amino acids

Summary

Summary: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.

Top Publications

  1. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
  2. ncbi Bayes empirical bayes inference of amino acid sites under positive selection
    Ziheng Yang
    Department of Biology, University College London, London, UK
    Mol Biol Evol 22:1107-18. 2005
  3. ncbi Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    Shao En Ong
    Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
    Mol Cell Proteomics 1:376-86. 2002
  4. doi Some remarks on protein attribute prediction and pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    J Theor Biol 273:236-47. 2011
  5. pmc Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids
    Yasemin Sancak
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 141:290-303. 2010
  6. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
  7. pmc AAindex: amino acid index database, progress report 2008
    Shuichi Kawashima
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai Minato ku Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D202-5. 2008
  8. pmc mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase
    Roberto Zoncu
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 334:678-83. 2011
  9. pmc Protein sectors: evolutionary units of three-dimensional structure
    Najeeb Halabi
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Cell 138:774-86. 2009
  10. pmc The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1
    Yasemin Sancak
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology MIT, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 320:1496-501. 2008

Detail Information

Publications388 found, 100 shown here

  1. ncbi Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen
    Center for Biological Sequence Analysis, BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Mol Biol 340:783-95. 2004
    ..The new method has been benchmarked against other available methods. Predictions can be made at the publicly available web server..
  2. ncbi Bayes empirical bayes inference of amino acid sites under positive selection
    Ziheng Yang
    Department of Biology, University College London, London, UK
    Mol Biol Evol 22:1107-18. 2005
    ..The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites...
  3. ncbi Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    Shao En Ong
    Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
    Mol Cell Proteomics 1:376-86. 2002
    ..Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins...
  4. doi Some remarks on protein attribute prediction and pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    J Theor Biol 273:236-47. 2011
    ....
  5. pmc Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids
    Yasemin Sancak
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 141:290-303. 2010
    The mTORC1 kinase promotes growth in response to growth factors, energy levels, and amino acids, and its activity is often deregulated in disease...
  6. ncbi A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    S Whelan
    Department of Zoology, University of Cambridge, Cambridge, England
    Mol Biol Evol 18:691-9. 2001
    ....
  7. pmc AAindex: amino acid index database, progress report 2008
    Shuichi Kawashima
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai Minato ku Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D202-5. 2008
    AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section...
  8. pmc mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase
    Roberto Zoncu
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 334:678-83. 2011
    The mTOR complex 1 (mTORC1) protein kinase is a master growth regulator that is stimulated by amino acids. Amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal ..
  9. pmc Protein sectors: evolutionary units of three-dimensional structure
    Najeeb Halabi
    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9050, USA
    Cell 138:774-86. 2009
    ..organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-..
  10. pmc The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1
    Yasemin Sancak
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology MIT, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 320:1496-501. 2008
    ..complex is the central component of a pathway that promotes growth in response to insulin, energy levels, and amino acids and is deregulated in common cancers...
  11. ncbi The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    Zsuzsanna Dosztanyi
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, PO Box 7, Hungary
    J Mol Biol 347:827-39. 2005
    ..This application we term IUPred and compare its performance with three generally accepted predictors, PONDR VL3H, DISOPRED2 and GlobPlot on a database of disordered proteins...
  12. pmc COI1 is a critical component of a receptor for jasmonate and the bacterial virulence factor coronatine
    Leron Katsir
    Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
    Proc Natl Acad Sci U S A 105:7100-5. 2008
    ..These findings demonstrate that COI1 is a critical component of the JA receptor and that COR exerts its virulence effects by functioning as a potent agonist of this receptor system...
  13. ncbi Identifying GPCRs and their types with Chou's pseudo amino acid composition: an approach from multi-scale energy representation and position specific scoring matrix
    - Zia-ur-Rehman
    Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences PIEAS, P O 45650, Nilore, Islamabad, Pakistan
    Protein Pept Lett 19:890-903. 2012
    ..We have compared our method with various other methods. The significance in performance of the proposed method depicts it to be useful for GPCRs classification...
  14. pmc Codon-substitution models for heterogeneous selection pressure at amino acid sites
    Z Yang
    Department of Biology, University College London, London NW1 2HE, United Kingdom
    Genetics 155:431-49. 2000
    ..However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets...
  15. ncbi A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
    Shao En Ong
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Protoc 1:2650-60. 2006
    Stable isotope labeling by amino acids in cell culture (SILAC) is a simple, robust, yet powerful approach in mass spectrometry (MS)-based quantitative proteomics...
  16. ncbi The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
    Jorn Kalinowski
    Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 104:5-25. 2003
    ..genomic sequence of Corynebacterium glutamicum ATCC 13032, well-known in industry for the production of amino acids, e.g. of L-glutamate and L-lysine was determined. The C...
  17. pmc Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila
    Richard C Grandison
    Institute of Healthy Ageing, Department of Genetics Evolution and Environment, University College London, UK
    Nature 462:1061-4. 2009
    ..Adding essential amino acids to the dietary restriction condition increased fecundity and decreased lifespan, similar to the effects of full ..
  18. 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...
  19. doi propy: a tool to generate various modes of Chou's PseAAC
    Dong Sheng Cao
    Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083, People s Republic of China
    Bioinformatics 29:960-2. 2013
    ..These features could be generally regarded as different Chou's PseAAC modes. In addition, it can also easily compute the previous descriptors based on user-defined properties, which are automatically available from the AAindex database...
  20. pmc Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1
    Liron Bar-Peled
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Cell 150:1196-208. 2012
    The mTOR Complex 1 (mTORC1) pathway regulates cell growth in response to numerous cues, including amino acids, which promote mTORC1 translocation to the lysosomal surface, its site of activation...
  21. pmc Plasma metabolomic profiles reflective of glucose homeostasis in non-diabetic and type 2 diabetic obese African-American women
    Oliver Fiehn
    Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 5:e15234. 2010
    ..small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e...
  22. ncbi Regulated translation initiation controls stress-induced gene expression in mammalian cells
    H P Harding
    Skirball Institute of Biomolecular Medicine The Department of Medicine, Kaplan Cancer Center New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 6:1099-108. 2000
    ..Mammalian cells thus utilize an ancient pathway to regulate gene expression in response to diverse stress signals...
  23. doi Adding new chemistries to the genetic code
    Chang C Liu
    The Scripps Research Institute, La Jolla, California 92037, USA
    Annu Rev Biochem 79:413-44. 2010
    ..of new orthogonal aminoacyl-tRNA synthetase/tRNA pairs has led to the addition of approximately 70 unnatural amino acids (UAAs) to the genetic codes of Escherichia coli, yeast, and mammalian cells...
