Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 10, 2011, Pages 947-958

  Tian, Feifei ^a,b   Lv, Yonggang ^a   Zhou, Peng ^c   Yang, Li ^a  

^a CHONGQING UNIVERSITY   (China)

^b SOUTHWEST JIAOTONG UNIVERSITY   (China)

^c UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Conformational entropy loss; Desolvation effect; Noncovalent interaction; PDZ domain; Protein peptide binding

Indexed keywords

BINDING ENERGY; COMPLEX NETWORKS; ENTROPY; FREE ENERGY; IONS; MOLECULAR MODELING; QUANTUM THEORY;

CONFORMATIONAL ENTROPY; CONFORMATIONAL ENTROPY LOSS; DESOLVATION; DESOLVATION EFFECT; ENTROPY LOSS; NON-COVALENT INTERACTION; PDZ DOMAINS; PROTEIN-PEPTIDE BINDING; QUANTUM MECHANICS/MOLECULAR MECHANICS; SURFACE AREA;

PEPTIDES;

AMINO TERMINAL TELOPEPTIDE; PDZ PROTEIN; PDZ3 PROTEIN; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; CONFORMATIONAL FREE ENERGY ANALYSIS; CONTROLLED STUDY; ENTROPY; MOLECULAR MECHANICS; POISSON BOLTZMANN SURFACE AREA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; QUANTUM MECHANICS;

EID: 84855201786     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9474-5     Document Type: Article

References (52)

