. The osmosensing mechanism is qualitatively described as an "ON/OFF switch" representing thermally relaxed and electrostatically locked protein conformations...
  93. ncbi Protein stability and surface electrostatics: a charged relationship
    Samantha S Strickler
    Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
    Biochemistry 45:2761-6. 2006
    ....
  94. ncbi Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    Keiji Takamoto
    Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA
    J Mol Biol 343:1195-206. 2004
    ..The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA...
  95. ncbi Macroscopic electrostatic models for protonation states in proteins
    Donald Bashford
    Department of Molecular Biotechnology, Hartwell Center for Bioinformatics and Biotechnology, Saint Jude Children s Research Hospital, Memphis, TN 38105 2794, USA
    Front Biosci 9:1082-99. 2004
    ..A tutorial approach is taken, the main aim of which is a thorough understanding of the method...
  96. pmc Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
    Susan Jones
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:7189-98. 2003
    ..This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set...
  97. ncbi Insertion selectivity of antimicrobial peptide protegrin-1 into lipid monolayers: effect of head group electrostatics and tail group packing
    Yuji Ishitsuka
    Department of Chemistry, The Institute for Biophysical Dynamics and the James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
    Biochim Biophys Acta 1758:1450-60. 2006
    ..However, the presence of PG-1 can still affect lipid morphology even with no observed PG-1 insertion. These results show the important role that lipid composition of the cell membrane plays in the activity of AMPs...
  98. ncbi Membrane and juxtamembrane targeting by PH and PTB domains
    Jonathan P DiNitto
    Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Two Biotech, Worcester, MA 01605, USA
    Biochim Biophys Acta 1761:850-67. 2006
    ..In this review, we highlight unifying recognition principles and further illustrate with examples how divergent mechanisms contribute to membrane and juxtamembrane targeting by PH and PTB domains...
  99. ncbi The role of electrostatics in protein-membrane interactions
    Anna Mulgrew-Nesbitt
    Weill Medical College of Cornell University, New York, NY 10021, USA
    Biochim Biophys Acta 1761:812-26. 2006
    Many experimental, structural and computational studies have established the importance of nonspecific electrostatics as a driving force for peripheral membrane association...
  100. pmc PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics
    Cyril Azuara
    Unité de Dynamique Structurale des Macromolécules, URA 2185 du C N R S, Institut Pasteur, 75015 Paris, France
    Nucleic Acids Res 34:W38-42. 2006
    ..These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes...
  101. ncbi Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
    V Zoete
    Laboratoire de Chimie Biophysique, Institut de Science et d Ingenierie Supramoleculaires, Universite Louis Pasteur, 8 allee Gaspard Monge, BP 70028 Strasbourg Cedex, France
    J Comput Aided Mol Des 17:861-80. 2003
    ..When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization...

Research Grants66

  1. Molecular Determinants of DNA Sliding and Hopping by a DNA Repair Glycosylase
    MENG MENG ROWLAND; Fiscal Year: 2013
    ..First, to test the role of DNA phosphate electrostatics, we will insert neutral methylphosphonate linkages in the DNA backbone between two uracil target sites ..
  2. SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
    Sharon Hammes Schiffer; Fiscal Year: 2010
    ..The calculations will probe the roles of electrostatics, hydrogen bonding, hydrogen tunneling, and protein motion in enzyme reactions...
  3. LIPID MODULATION OF RHODOPSIN SIGNALING IN MEMBRANES
    Michael F Brown; Fiscal Year: 2010
    ..An additional aspect entails the interplay of the bilayer electrostatics including the surface charge density and the electrical double layer with the above bilayer properties...
  4. Mechanisms of Viral DNA Packaging
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2013
    ..the packaging process the DNA is compacted to near-crystalline density-overcoming energetic penalties due to electrostatics repulsion, DNA bending stiffness, and entropy...
  5. Quantum Chemistry of Proton Pumping by Cytochrome c Oxidases
    Louis Noodleman; Fiscal Year: 2013
    ..The proposed work involves density functional theory (DFT) calculations of geometric and electronic structure, electrostatics calculations, and quantum mechanics\molecular mechanics\molecular dynamics (QM/MM/MD) simulations to provide a ..
  6. The interaction between outer membrane porins and toll-like receptors
    T M Iverson; Fiscal Year: 2011
    ..The goal of this 2-year proposal is to identify how electrostatics contribute to the recognition of OMPs by TLRs. Specifically, we plan to: 1...
  7. Functional mapping of SNARE-dependent trafficking and fusion
    Jeffrey E Pessin; Fiscal Year: 2013
    ..we will use a series of biophysical and cell biological approaches to determine the role of membrane electrostatics and the tandem VAMP2 tryptophans in this key biological process...
  8. SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES
    Sharon Hammes-Schiffer; Fiscal Year: 2013
    ..These calculations will probe the roles of hydrogen bonding, electrostatics, active site reorganization, and conformational sampling in both protein and RNA enzyme catalysis...
  9. Specificity in the Synthesis of Aminoacyl-tRNA
    John J Perona; Fiscal Year: 2012
    ..This overall study will then be followed with an in-depth analysis of the roles of indirect readout, electrostatics, and conformational strain in communication between the tRNA acceptor stem interface and the adjacent ..
  10. Understanding pH-Dependent Protein Behavior Using Advanced Continuum Theory
    JAYDEEP PORTER BARDHAN; Fiscal Year: 2013
    ..The new approach, called nonlocal electrostatics, is an example of a multiscale model because it captures physics that are important at very small length ..
  11. Electrostatics and Dynamics in Proteins
    Steven G Boxer; Fiscal Year: 2013
    ..Applications of these novel systems for advanced imaging and as modulators of enzyme function that affect cell physiology with light are described. ..
  12. Prediction of the Structure of Therapeutic Antibodies with their Antigens
    Jeffrey J Gray; Fiscal Year: 2013
    ..web, and (3) develop methods to quantitatively predict protein-protein binding affinity using improved electrostatics treatments...
  13. Nonheme diiron enzymes: understanding oxygen activation in human deoxyhypusine hy
    Lisa Engstrom; Fiscal Year: 2013
    ..site Glu ligands (Glu57, Glu90, Glu208, Glu241) to Asp and Gln will be performed to assess the contribution of electrostatics and sterics on hDOHHperoxo stability...
  14. Preferential cytotoxic actions of metal oxide nanoparticles against cancer
    Denise G Wingett; Fiscal Year: 2010
    ..Specific aim 3 will determine the extent to which alterations in nanoparticle electrostatics, antibody functionalization, and iron-doping to promote greater intracellular reactive oxygen species ..
  15. Probing Nucleotide Recognition in the Genetic Information Pathway
    Eric T Kool; Fiscal Year: 2012
    ..to studying these biological processes is to develop and study new DNA and RNA base analogs that modulate electrostatics and shape in a systematic way...
  16. Approaches to Modeling Key Elements in Glutamate Receptors Activation Mechanism
    Maria G Kurnikova; Fiscal Year: 2012
    ..We will use methods of computational chemistry: molecular dynamics simulations and continuum electrostatics to compute free energies of distinct conformational states of the ligand binding and transmembrane domains and ..
  17. Unnatural Base Pairs as DNA Bioprobes
    KATHERINE RADTKE; Fiscal Year: 2009
    ..questions by providing new insights into the physical aspects of DNA helix stability and the role that electrostatics and base stacking play...
  18. Electronic Structure and Reactions of Fe-oxo Enzymes
    Louis Noodleman; Fiscal Year: 2010
    ..density functional theory (DFT) methods to describe and analyze active site properties, and link this to an electrostatics-based representation of the longer range protein and solvent environment...
  19. ELECTROSTATIC SURFACE OPTIMIZATION FOR OSSEOINTEGRATION
    Michele Marcolongo; Fiscal Year: 2000
    ..Previous studies have been limited in this regard as they have not uncoupled the electrostatics from functionality and surface energy due to surface chemistry...
  20. Mechanistic Basis for Amino Acid Discrimination by the Translational Machinery
    Virginia W Cornish; Fiscal Year: 2013
    ..hypothesis, the ribosome is exquisitely specific not only for the tRNA adaptor, but also for the structure and electrostatics of the amino acid covalently attached to the tRNA...
  21. COMPUTATIONAL STUDIES OF ION CHANNELS
    Benoit Roux; Fiscal Year: 2012
    ..concerning the nature of ion diffusion through wide aqueous vestibules and its sensitivity to pore shape and electrostatics. The proposed projects are designed to address fundamental issues about ion permeation, inactivation and ..
  22. RNA-ligand interactions: simulation and experiment
    Carlos Simmerling; Fiscal Year: 2013
    ..flexible loop that undergoes a conformational change when it binds to ions, and acts as a model system to test electrostatics, sampling, structural accuracy, and the ability of the simulations to model the subtle influences of ions on ..
  23. Refinement of Macromolecular Assembly Structure using Electron Microscopy
    Michael S Chapman; Fiscal Year: 2010
    ..This work will include development of restraints for continuum electrostatics and hydrogen bonding, and a comparison of atomistic restraints with heuristics that might enhance convergence ..
  24. Computational/Experimental Modeling of Aqueous Environments in Biology
    John W Brady; Fiscal Year: 2013
    ..SSDQO reproduces numerous properties of liquid water over a wide range of conditions, mimics the electrostatics of the quantum mechanical electron density of a water molecule better than typical models, and yet is ..
  25. Level-Set Variational Implicit-Solvent Approach to Biomolecular Interactions
    Bo Li; Fiscal Year: 2013
    ..Sophisticated numerical methods for electrostatics are developed to couple with the level-set method...
  26. Modeling macromolecular transport through protein and solid-state nanopores
    Murugappan Muthukumar; Fiscal Year: 2013
    ..and numerical computation of coupled nonlinear equations to address polyelectrolyte statistics and dynamics, electrostatics, and hydrodynamics in the phenomena of DNA translocation...
  27. All-optical molecular voltmeter for measuring electric fields in proteins
    Aleksander Rebane; Fiscal Year: 2013
    ..Here we are taking next logical step: determine if and how can we use the sensitivity of 2PA to measure electrostatics in complex proteins...
  28. Kinome-Wide Spectroscopic Study of Drug Binding Site Electrostatics
    NICHOLAS MARK LEVINSON; Fiscal Year: 2013
    ..1, a new spectroscopic technique called vibrational Stark spectroscopy will be used to construct a map of the electrostatics of the ATP-binding site and how it varies across the ~500 members of this protein family...
  29. Structural Mechanisms for the Inhibition of Thrombosis
    JAMES HUNTINGTON; Fiscal Year: 2009
    ..monomeric native and activated AT;d) the role of hinge region expulsion in heparin binding;and, e) the role of electrostatics in propagating the conformational change...
  30. Fundamental Studies of RNA Folding
    Daniel Herschlag; Fiscal Year: 2013
    ..simple helices and uses an integrated experimental-computational feedback loop to develop an understanding of electrostatics, the largest and most general force influencing the behavior and interactions of RNA...
  31. Predicting protein flexibility and stability
    Donald Jacobs; Fiscal Year: 2010
    ..of essential entropy-compensation mechanisms that include (a) hydration, (b) hydrophobic interactions, (c) electrostatics interactions, with (d) a residue-specific parameterization...
  32. De novo design of alpha-helical bundles
    William F Degrado; Fiscal Year: 2013
    ..In the coming period we will determine how systematic changes to the solvent-accessibility, electrostatics, and polarity of the dimetal site affect its reactivity and catalytic properties. Aim 2...
  33. DelPhi: Software for Electrostatic Modeling of Biomolecules and Objects
    EMIL GEORGIEV ALEXOV; Fiscal Year: 2013
    ..The role of electrostatics is two fold: providing long-range interactions steering biological molecules toward their pre-binding ..
  34. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2011
    ..We will utilize and optimize a novel potential energy function with explicit polarization and atomic multipole electrostatics for predicting ligand-protein binding...
  35. Modeling Membrane Binding and Permeabilization by Antimicrobial Peptides
    Themis Lazaridis; Fiscal Year: 2012
    ..These studies will test the hypothesis that electrostatics is a major determinant of target selectivity. 2. Investigate mechanisms of membrane permeabilization by AMPs...
  36. Structure-Energy Correlation in Proteins
    BERTRAND GARCIA-MORENO; Fiscal Year: 2013
    ..The specific aims of this proposal describe experimental studies to examine fundamental aspects of protein electrostatics. The studies are focused on the properties of internal ionizable groups because those are the ones that are ..