  24. doi How Saccharomyces responds to nutrients
    Shadia Zaman
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Annu Rev Genet 42:27-81. 2008
    ....
  25. pmc Relationships between circulating metabolic intermediates and insulin action in overweight to obese, inactive men and women
    Kim M Huffman
    Physical Medicine and Rehabilitation, Veterans Affairs Medical Center, Durham, North Carolina, USA
    Diabetes Care 32:1678-83. 2009
    ..To determine whether circulating metabolic intermediates are related to insulin resistance and beta-cell dysfunction in individuals at risk for type 2 diabetes...
  26. pmc Identification of amino acids in HA and PB2 critical for the transmission of H5N1 avian influenza viruses in a mammalian host
    Yuwei Gao
    Animal Influenza Laboratory of the Ministry of Agriculture and National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People s Republic of China
    PLoS Pathog 5:e1000709. 2009
    ..These amino acids changes in PB2 and HA could serve as important molecular markers for assessing the pandemic potential of H5N1 ..
  27. pmc Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    R Nielsen
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 148:929-36. 1998
    ..Positively selected sites are found in both the V3 region and the flanking regions...
  28. pmc Amino acids and mTORC1: from lysosomes to disease
    Alejo Efeyan
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Trends Mol Med 18:524-33. 2012
    ..findings have placed the lysosome, a key mediator of cellular catabolism, at the core of mTORC1 regulation by amino acids. A multiprotein complex that includes the Rag GTPases, Ragulator, and the v-ATPase forms an amino acid-sensing ..
  29. doi PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions
    Pufeng Du
    School of Computer Science and Technology, Tianjin University, Tianjin 300072, China
    Anal Biochem 425:117-9. 2012
    ..net), which can be used to generate various modes of Chou's pseudo-amino acid composition in a much more efficient and flexible way. It is anticipated that PseAAC-Builder may become a useful tool for studying various protein attributes...
  30. pmc Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting
    Karsten Suhre
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
    PLoS ONE 5:e13953. 2010
    ....
  31. pmc The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis
    Paul E Staswick
    Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583, USA
    Plant Cell 16:2117-27. 2004
    ..produced in vitro by recombinant JAR1 demonstrated that this enzyme forms JA-amido conjugates with several amino acids, including JA-Ile. JA-Val, -Leu, -Ile, and -Phe were each quantified in Arabidopsis seedlings by GC-MS...
  32. doi iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types
    Xuan Xiao
    Computer Department, Jing De Zhen Ceramic Institute, Jing De Zhen 333403, China
    Anal Biochem 436:168-77. 2013
    ..For the conveniences of users, a user-friendly web-server for iAMP-2L was established at http://www.jci-bioinfo.cn/iAMP-2L...
  33. ncbi Very fast empirical prediction and rationalization of protein pKa values
    Hui Li
    Department of Chemistry, Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA
    Proteins 61:704-21. 2005
    ..89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values...
  34. doi Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition
    Yen Kuang Chen
    Institute of Biomedical Informatics, National Yang Ming University, No 155, Sec 2, Lih Nong Street, Taipei, 112, Taiwan, ROC
    J Theor Biol 318:1-12. 2013
    ..The classifier has been deployed as a web server and can be accessed at http://bsaltools.ym.edu.tw/predmpt...
  35. pmc PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Biochim Biophys Acta 1804:996-1010. 2010
    ..Increased understanding of the underlying mechanism by which such meta-predictors give improved predictions will likely promote the further development of protein disorder predictors. Access to PONDR-FIT is available at www.disprot.org...
  36. doi Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform
    Xing Yu Sun
    Department of Chemistry, Nanchang University, Nanchang 330031, P R China
    Mol Biosyst 8:3178-84. 2012
    ..60%. The overall accuracy of the 2nd layer varies from 88.23 to 100%. The results suggest that this newly developed protocol (DWT_DT) is very promising in predicting quaternary structures with complicated composition...
  37. pmc Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Yanzhi Guo
    College of Chemistry, Sichuan University, Chengdu 610064 and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P R China
    Nucleic Acids Res 36:3025-30. 2008
    ..The prediction software and all data sets used in this article are freely available at http://www.scucic.cn/Predict_PPI/index.htm...
  38. doi Supersecondary structure prediction using Chou's pseudo amino acid composition
    Dongsheng Zou
    College of Computer Science, Chongqing University, Chongqing 400044, China
    J Comput Chem 32:271-8. 2011
    ..Our method is trained and tested on ArchDB40 dataset containing 3088 proteins. The highest overall accuracy for the training dataset and the independent testing dataset are 77.7 and 69.4%, respectively...
  39. doi Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition
    D N Georgiou
    Department of Mathematics, University of Patras, 265 00 Patras, Greece
    J Theor Biol 257:17-26. 2009
    In this paper we present a study of classification of the 20 amino acids via a fuzzy clustering technique...
  40. doi Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine
    Hassan Mohabatkar
    Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
    J Theor Biol 281:18-23. 2011
    ..Based on our results, using the concept of Chou's pseudo-amino acid composition and support vector machine is an effective approach for the prediction of GABA(A)Rs...
  41. pmc Hyperglycemia and a common variant of GCKR are associated with the levels of eight amino acids in 9,369 Finnish men
    Alena Stancakova
    Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
    Diabetes 61:1895-902. 2012
    ..Plasma levels of eight amino acids were measured with proton nuclear magnetic resonance spectroscopy...
  42. pmc Distinct pathways for modification of the bacterial cell wall by non-canonical D-amino acids
    Felipe Cava
    Department of Microbiology and Molecular Genetics, Channing Laboratory, Brigham and Women s Hospital, Harvard Medical School and HHMI, Boston, MA, USA
    EMBO J 30:3442-53. 2011
    Production of non-canonical D-amino acids (NCDAAs) in stationary phase promotes remodelling of peptidoglycan (PG), the polymer that comprises the bacterial cell wall...
  43. doi Host proteasomal degradation generates amino acids essential for intracellular bacterial growth
    Christopher T D Price
    Department of Microbiology and Immunology, College of Medicine, University of Louisville, KY 40202, USA
    Science 334:1553-7. 2011
    ..proteasomal degradation of Lys(48)-linked polyubiquitinated proteins, assembled on the LCV by AnkB, generates amino acids required for intracellular bacterial proliferation...
  44. doi MemHyb: predicting membrane protein types by hybridizing SAAC and PSSM
    Maqsood Hayat
    Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences PIEAS, Islamabad, Pakistan
    J Theor Biol 292:93-102. 2012
    ..The web server for the proposed MemHyb-SVM is accessible at http://111.68.99.218/MemHyb-SVM...
  45. ncbi Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    Tal Pupko
    The Institute of Statistical Mathematics, 4 6 7 Minami Azabu, Minato ku, Tokyo 106 8569, Japan
    Bioinformatics 18:S71-7. 2002
    ..Functionally important regions often correspond to surface patches of slowly evolving residues...
  46. pmc Amino acid regulation of TOR complex 1
    Joseph Avruch
    Department of Molecular Biology and Diabetes Research Unit, Medical Service, Massachusetts General Hospital, and Department of Medicine, Harvard Medical School, Simches Research Center, Boston, MA 02114, USA
    Am J Physiol Endocrinol Metab 296:E592-602. 2009
    ..the biochemical mechanisms that regulate mTORC1 kinase activity, with special emphasis on mTORC1 regulation by amino acids. The dominant positive regulator of mTORC1 is the GTP-charged form of the ras-like GTPase Rheb...
  47. ncbi Not so different after all: a comparison of methods for detecting amino acid sites under selection
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California San Diego, USA
    Mol Biol Evol 22:1208-22. 2005
    ..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
  48. pmc Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility
    Tomoko Kobayashi
    Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara cho, Sakyo ku, Kyoto 606 8507, Japan
    J Virol 85:932-45. 2011
    ..These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu...
  49. pmc Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase
    Takahiro Nobukuni
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
    Proc Natl Acad Sci U S A 102:14238-43. 2005
    ..Unexpectedly, we found that a major pathway by which amino acids control mTOR signaling is distinct from that of insulin and that, instead of signaling through components of ..
  50. pmc A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1
    Liron Bar-Peled
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02142, USA
    Science 340:1100-6. 2013
    The mTOR complex 1 (mTORC1) pathway promotes cell growth in response to many cues, including amino acids, which act through the Rag guanosine triphosphatases (GTPases) to promote mTORC1 translocation to the lysosomal surface, its site of ..
  51. ncbi Prediction of allergenic proteins by means of the concept of Chou's pseudo amino acid composition and a machine learning approach
    Hassan Mohabatkar
    Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
    Med Chem 9:133-7. 2013
    ..Interestingly, in our study all six characters (hydrophobicity, hydrophilicity, side chain mass, pK1, pK2 and pI) are present among the 10 higher ranked features obtained from the mRMR feature selection method...
  52. doi Amino acids: metabolism, functions, and nutrition
    Guoyao Wu
    Department of Animal Science, Faculty of Nutrition, Texas A and M University, College Station, TX, 77843, USA
    Amino Acids 37:1-17. 2009
    Recent years have witnessed the discovery that amino acids (AA) are not only cell signaling molecules but are also regulators of gene expression and the protein phosphorylation cascade...
  53. 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
    ..Our results indicate that direct protein-lipid interactions are critical during translocon-mediated membrane insertion...
  54. pmc Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid
    Paul E Staswick
    Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583, USA
    Plant Cell 17:616-27. 2005
    ..In vitro reactions with six recombinant GH3 enzymes produced IAA conjugates with several amino acids, based on thin layer chromatography...
  55. pmc Amino acids activate mammalian target of rapamycin complex 2 (mTORC2) via PI3K/Akt signaling
    Irantzu Tato
    Departament de Ciències Fisiològiques II, Campus de Bellvitge, Institut d Investigació Biomèdica de Bellvitge IDIBELL, Universitat de Barcelona, L Hospitalet de Llobregat, Barcelona E 08907, Spain
    J Biol Chem 286:6128-42. 2011
    ..Nutrients such as amino acids are important regulators of mTOR complex 1 (mTORC1) activation, thus affecting cell growth, protein synthesis, ..
  56. ncbi Network analysis of protein structures identifies functional residues
    Gil Amitai
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 344:1135-46. 2004
    ..Closeness integrates the effect of the entire protein on single residues. Such natural structural design may be evolutionary maintained to preserve interaction redundancy and contribute to optimal setting of functional sites...
  57. ncbi An integrated stress response regulates amino acid metabolism and resistance to oxidative stress
    Heather P Harding
    Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 11:619-33. 2003
    ..A signaling pathway initiated by eIF2alpha phosphorylation protects cells against metabolic consequences of ER oxidation by promoting the linked processes of amino acid sufficiency and resistance to oxidative stress...
  58. pmc Regulation of TORC1 by Rag GTPases in nutrient response
    Eunjung Kim
    Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093 081, USA
    Nat Cell Biol 10:935-45. 2008
    ..A wide range of signals, including amino acids, is known to activate TORC1...
  59. doi A role for codon order in translation dynamics
    Gina Cannarozzi
    Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
    Cell 141:355-67. 2010
    ..They also establish that the dynamics of translation leave a significant signature at the level of the genome...
  60. pmc Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases
    C L Bender
    Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma 74078 3032, USA
    Microbiol Mol Biol Rev 63:266-92. 1999
    ..Genetic reprogramming of peptide and polyketide synthetases has been successful, and portions of the coronatine and syringomycin gene clusters could be valuable resources in developing new antimicrobial agents...
  61. doi Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome
    Heinz Neumann
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 464:441-4. 2010
    The in vivo, genetically programmed incorporation of designer amino acids allows the properties of proteins to be tailored with molecular precision...
  62. pmc Inhibitory effects of D-amino acids on Staphylococcus aureus biofilm development
    Allon I Hochbaum
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138 1903, USA
    J Bacteriol 193:5616-22. 2011
    ..A natural signal for biofilm disassembly in Bacillus subtilis is certain D-amino acids, which are incorporated into the peptidoglycan and trigger the release of the protein component of the matrix...
  63. pmc D-amino acids trigger biofilm disassembly
    Ilana Kolodkin-Gal
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Science 328:627-9. 2010
    ..Mutants able to form biofilms in the presence of D-amino acids contained alterations in a protein (YqxM) required for the formation and anchoring of the fibers to the cell...
  64. ncbi Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism
    K Hara
    Diabetes Unit and Medical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02129, USA
    J Biol Chem 273:14484-94. 1998
    ..Withdrawal of amino acids from the nutrient medium of CHO-IR cells results in a rapid deactivation of p70 S6 kinase and dephosphorylation ..
  65. pmc BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
    Liangjiang Wang
    Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
    Nucleic Acids Res 34:W243-8. 2006
    ..BindN provides a useful tool for understanding the function of DNA and RNA-binding proteins based on primary sequence data...
  66. ncbi Restriction of amino acids extends lifespan in Drosophila melanogaster
    Kyung Jin Min
    Department of Ecology and Evolutionary Biology, Brown University, Box G W, Providence, RI 02912, USA
    Mech Ageing Dev 127:643-6. 2006
    ..Here we vary the concentration of casein as a source of amino acids in adult diet to uncover a quality of nutrient yeast responsible for longevity control...
  67. pmc Metabolic signatures of extreme longevity in northern Italian centenarians reveal a complex remodeling of lipids, amino acids, and gut microbiota metabolism
    Sebastiano Collino
    Proteomics and Metabonomics, Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de l Innovation, Lausanne, Switzerland
    PLoS ONE 8:e56564. 2013
    ....
  68. doi An enhanced system for unnatural amino acid mutagenesis in E. coli
    Travis S Young
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    J Mol Biol 395:361-74. 2010
    We report a new vector, pEVOL, for the incorporation of unnatural amino acids into proteins in Escherichia coli using evolved Methanocaldococcus jannaschii aminoacyl-tRNA synthetase(s) (aaRS)/suppressor tRNA pairs...
  69. pmc In Situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent D-amino acids
    Erkin Kuru
    Indiana University, Bloomington, IN 47405, USA
    Angew Chem Int Ed Engl 51:12519-23. 2012
    ..of diverse bacteria is labeled by exploiting the tolerance of cells for incorporating different non-natural D-amino acids. These nontoxic D-amino acids preferably label the sites of active PG synthesis, thereby enabling fine ..
  70. doi Exercising before protein intake allows for greater use of dietary protein-derived amino acids for de novo muscle protein synthesis in both young and elderly men
    Bart Pennings
    Top Institute Food and Nutrition, Wageningen, Netherlands
    Am J Clin Nutr 93:322-31. 2011
    ..This blunted response could be the result of impaired protein digestion and absorption kinetics and lead to lower postprandial plasma amino acid availability...
  71. ncbi Using the concept of Chou's pseudo amino acid composition to predict protein subcellular localization: an approach by incorporating evolutionary information and von Neumann entropies
    Shao Wu Zhang
    College of Automation, Northwestern Polytechnical University, No 127 Youyi West Road, Xi an 710072, China
    Amino Acids 34:565-72. 2008
    ..Compared with the results reported by the previous investigators, higher success rates were obtained, suggesting that the current approach is quite promising, and may become a useful high-throughput tool in the relevant areas...
  72. pmc Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels
    Mario Hlevnjak
    Department of Structural and Computational Biology, Max F Perutz Laboratories, University of Vienna, Vienna 1030, Austria
    Nucleic Acids Res 40:8874-82. 2012
    ..The latter is captured by polar requirement, a measure of solubility of amino acids in aqueous solutions of pyridines, heterocycles closely related to pyrimidines...
  73. doi Metabolic diversity in Campylobacter jejuni enhances specific tissue colonization
    Dirk Hofreuter
    Section of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
    Cell Host Microbe 4:425-33. 2008
    ..In addition, these studies revealed remarkably specific nutritional requirements for a pathogen to effectively colonize different tissues...
  74. ncbi A nutrient sensor mechanism controls Drosophila growth
    Julien Colombani
    Institute for Signaling, Developmental Biology and Cancer Research, UMR6543 CNRS Parc Valrose, 06108, Cedex 2, Nice, France
    Cell 114:739-49. 2003
    ..Our results demonstrate that the fat body functions as a nutrient sensor that restricts global growth through a humoral mechanism...
  75. ncbi Rotamer libraries in the 21st century
    Roland L Dunbrack
    Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia PA 19111, USA
    Curr Opin Struct Biol 12:431-40. 2002
    ....
  76. doi Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization
    Loris Nanni
    DEIS, IEIIT CNR, Universita di Bologna, Viale Risorgimento 2, 40136 Bologna, Italy
    Amino Acids 34:653-60. 2008
    ..2%) using the same dataset. While the overall prediction accuracy obtained by ALL-Loc is 83.9%...
  77. pmc The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
    Barbara A Methe
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:10913-8. 2005
    ..Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition...
  78. pmc Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages
    Michael D Urbaniak
    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom
    PLoS ONE 7:e36619. 2012
    ..for growing Trypanosoma brucei procyclic form cells in conditions suitable for stable isotope labeling by amino acids in culture (SILAC) and report a comparative proteomic analysis of cultured procyclic form and bloodstream form ..
  79. ncbi A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..Limitations of the new method are discussed...
  80. ncbi Prediction of linear B-cell epitopes using amino acid pair antigenicity scale
    J Chen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
    Amino Acids 33:423-8. 2007
    ..It is anticipated that with the continuous increase of the known epitope data, the power of the AAP antigenicity scale approach will be further enhanced...
  81. ncbi Translational regulation of GCN4 and the general amino acid control of yeast
    Alan G Hinnebusch
    Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
    Annu Rev Microbiol 59:407-50. 2005
    ..This dual regulatory response enables cells to limit their consumption of amino acids while diverting resources into amino acid biosynthesis in nutrient-poor environments...
  82. doi Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses
    Maryam Esmaeili
    Department of Biology, College of Sciences, Shiraz University, Shiraz 71454, Iran
    J Theor Biol 263:203-9. 2010
    ..Risk type of 4 unknown HPV types and 25 non-reported HPV types were also predicted. These results show that bioinformatics based theoretical approaches can direct and simplify experimental studies...
  83. doi Muscle full effect after oral protein: time-dependent concordance and discordance between human muscle protein synthesis and mTORC1 signaling
    Philip J Atherton
    School of Graduate Entry Medicine and Health, Division of Clinical Physiology, University of Nottingham, Royal Derby Hospital, Derby, United Kingdom
    Am J Clin Nutr 92:1080-8. 2010
    We previously showed that human muscle protein synthesis (MPS) increased during infusion of amino acids (AAs) and peaked at ≈120 min before returning to baseline rates, despite elevated plasma AA concentrations.
  84. ncbi Metabolic effects of amino acid mixtures and whey protein in healthy subjects: studies using glucose-equivalent drinks
    Mikael Nilsson
    Division of Applied Nutrition and Food Chemistry, Lund University, Lund, Sweden
    Am J Clin Nutr 85:996-1004. 2007
    ..In parallel to the hyperinsulinemia, a pronounced postprandial rise of certain amino acids and of glucose-dependent insulinotrophic polypeptide (GIP) was observed in plasma.
  85. pmc Prediction of RNA binding sites in proteins from amino acid sequence
    Michael Terribilini
    Bioinformatics and Computationa Biology, Graduate Program, Iowa State University, Ames, Iowa 50010, USA
    RNA 12:1450-62. 2006
    ..We have developed a computational tool for predicting which amino acids of an RNA binding protein participate in RNA-protein interactions, using only the protein sequence as input...
  86. ncbi ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
    Fabian Glaser
    The George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Bioinformatics 19:163-4. 2003
    ..We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins...
  87. pmc The importance of intrinsic disorder for protein phosphorylation
    Lilia M Iakoucheva
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Nucleic Acids Res 32:1037-49. 2004
    ....
  88. ncbi Hot spots--a review of the protein-protein interface determinant amino-acid residues
    Irina S Moreira
    REQUIMTE Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, 4169 007 Porto, Portugal
    Proteins 68:803-12. 2007
    ..epitopes, and demonstrated that most of the protein-protein binding energy is related only to a group of few amino acids at intermolecular protein interfaces: the hot spots...
  89. ncbi ISIS: interaction sites identified from sequence
    Yanay Ofran
    CUBIC and North East Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Bioinformatics 23:e13-6. 2007
    ..Therefore, for the vast majority of proteins, for which there is no high-resolution structure, there is no effective way of identifying interface residues...
  90. pmc Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    A A Schaffer
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 29:2994-3005. 2001
    ..The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST...
  91. doi Feast or famine: the host-pathogen battle over amino acids
    Yanjia J Zhang
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
    Cell Microbiol 15:1079-87. 2013
    ..These processes provide both key insights into immune subversion and new targets for drug development...
  92. doi AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties
    Krishna Kumar Kandaswamy
    Institute for Neuro and Bioinformatics, University of Lubeck, 23538 Lubeck, Germany
    J Theor Biol 270:56-62. 2011
    ..High prediction accuracy and successful of prediction of hypothetical proteins suggests that AFP-Pred can be a useful approach to identify antifreeze proteins from sequence information, irrespective of their sequence similarity...
  93. ncbi Functional and quantitative proteomics using SILAC
    Matthias Mann
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nat Rev Mol Cell Biol 7:952-8. 2006
    ..Among the many formats for quantitative proteomics, stable-isotope labelling by amino acids in cell culture (SILAC) has emerged as a simple and powerful one...
  94. pmc CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Joe Dundas
    Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Nucleic Acids Res 34:W116-8. 2006
    ..The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins...
  95. pmc Amino acid transceptors: gate keepers of nutrient exchange and regulators of nutrient signaling
    Harinder S Hundal
    Division of Molecular Physiology, Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
    Am J Physiol Endocrinol Metab 296:E603-13. 2009
    ..endocrine controls in higher eukaryotes, alongside their frequent inability to synthesize all proteinaceous amino acids (and, hence, the requirement for indispensable amino acids in their diet), appears to have lessened the ..
  96. pmc Disassociation between the effects of amino acids and insulin on signaling, ubiquitin ligases, and protein turnover in human muscle
    P L Greenhaff
    Centre for Integrated Systems Biology and Medicine, Univ of Nottingham, Queen s Medical Centre, Nottingham NG7 2UH, UK
    Am J Physiol Endocrinol Metab 295:E595-604. 2008
    We determined the effects of intravenous infusion of amino acids (AA) at serum insulin of 5, 30, 72, and 167 mU/l on anabolic signaling, expression of ubiquitin-proteasome components, and protein turnover in muscles of healthy young men...
  97. ncbi Glycemia and insulinemia in healthy subjects after lactose-equivalent meals of milk and other food proteins: the role of plasma amino acids and incretins
    Mikael Nilsson
    Department of Applied Nutrition and Food Chemistry, Lund University, Sweden
    Am J Clin Nutr 80:1246-53. 2004
    ..Milk products deviate from other carbohydrate-containing foods in that they produce high insulin responses, despite their low GI. The insulinotropic mechanism of milk has not been elucidated...
  98. ncbi Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
    R S Stephens
    Program in Infectious Diseases, University of California, Berkeley, CA 94720, USA
    Science 282:754-9. 1998
    ..The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism...
  99. doi Protein-protein interaction and quaternary structure
    Joel Janin
    Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Universite Paris Sud, Orsay, France
    Q Rev Biophys 41:133-80. 2008
    ....
  100. ncbi Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Simon C Lovell
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 50:437-50. 2003
    ..To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage)...
  101. ncbi Cell-free translation reconstituted with purified components
    Y Shimizu
    Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bldg FSB401, Kasiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
    Nat Biotechnol 19:751-5. 2001
    ..Moreover, omission of a release factor allowed efficient incorporation of an unnatural amino acid using suppressor transfer RNA (tRNA)...

Research Grants74

  1. AMINO ACIDS IN URINE, DIET & BP: INT'L POPULATION STUDY
    Martha Daviglus; Fiscal Year: 2003
    ..protein intake; arginine -- source in cells for nitric oxide (NO), implicated in vasodilation; other urinary amino acids. The study has already collected standardized comprehensive dietary and BP data on all individuals in its 17 ..
  2. Pyruvate Dehydrogenase kinase as Therapeutic Target for Hepatic Steatosis, Obesit
    Robert A Harris; Fiscal Year: 2012
    ..blood glucose levels, glucose tolerance, insulin sensitivity, hepatic steatosis, adiposity, branched chain amino acids (BCAAs), free fatty acids (FFAs), ketone bodies, triacylglcyerols (TAG), cholesterol, blood pH, and markers of ..
  3. H1R Signaling and Immune Deviation in EAE
    Cory Teuscher; Fiscal Year: 2013
    ..H1R alleles differ by three amino acids in the third intracellular loop (H1RS: Pro263Val312Pro330;H1RR: Leu263Met312Ser330)...
  4. Phosphorylation of FGF23 coordinates crosstalk between the skeleton and kidney
    VINCENT SCOTT TAGLIABRACCI; Fiscal Year: 2013
    ..and 3) Fam20C phosphorylates FGF23 at Ser180 within an important regulatory motif and at 3 highly conserved amino acids within the C terminus that may affect binding of the hormone to its cognate receptor (preliminary data, ..
  5. Tyrosine Availability Influences Mesocortico-Limbic Catecholamines
    GEORGE EUGENE JASKIW; Fiscal Year: 2012
    ..Tyrosine levels will be raised by administering tyrosine and lowered by giving a mixture of amino acids that limit entry of tyrosine into the brain...
  6. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..The malignant brain tumor (MBT) repeat is a structural domain of ca. 100 amino acids and occurs in 11 human proteins which recognize mono- and dimethyl-lysine modifications of histones...
  7. Role of SCD1 and Dietary Methionine Restriction on Energy Homeostasis
    ERIC PAUL PLAISANCE; Fiscal Year: 2011
    ..of the integrated responses of the brain and peripheral tissues to the intake of specific nutrients such as amino acids and fats in the diet...
  8. IMMUNOGENETICS OF COLLAGEN INDUCED ARTHRITIS IN MICE
    Chella David; Fiscal Year: 2009
    ..addition, we will use DRB1*0401 and DRB1*0402 mice to determine the mechanism of protection to understand how 3 amino acids difference in both molecules lead to protection by the latter...
  9. Insulin Signaling and the Heart in Diabetes
    EVAN DALE ABEL; Fiscal Year: 2011
    ..if the suppression of cardiomyocyte autophagy by insulin signaling requires increased uptake of glucose or amino acids. Aim 4: will determine if insulin signaling suppresses cardiomyocyte autophagy by disrupting initiation of ..
  10. BIOSYNTHESIS OF TRACHEAL MUCOUS GLYCOPROTEINS
    Pi Wan Cheng; Fiscal Year: 2010
    ..We propose to: 1. Determine the active site of C2GnT-M by X-ray crystallography and then confirm the amino acids involved in catalysis by site-directed mutagenesis followed by measurement of enzyme activities using core 1, ..
  11. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2013
    ..reduction of IKACh can be achieved through two mechanisms: (1) direct channel blockade involving specific amino acids in the cytoplasmic domain of the channel;and (2) internalization of Kir3.1/Kir3...
  12. Structural and molecular basis of drug-induced IKACh reduction
    SAMI FOUAD NOUJAIM; Fiscal Year: 2012
    ..reduction of IKACh can be achieved through two mechanisms: (1) direct channel blockade involving specific amino acids in the cytoplasmic domain of the channel;and (2) internalization of Kir3.1/Kir3...
  13. Role for Na,K-ATPase in Nucleoplasmic Calcium Homeostasis
    Craig Gatto; Fiscal Year: 2010
    ..The Na,K-ATPase is a heterodimeric integral membrane protein consisting of a catalytic a-subunit (~1000 amino acids) and a glycosylated [unreadable]-subunit (~300 amino acids)...
  14. Novel Peptide MPO Inhibitors for Treating Atherosclerosis
    Kirkwood A Pritchard; Fiscal Year: 2012
    ..MPO also oxidizes aromatic amino acids such as tyrosine and tryptophan to generate cytotoxic tyrosyl and tryptophanyl radicals...
  15. BONE MATRIX AND BONE RESORPTION
    Paul R Odgren; Fiscal Year: 2012
    ..We will also study the effects of point mutations of candidate amino acids to determine if specific aa in the PH and C-1 domains impact their important biological binding activities...
  16. Pathogenesis of the Metabolic Syndrome
    W Timothy Garvey; Fiscal Year: 2013
    ..Metabolomic profiles will be assessed for acylcarnitines, fatty acids, organic acids, amino acids, and LCFA-CoAs in plasma, urine, and in biopsied muscle tissue...
  17. TARGETING THE MARCKS-FAMILY PROTEINS TO INHIBIT NEUTROPHIL MIGRATION
    Mary K Sheats; Fiscal Year: 2013
    ..MARCKS or MARCKSL1 inhibition will be accomplished using: cell permeant peptides identical to the 24 amino acids of the N-terminus of each protein, transgenic expression of a truncated fluorescently-tagged N-terminus MARCKS ..
  18. A quantitative proteomics approach to understand viral immune evasion strategies
    Michele E Hardy; Fiscal Year: 2010
    ..We will employ stable isotope labeling of amino acids in culture (SILAC) followed by high resolution chromatographic separation and tandem mass spectrometry...
  19. C5a as an Anti-HIV Microbicidal Candidate
    PHILIPPE ANDRE GALLAY; Fiscal Year: 2013
    ..C5A corresponds to a small (18 amino acids) N-terminal region (aa 3-20) of the hepatitis C virus (HCV) nonstructural protein 5A (NS5A) (477 amino acids)...
  20. Present Homologous and Heterologous Antigen with Hepatitis E Virus
    R Holland Cheng; Fiscal Year: 2012
    ..By carrying insertion of 15 amino acids at an antibody-binding site, the chimeric VLP reduces the reactivity to anti-HEV antibodies meanwhile retains ..
  21. The genetics and pathophysiology of impaired Wnt signaling in metabolic syndrome
    Arya Mani; Fiscal Year: 2012
    ..we have identified the disease causing mutations that substitute evolutionarily highly conservative amino acids in the LDL receptor like protein (LRP6), a co-receptor in the Wnt signaling pathway...
  22. Development of Vaccines against Clostridium difficile Infection
    SAUL R TZIPORI; Fiscal Year: 2013
    ..cTxAB has a small deletion (97 amino acids) in transmembrane domain rendering it non-toxic...
  23. Genetics of the Neuromuscular Junction: Mechanisms and Disease Models
    Robert W Burgess; Fiscal Year: 2013
    ..These enzymes are well characterized for their function in charging amino acids onto their cognate tRNAs for translation...
  24. Regulation of K-Ras by a Farnesyl-electrostatic Switch
    MARK REID PHILIPS; Fiscal Year: 2013
    ..We found that phosphorylation of K-Ras at serine 181 partially neutralized the adjacent polybasic stretch of amino acids and thereby activated a farnesyl-electrostatic switch that resulted in release of K-Ras from the plasma ..
  25. Novel Therapy for Preeclampsia
    James W Larrick; Fiscal Year: 2012
    ..Affinity maturation, in combination with targeted in vitro mutagenesis of specific amino acids known to modify specificity of the binding site for digoxin, will yield multipe clones...
  26. FUNCTIONAL PROPERTIES OF HEMOGLOBINS AND MYOGLOBINS
    John S Olson; Fiscal Year: 2010
    ..We and others have identified the roles of specific amino acids, structural motifs, and stereochemical effects in regulating O2 affinity, ligand discrimination, rates of ..
  27. Combined BAC Transgenic and Knock-Out Mouse Model of Lowe Syndrome Nephropathy
    Robert L Nussbaum; Fiscal Year: 2013
    ..levels of phosphatidylinositol(4,5)P2 and altered renal transport of low molecular weight proteins and amino acids. We will also use recombination in mouse embryonic stem cells to dissect and identify the differences between ..
  28. Citrulline to Prevent or Mitigate Acute Lung Injury in Severe Sepsis
    Todd W Rice; Fiscal Year: 2013
    ..Laboratory resources are available to investigate changes in biochemical responses, including plasma levels of amino acids, nitric oxide metabolites, and inflammatory cytokines...
  29. Nutrition and Anabolic Interventions in Cancer Cachexia
    Melinda Sheffield-Moore; Fiscal Year: 2013
    ..Our preliminary data show that the response of skeletal muscle protein to the anabolic stimulus of amino acids is impaired in cancer patients...
  30. Controlled delivery of polypeptide hormone calcitonin
    Jagdish Singh; Fiscal Year: 2013
    ..Calcitonin isa polypeptide hormone with 32 amino acids and has a molecular mass of about 3500...
  31. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
    ..Minor groove DNA binding polyamides containing aromatic amino acids form the basis of a modular code to control sequence specificity...
  32. STRESS, ADRENAL STEROIDS AND THE BRAIN
    Bruce S McEwen; Fiscal Year: 2013
    ..effects on structural plasticity and other functions involve interactions among endocannabinoids, excitatory amino acids and glucocorticoids and neuroprotective agents, such as the chaperone, BAG1...
  33. Vitamin B6 Effects on One-Carbon Metabolism
    Jesse F Gregory; Fiscal Year: 2013
    ..units by the glycine cleavage system and serine hydroxymethyltransferase, inter conversion and catabolism of amino acids, control of homocysteine, and production of glucose and cysteine...
  34. Reversing Corticosteroid-Induced Memory Impairment
    E Sherwood Brown; Fiscal Year: 2013
    ..hippocampal changes secondary to corticosteroids can be attenuated with agents that modulate excitatory amino acids. Histological changes can be prevented and reversed with phenytoin, a glutamate release inhibitor, or an N-..
  35. Potentiation of Glycine Receptors by Ethanol
    LUIS GERARDO AGUAYO; Fiscal Year: 2010
    ..More importantly, preliminary results show that basic amino acids in the main intracellular loop of the GlyR determine the sensitivity of the receptor to clinically relevant ..
  36. Electron Transfer in Iron and Copper Proteins
    Jay R Winkler; Fiscal Year: 2013
    ..and production, require the transfer of holes at high potentials where the sidechains of redox-active amino acids can become involved...
  37. Characterization of IL36, a novel cytokine
    Albert Zlotnik; Fiscal Year: 2012
    ..We have tentatively called this protein Interleukin 36. IL36 is a small protein of 311 amino acids and exhibits a signal peptide of 45 amino acids, predicting a mature protein of 266 amino acids, with an ..
  38. DRUG RESISTANCE AND PTERIDINE METABOLISM IN LEISHMANIA
    Stephen M Beverley; Fiscal Year: 2010
    ..metabolites needed to make essential metabolites in intermediary metabolism including DNA, RNA, and amino acids. Our studies have disclosed an unanticipated richness in the folate pathway, revealing an unanticipated ..
  39. MRI of Acute Vascular Injury and Hemorrhagic Transformation in Ischemic Stroke
    Robert A Knight; Fiscal Year: 2010
    ..Injury to the BBB in ischemic stroke often leads to the leakage of ions, water, amino acids, and plasma proteins into the brain and as a result in large strokes significant brain swelling may occur ..
  40. Fnip1 Function in Lymphocyte Development, Activation and Metabolism
    Brian M Iritani; Fiscal Year: 2013
    ..which efficiently produces energy, to aerobic glycolysis, which generates bio-precursors (such as lipids, amino acids, and nucleotides) required to fuel cell division...
  41. Maternal Obesity and Gestational Diabetes: Impact on Metabolome
    William L Lowe; Fiscal Year: 2013
    ..Aim of the proposed HAPO Metabolomics Study is to use a targeted mass spectrometry- based platform to measure amino acids, acylcarnitines, and conventional metabolites and a gas chromatography:mass spectrometry-based non-targeted ..
  42. Remodeling of Lipid Metabolism by Dietary Methionine Restriction
    ERIC PAUL PLAISANCE; Fiscal Year: 2012
    ..control non-derepressible 2 (GCN2) kinase, a protein which is activated when any one of the 9-10 essential amino acids (EAAs) in the diet are removed...
  43. Development of a novel method for inhibiting diabetic retinopathy
    David R Clemmons; Fiscal Year: 2012
    ..We will determine if a polyclonal antibody direct against amino acids 71-80 in rat IAP has efficacy in vivo...
  44. Thrombospondin 4 A1
    JOHN W LAWLER; Fiscal Year: 2010
    ..Specific focus for the next period of support will be on the following areas. Specific Aim 1. To identify key amino acids for the interactions of COMP with proteins and proteoglycans (PGs)...
  45. Biosynthetic Protein Models of Heme-copper Oxidases and Nitric Oxide Reductases
    Yi Lu; Fiscal Year: 2013
    ..mutagenesis and expressed protein ligation (EPL) will be employed to introduce natural or unnatural amino acids into the metal-binding sites...
  46. Food(cassava) cyanogen exposure and motor neuron degeneration
    DANIEL DESIRE TSHALA KATUMBAY; Fiscal Year: 2010
    ..In addition, affected subjects have a low intake in sulfur amino acids (SAA) needed to detoxify endogenously produced cyanide (CN)...
  47. Inhibition of the MLL-AF4-AF9 Interaction in Pediatric Leukemia
    Andrew Napper; Fiscal Year: 2012
    ..A recent study showed that peptides containing as few as 10 amino acids derived from the AF9 binding site in AF4 bind to AF9 with low nanomolar potency and selectively kill an MLL-AF4-..
  48. Influence of Heme on Hepatic Cytochrome P450 Turnover
    Maria Almira Correia; Fiscal Year: 2013
    ..Studies are proposed in Hri-/- and Hri+/+ hepatocytes using SILAC (stable isotope labeling of amino acids in culture) coupled with proteomics to identify and quantify the hepatic proteins whose synthesis and/or ..
  49. Mitochondrial function and antifungal photodynamic therapy
    Constantine G Haidaris; Fiscal Year: 2011
    ..The sulfur containing amino acids cysteine and methionine are primary targets of oxidative damage in proteins...
  50. PET TUMOR AND PROLIFERATION IMAGING VIA CATIONIC AMINO ACID TRANSPORT
    JONATHAN EDWARD MCCONATHY; Fiscal Year: 2013
    ..and preliminary preclinical evaluation of PET tracers for brain monoamine transporters and 18F-labeled amino acids (AAs) for tumor imaging...
  51. MECHANISM AND CONTROL OF UREA BIOSYNTHESIS
    Frank M Raushel; Fiscal Year: 2011
    ..members of the amidotransferase superfamily are critical for the biosynthesis of carbohydrates, nucleic acids, amino acids and essential coenzymes and thus these enzymes are attractive targets for pharmaceutical intervention and ..
  52. HMG in Post Operative and Traumatic Stress
    Kevin J Tracey; Fiscal Year: 2013
    ..strategy based on surface plasmon resonance to study HMGB1 binding to TLR4 and RAGE, substitution of specific amino acids to modify binding and signaling, proximity ligation assays to study intracellular binding of HMGB1 to TLR4 and ..
  53. Hepatitis C virus and liver fibrogenesis
    Gulam Waris; Fiscal Year: 2010
    ..The HCV genome is a positive-sense single stranded RNA molecule that encodes a polyprotein precursor of ~3000 amino acids which is post- translationally cleaved by host and virus-encoded proteases into structural proteins (core, E1, ..
  54. GENETIC APPROACHES TO PROTEIN-NUCLEIC ACID INTERACTIONS
    Paul R Schimmel; Fiscal Year: 2012
    ..of transfer RNAs and thereby establish the genetic code relationship between trinucleotide codons and amino acids. The enzymes appeared early in evolution and are essential to all life forms...
  55. Novel Catalases and their Products
    Alan R Brash; Fiscal Year: 2013
    ..We also propose to change the AOS activity of these enzymes by site-direct mutagenesis of active site amino acids, a hypothesis supported by the array of products of CYP74 relatives of the P450 AOS...
  56. Human VGF Polymorphisms and Depression
    Stephen R Salton; Fiscal Year: 2010
    ..two mouse models that knock human VGF alleles into the mouse Vgf locus, encoding either full length human VGF (amino acids 1-615) or SNP-truncated VGF (amino acids 1-524)...
  57. METABOLIC CONTROL OF SUGAR TRANSPORT
    Anthony Carruthers; Fiscal Year: 2012
    ..GLUT1 covalently modified with photoreactive nucleotide analogs and by mutagenesis of identified, labeled amino acids. Specific Aim 2 tests the hypothesis that the C-terminus and cytoplasmic loop 6 play a primary role in GLUT1 ..
  58. MAP KINASE IN ISLET FUNCTION
    Melanie H Cobb; Fiscal Year: 2013
    ..This receptor, identified in gustatory neurons, binds to a variety of amino acids, but has not been studied on cells...
  59. Gluconeogenesis and Glycogenolysis - Role and Regulation
    Alan D Cherrington; Fiscal Year: 2013
    ..Metabolic clamps (glucose, NEFA, amino acids) will be used as needed to fix substrate levels. Surgical (hepatic denervation etc) and pharmacologic (i.e...
  60. PHOSPHOPEPTIDE METABOLISM IN ADIPOCYTES
    Joseph Avruch; Fiscal Year: 2013
    ..cells TOR retains these functions, but regulation by the insulin/IGF system is superimposed on regulation by amino acids, especially leucine...
  61. ANALYSIS OF MEIOTIC CHROMOSOME SYNAPSIS IN YEAST
    Nancy M Hollingsworth; Fiscal Year: 2013
    ..Development of a novel protocol has allowed the powerful proteomic approach of Stable Isotope Labeling by Amino acids in Cell culture or SILAC, to be applied to meiotic budding yeast cells for the first time...
  62. Microdialysis Studies of Seizure-Induced Oxidative Stress
    Craig E Lunte; Fiscal Year: 2013
    ..to monitor formation of ROS and RNS, biomarkers for DNA damage and lipid peroxidation, and the neurotransmitter amino acids and catecholamines...
  63. Mechanisms of ENaC Inhibition by Replicating Influenza Virus: Role of M2 Protein
    Sadis Matalon; Fiscal Year: 2012
    ..comprehensive in vitro and in vivo studies listed in four specific aims: (1) Identify regions and specific amino acids of the influenza strain A/Udorn/72 M2 proton (H+) channel responsible for ENaC down-regulation in Xenopus ..
  64. PLASMA PROTEINS: MARKERS OF CHEMICAL EXPOSURE
    GHULAM ANSARI; Fiscal Year: 1991
    ..Spectral methods will involve identification and quantitation of chemically modified amino acids in blood proteins such as al-proteinase inhibitor and hemoglobin using gas chromatography-mass spectrometry...
  65. Molecular Modulation of Catalytic Sites of Escherichia coli F1Fo ATP Synthase
    Zulfiqar Ahmad; Fiscal Year: 2009
    ..function of this nanomotor, it is paramount to identify and characterize the role of phosphate binding amino acids and their interactions. So far, six amino acids from the catalytic sites have been characterized...
  66. MOLECULAR MECHANISMS OF OXIDATION OF LDL
    Sampath Parthasarathy; Fiscal Year: 1999
    ..g., BSA), polyamino acids, amino acids, apolipoproteins and alkylamines. Some incubations will be conducted in the presence of antioxidants...
  67. Development of Novel Fluorinated Amino Acids
    Mark Goodman; Fiscal Year: 2004
    ..Our approach will focus on the development of [18F]cyclobutyl and [18F]branched nonmetabolized amino acids that move across tumor capillaries by carrier-mediated facilitated transport involving either the "L" large-..
  68. Substrate Selection in Homologous Bacterial Transporters
    Manuel Varela; Fiscal Year: 2004
    ..It is unclear whether amino acids that confer sugar specificity in the lactose permease of E...
  69. NEONATAL PARENTERAL NUTRITION AND HEPATIC DYSFUNCTION
    Jatinder Bhatia; Fiscal Year: 1990
    ..In vivo studies indicate a role for amino acids in the induction of TPN-associated hepatic dysfunction, but the mechanisms involved are unknown...
  70. ONTOGENY OF FETAL HEPATIC SERINE AND GLYCINE METABOLISM
    Michael Narkewicz; Fiscal Year: 1999
    ..Disorders of the metabolism of a variety of amino acids are associated with the development of intrauterine growth retardation or neurologic disease...
  71. Investigation of Reactions of Physiological Importance
    Paul R Schimmel; Fiscal Year: 2011
    ..Here, the 20 aminoacyl tRNA synthetases-one for each amino acid-catalyze the attachments of amino acids to their cognate transfer RNAs...
  72. Nutritional Intervention for Age-Related Muscular Function and Strength Losses
    John A Rathmacher; Fiscal Year: 2010
    ..have demonstrated the efficacy of 2-hydroxy-2-methylbutyrate (HMB) alone or in combination with other amino acids in enhancing muscle strength and function in young athletes...
  73. Dosimetry of Lipid-Derived Amino Acid Adducts by LC/MS
    Ian Blair; Fiscal Year: 2006
    ..Previous studies have demonstrated 4-hydroxy-2-nonenal can induce covalent modifications with model amino acids. However, the efficiency of this process is much lower than we observed with 4-oxo-2-nonenal The ability to ..
  74. Amino Acids and Muscle Protein Synthesis
    Robert Wolfe; Fiscal Year: 2006
    ..control of muscle protein synthesis are responsive not only to the prevailing plasma concentrations of amino acids, but also to the direction in which concentration of leucine changes...