1. V Neduva R Linding I Su Angrand A Stark F de Masi TJ Gibson J Lewis L Serrano RB Russell 2005 Systematic discovery of new recognition peptides mediating protein interaction networks PLoS Biol 3 e405 10.1371/journal.pbio. 0030405 (Pubitemid 41796329)
2. E Petsalaki RB Russell 2008 Peptide mediated interactions in biological systems: new discoveries and applications Curr Opin Biotechnol 19 344 350 10.1016/j.copbio.2008.06.004 1:CAS:528:DC%2BD1cXhtValsL7E
3. P Vanhee F Stricher L Baeten E Verschueren T Lenaerts L Serrano F Rousseau J Schymkowitz 2009 Protein-peptide interactions adopt the same structural motifs as monomeric protein folds Structure 17 1128 1136 10.1016/j.str.2009.06.013 1:CAS:528:DC%2BD1MXps1CltL0%3D
4. T Hou W Zhang DA Case W Wang 2008 Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain J Mol Biol 376 1201 1214 10.1016/j.jmb.2007.12.054 1:CAS:528:DC%2BD1cXhsleju7Y%3D
5. AY Hung M Sheng 2002 PDZ domains: structural modules for protein complex assembly J Biol Chem 277 5699 5702 10.1074/jbc.R100065200 1:CAS:528: DC%2BD38XhvFyrs7o%3D (Pubitemid 34968344)
6. MB Kennedy 1995 Origin of PDZ (DHR, GLGF) domains Trends Biochem Sci 20 350 10.1016/S0968-0004(00)89074-X 1:CAS:528:DyaK2MXotF2rsL4%3D
7. CP Ponting 1997 Evidence for PDZ domains in bacteria, yeast, and plants Protein Sci 6 46 468
8. Nourry C, Grant SGN, Borg JP (2003) PDZ domain proteins: plug and play! Sci STKE 2003(179):RE7
9. R Tonikian Y Zhang SL Sazinsky B Currell JH Yeh B Reva HA Held BA Appleton M Evangelista Y Wu X Xin AC Chan S Seshagiri LA Lasky C Sander C Boone GD Bader SS Sidhu 2008 A specificity map for the PDZ domain family PLoS Biol 6 e239 10.1371/journal.pbio.0060239
10. KK Dev 2004 Making protein interactions druggable: targeting PDZ domains Nat Rev Drug Discov 3 1047 1056 10.1038/nrd1578 1:CAS:528:DC%2BD2cXhtVarsL3J (Pubitemid 39642367)
11. C Giallourakis Z Cao T Green H Wachtel X Xie M Lopez-Illasaca M Daly J Rioux R Xavier 2006 A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands Genome Res 16 1056 1072 10.1101/gr.5285206 1:CAS:528:DC%2BD28Xot1Kkurw%3D (Pubitemid 44162265)
12. U Wiedemann P Boisguerin R Leben D Leitner G Krause K Moelling R Volkmer-Engert H Oschkinat 2004 Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides J Mol Biol 343 703 718 10.1016/j.jmb.2004.08.064 1:CAS:528:DC%2BD2cXot1WrtL8%3D (Pubitemid 39311616)
13. DA Doyle A Lee J Lewis E Kim M Sheng R MacKinnon 1996 Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ Cell 85 1067 1076 10.1016/S0092-8674(00)81307-0 1:CAS:528:DyaK28XjvF2iu7s%3D (Pubitemid 26231173)
14. MA Stiffler JR Chen VP Grantcharova Y Lei D Fuchs JE Allen LA Zaslavskaia G MacBeath 2007 PDZ domain binding selectivity is optimized across the mouse proteome Science 317 364 369 10.1126/science.1144592 1:CAS:528: DC%2BD2sXnslGrs78%3D (Pubitemid 47106375)
15. JR Chen BH Chang JE Allen MA Stiffler G MacBeath 2008 Predicting PDZ domain-peptide interactions from primary sequences Nat Biotechnol 26 1041 1045 10.1038/nbt.1489 1:CAS:528:DC%2BD1cXhtVygtLvM
16. K Kaufmann N Shen L Mizoue J Meiler 2011 A physical model for PDZ-domain/peptide interactions J Mol Model 17 315 324 10.1007/s00894-010-0725-5 1:CAS:528:DC%2BC3MXht1Wjsrg%3D
17. D Saro E Klosi A Paredes MR Spaller 2004 Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands Org Lett 6 3429 3432 10.1021/ol049181q 1:CAS:528:DC%2BD2cXntVCrt7Y%3D (Pubitemid 39406906)
18. D Saro T Li C Rupasinghe A Paredes N Caspers MR Spaller 2007 A thermodynamic ligand binding study of the third PDZ domain (PDZ3) from the mammalian neuronal protein PSD-95 Biochemistry 46 6340 6352 10.1021/bi062088k 1:CAS:528:DC%2BD2sXkvValsbo%3D (Pubitemid 46842877)
19. GG Krivov MV Shapovalov RL Dunbrack Jr 2009 Improved prediction of protein side-chain conformations with SCWRL4 Proteins 77 778 795 10.1002/prot.22488 1:CAS:528:DC%2BD1MXhtlSru7nN
20. JM Word SC Lovell JS Richardson DC Richardson 1999 Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J Mol Biol 285 1735 1747 10.1006/jmbi.1998.2401 1:CAS:528: DyaK1MXhtV2ht7g%3D (Pubitemid 29060467)
21. B Knapp U Omasits W Schreiner 2008 Side chain substitution benchmark for peptide/MHC interaction Protein Sci 17 977 982 10.1110/ps.073402508 1:CAS:528:DC%2BD1cXmvFKht7Y%3D (Pubitemid 351749203)
22. P Zhou F Tian F Lv Z Shang 2009 Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins Proteins 76 151 163 10.1002/prot.22327 1:CAS:528:DC%2BD1MXmtFKhtLY%3D
23. Y Duan C Wu S Chowdhury MC Lee G Xiong W Zhang R Yang P Cieplak R Luo T Lee J Caldwell J Wang P Kollman 2003 A point-charge force field for molecular mechanics simulations of proteins based on condensed phase quantum mechanical calculations J Comput Chem 24 1999 2012 10.1002/jcc.10349 1:CAS:528: DC%2BD3sXovVygsbc%3D
24. F Tian L Yang F Lv X Luo P Pan 2011 Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR Analyses Amino Acids 40 493 503 10.1007/s00726-010-0661-9 1:CAS:528:DC%2BC3MXlt12jtA%3D%3D
25. M Svensson S Humbel RDJ Froese T Matsubara S Sieber K Morokuma 1996 ONIOM: a multilayered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3))(2) + H-2 oxidative addition J Phys Chem 100 19357 19363 10.1021/jp962071j 1:CAS:528:DyaK28XntVWmt7Y%3D (Pubitemid 126786970)
26. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson BG, Chen W, Wong MW, Andres JL, