ProtSA: A web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Estrada, Jorge ^a   Bernadó, Pau ^b   Blackledge, Martin ^c   Sancho, Javier ^a  

^a UNIVERSITY OF ZARAGOZA   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c INSTITUT DE BIOLOGIE STRUCTURALE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTICAL SOFTWARE; CALCULATION PROTOCOLS; HYDROPHOBIC EFFECT; PROTEIN STABILITY; SCIENTIFIC COMMUNITY; SOLVENT ACCESSIBILITY; SOLVENT ACCESSIBLE SURFACE AREAS;

AMINO ACIDS; APPLICATIONS; ATOMS; PROTEIN FOLDING; SOLVENTS; WORLD WIDE WEB;

PROTEINS;

SOLVENT; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; ENERGY TRANSFER; MATHEMATICAL COMPUTING; PROTEIN CONFORMATION; PROTEIN FOLDING; BINDING SITE; CHEMISTRY; HYDROPHOBICITY; INTERNET; THERMODYNAMICS;

BINDING SITES; HYDROPHOBICITY; INTERNET; PROTEIN FOLDING; PROTEINS; SOFTWARE; SOLVENTS; THERMODYNAMICS;

EID: 65449171120     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-104     Document Type: Article

References (33)

1. Baldwin RL Energetics of protein folding J Mol Biol 2007, 371:283-301. 10.1016/j.jmb.2007.05.078 17582437
2. Chen Y Ding F Nie H Serohijos AW Sharma S Wilcox KC Yin S Dokholyan NV Protein folding: Then and now Arch Biochem Biophys 2008, 469:4-19. 2173875 17585870 10.1016/j.abb.2007.05.014
3. Wesson L Eisenberg D Atomic solvation parameters applied to molecular dynamics of proteins in solution Protein Sci 1992, 1:227-235. 2142195 1304905
4. Robertson AD Murphy KP Protein structure and the energetics of protein stability Chem Rev 1997, 97:1251-1268. 10.1021/cr960383c 11851450
5. Myers JK Pace CN Scholtz JM Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding Protein Sci 1995, 4:2138-2148. 2142997 8535251 10.1002/ pro.5560041020
6. Lee B Richards FM The interpretation of protein structures: Estimation of static accessibility J Mol Biol 1971, 55:379-400. 10.1016/ 0022-2836(71)90324-X 5551392
7. Miller S Janin J Lesk AM Chothia C Interior and surface of monomeric proteins J Mol Biol 1987, 196:641-656. 10.1016/0022-2836(87)90038-6 3681970
8. Shrake A Rupley JA Environment and exposure to solvent of protein atoms. Lysozyme and insulin J Mol Biol 1973, 79:351-371. 10.1016/ 0022-2836(73)90011-9 4760134
9. Rose GD Geselowitz AR Lesser GJ Lee RH Zehfus MH Hydrophobicity of amino acid residues in globular proteins Science 1985, 229:834-838. 10.1126/ science.4023714 4023714
10. Creamer TP Srinivasan R Rose GD Modeling unfolded states of peptides and proteins Biochemistry 1995, 34:16245-16250. 10.1021/bi00050a003 8845348
11. Creamer TP Srinivasan R Rose GD Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility Biochemistry 1997, 36:2832-2835. 10.1021/bi962819o 9062111
12. Gong H Rose GD Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model Proc Natl Acad Sci USA 2008, 105:3321-3326. 2265189 18305164 10.1073/pnas.0712240105
13. Goldenberg DP Computational simulation of the statistical properties of unfolded proteins J Mol Biol 2003, 326:1615-1633. 10.1016/ S0022-2836(03)00033-0 12595269
14. Bernadó P Blackledge M Sancho J Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles Biophys J 2006, 91:4536-4543. 1779920 17012314 10.1529/ biophysj.106.087528
15. Bernadó P Blanchard L Timmins P Marion D Ruigrok RW Blackledge M A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering Proc Natl Acad Sci USA 2005, 102:17002-17007. 1287987 16284250 10.1073/pnas.0506202102
16. Bernadó P Bertoncini CW Griesinger C Zweckstetter M Blackledge M Defining long-range order and local disorder in native α-synuclein using residual dipolar couplings J Am Chem Soc 2005, 127:17968-17969. 10.1021/ja055538p 16366524
17. Mukrasch MD Markwick P Biernat J Bergen M Bernadó P Griesinger C Mandelkow E Zweckstetter M Blackledge M Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation J Am Chem Soc 2007, 129:5235-5243. 10.1021/ja0690159 17385861
18. Wells M Tidow H Rutherford TJ Markwick P Jensen MR Mylonas E Svergun DI Blackledge M Fersht AR Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain Proc Natl Acad Sci USA 2008, 105:5762-5767. 2311362 18391200 10.1073/ pnas.0801353105
19. Jensen MR Houben K Lescop E Blanchard L Ruigrok RW Blackledge M Quantitative conformational analysis of partially folded proteins from residual dipolar couplings: Application to the molecular recognition element of Sendai virus nucleoprotein J Am Chem Soc 2008, 130:8055-8061. 10.1021/ja801332d 18507376
20. Geierhaas CD Nickson AA Lindorff-Larsen K Clarke J Vendruscolo M BPPred: a Web-based computational tool for predicting biophysical parameters of proteins Protein Sci 2007, 16:125-134. 2222837 17123959 10.1110/ ps.062383807
21. Eyal E Najmanovich R McConkey BJ Edelman M Sobolev V Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins J Comput Chem 2004, 25:712-724. 10.1002/ jcc.10420 14978714
22. Edelsbrunner H Koehl P The weighted-volume derivative of a space-filling diagram Proc Natl Acad Sci USA 2003, 100:2203-2208. 151318 12601153 10.1073/pnas.0537830100
23. Hubbard SJ Thornton JM NACCESS Computer Program Department of Biochemistry and Molecular Biology, University College London, London, UK 1993.
24. Lovell SC Davis IW Arendall WB 3rd de Bakker PI Word JM Prisant MG Richardson JS Richardson DC Structure validation by Cα geometry: Φ,Ψ and Cβ deviation Proteins 2003, 50(3):437-450. 12557186 10.1002/prot.10286
25. Levitt M A simplified representation of protein conformations for rapid simulation of protein folding J Mol Biol 1976, 104:59-107. 10.1016/ 0022-2836(76)90004-8 957439
26. Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22:2577-2637. 10.1002/bip.360221211 6667333
27. ProtSA: A web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble http://webapps.bifi.es/ protsa/
28. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28:235-242. 102472 10592235 10.1093/nar/28.1.235
29. Pakula AA Sauer RT Reverse hydrophobic effects relieved by amino-acid substitutions at a protein surface Nature 1990, 344:363-364. 10.1038/ 344363a0 2314475
30. Ohlendorf DH Tronrud DE Matthews BW Refined structure of Cro repressor protein from bacteriophage λ suggests both flexibility and plasticity J Mol Biol 1998, 280:129-136. 10.1006/jmbi.1998.1849 9653036
31. Takano K Scholtz JM Sacchettini JC Pace CN The contribution of polar group burial to protein stability is strongly context-dependent J Biol Chem 2003, 278:31790-31795. 10.1074/jbc.M304177200 12799387
32. Persistence of Vision Raytracer http://www.povray.org/
33. Pettersen EF Goddard TD Huang CC Couch GS Greenblatt DM Meng EC Ferrin TE UCSF Chimera - A visualization system for exploratory research and analysis J Comput Chem 2004, 25:1605-1612. 10.1002/jcc.20084 15264254