  37. Fast and Accurate Numerical Methods of Electrostatic Interactions in Biomolecules
    Wei Cai; Fiscal Year: 2010
    ..The main challenge for modeling electrostatics, as the core calculation of Molecular Dynamics and Monte Carlo simulations, is to balance the accuracy of ..
  38. APBS: Nanoscale Biomolecular Electrostatics Software
    Nathan A Baker; Fiscal Year: 2013
    ..APBS is a unique software package which solves the equations of continuum electrostatics for large biomolecular assemblages...
  39. Electrostatic effects of the native state ensemble
    BERTRAND GARCIA-MORENO; Fiscal Year: 2012
    ..of pKa values and electrostatic energies, and the development of computational methods for structure- based electrostatics calculations, continues to be of great interest...
  40. Analytical Electrostatics: Methods and Biological Applications
    ALEXEY VLAD ONUFRIEV; Fiscal Year: 2013
    ..of practical analytical electrostatic models -- the Poisson formalism of continuum, linear, local response electrostatics. The proposed fully implicit, analytical models will retain most of the solvation effects of the first ..
  41. High Performance Computing in Computational Biology
    Dennis R Livesay; Fiscal Year: 2010
    ..efforts, including projects in protein stability/flexibility relationships, molecular dynamics, protein electrostatics, RNA secondary structure prediction, and digital processing of biological images...
  42. ELECTROSTATICS AND DYNAMICS IN MYOGLOBIN MUTANTS
    STEVEN BOXER; Fiscal Year: 2003
    ..a request for continuing support of a research program aimed at understanding the role of protein dynamics and electrostatics in biological function...
  43. MUTATIONAL EFFECTS ON COLLAGEN'S STRUCTURE & STABILITY
    TERI KLEIN; Fiscal Year: 2003
    ..mutants for a type I collagen fragment; (4) determine the neighborhood effects and individual contributions of electrostatics including hydrogen bonds and conformational changes for the OI regional phenotype model; and (5) determine the ..
  44. Numerical Methods that Solve the PBE for Biomolecular Electrostatics
    ALEXANDER BOSCHITSCH; Fiscal Year: 2007
    ..In Phase II, this model will be further refined, incorporated into an electrostatics modeling software package and used to study biologically significant systems requiring the mPBE-based level of ..
  45. Workshop on Methods for Macromolecular Modeling
    Tamar Schlick; Fiscal Year: 2004
    ..Advances in simulation techniques, most notably in the areas of conformational sampling, fast electrostatics, molecular dynamics integration, and quantum-mechanical calculations, are having significant impact on ..
  46. Structure and Interactions of Gas Vesicles by SSNMR
    Judith Herzfeld; Fiscal Year: 2007
    ..The role of electrostatics will be explored by identifying the cation displacements and protonation changes that induce vesicle collapse ..
  47. BIOCHEMISTRY AND BIOPHYSICS OF BPTI FOLDING MUTANTS
    Stephen Anderson; Fiscal Year: 1993
    ..the resulting mutants; 3) Test the "cardboard box" model of protein folding by measuring the contribution of electrostatics to 5-55 disulfide bond formation and to global polypeptide stability; 4) Facilitate ongoing work in ..
  48. Validating polarizability models in macromolecular force fields: The Stark effect
    ASHLEY LAUREN RINGER; Fiscal Year: 2011
    ..The proper description of electrostatics and treatment of molecular polarizability in macromolecular force fields is critical to the development of ..
  49. Regulatory Mechanisms of Secretory Phospholipases A2
    SUREN TATULIAN; Fiscal Year: 2004
    ..Our specific aims are: 1. Identify the roles of membrane electrostatics, membrane binding strength, orientation of membrane-bound PLA2 and membrane-induced structural changes in PLA2 ..
  50. HEAD GROUP INTERACTIONS IN MEMBRANES AND MICELLES
    KENNETH DILL; Fiscal Year: 1991
    ..This will require coupling this electrostatics treatment with recent efforts of ours and others on chain conformations in interfacial systems, in a relevant ..
  51. Workshop on Methods for Macromolecular Modeling
    Tamar Schlick; Fiscal Year: 2000
    ..Advances in simulation techniques, most notably in the areas of conformational sampling, fast electrostatics, molecular dynamics integration, and quantum-mechanical calculations are having significant impact on ..
  52. Electrostatic Modulation of Protein Stability and Folding
    JANA SHEN; Fiscal Year: 2013
    ..the native-centric paradigm of protein stability and function and transform the static-structure based view of protein electrostatics. They will also help establish general principles for computational protein design.
  53. INHALATIONAL ANESTHETIC BINDING STUDIES
    Roderic Eckenhoff; Fiscal Year: 2007
    ..binding to protein relies on internal cavity volume, hydrophobic and weak van der Waals forces, whereas full electrostatics reduce affinity...
  54. Nanofabrication of high performance AFM cantilevers
    JAN HOH; Fiscal Year: 2003
    ..tool for biomedical research, and has found applications that include imaging of DNA, measuring local surface electrostatics on membranes, mapping mechanical properties of cells and single molecule protein mechanics...
  55. Theoretical and MD Simulation Studies of U1A-RNA Binding and Specificity
    David Beveridge; Fiscal Year: 2006
    ..models of dynamical structures obtained from molecular dynamics (MD) simulation and corresponding continuum electrostatics and free energy calculations using several methods as a cross check on results...
  56. Computational analysis of protein/membrane interactions
    Diana Murray; Fiscal Year: 2006
    ..membrane-interacting proteins in parallel, two hypotheses will be tested: 1) that two physical factors-electrostatics and hydrophobicity-are the major determinants of membrane binding, and 2) that these physical factors are ..
  57. THEORETICAL STUDIES OF PROTEIN ELECTROSTATICS
    Donald Bashford; Fiscal Year: 2003
    ..In bacteriorhodopsin, the modulation of several pKa values and proton transfer energies within the molecule during its photocycle is crucial to its function as a proton pump. ..
  58. 500 MHZ SPECTROMETER
    HARDEN MC CONNELL; Fiscal Year: 1990
    ..Professor Boxer's research involves studies of electrostatics and dynamics in recombinant human and sperm whale myoglobins...
  59. Computational Prediction of Protein-Protein Docking
    Jeffrey Gray; Fiscal Year: 2005
    ..2000, and he is an expert in scientific computation and colloid science including self-assembly processes and electrostatics. The goal of the training period is to make Gray an expert in genomics and protein biophysics...
  60. CRYSTALLOGRAPHIC ANALYSIS OF PROTEIN ELECTROSTATICS
    Robert Blessing; Fiscal Year: 2006
    ..for the development of these new biocrystallographic methodologies will be analyses of the roles of structured electrostatics and structured dynamical modes in the phenomena of insulin hexamer allosterism and ribonuclease...
  61. Computational analysis of phosphoinositide signaling
    Diana Murray; Fiscal Year: 2009
    ..Our overall hypothesis for the current proposal is that electrostatics plays a general role in phosphoinositide signaling and is manifested through phosphoinositide-mediated ..
  62. FREE SOLUTION MOBILITY AS A PROBE OF DNA ELECTROSTATICS
    Nancy Stellwagen; Fiscal Year: 2004
    DESCRIPTION: This amended new application seeks funding to characterize features of DNA electrostatics by observation of the free solution mobilities of a number of DNA molecules...
  63. Static & dynamic electrostatic interactions in proteins
    ZINAIDA ROMANOVA; Fiscal Year: 2003
    ..ultimate goal of designing molecular probes capable of mapping proteins and reporting on protein dynamics and electrostatics Specifically to: 1) design and synthesize new cysteine (Cys)-specific labels, generic probes that will allow ..
  64. POLARIZABLE FORCE FIELDS FOR PEPTIDES AND PROTEINS
    MURCO RINGNALDA; Fiscal Year: 2000
    ..FQ model to construct a full polarizable force field by constructing a transferable functional form for the electrostatics and then adding van der Waals and valence terms...
  65. Nanoscale Electrocatalytic Protein Detection
    SHANA KELLEY; Fiscal Year: 2006
    ..Because the reporter system responds to changes in the electrostatics of an electrode surface, it will enable the analysis of nucleic acids/protein and peptide/protein complexes...
  66. ELECTROSTATIC STABILIZATION OF A PROTEIN-DNA COMPLEX
    Shari Spector; Fiscal Year: 2002
    ..goal of the project described in this proposal is to identify a set of general rules describing the role of electrostatics in the stability and binding affinity of protein- DNA complexes...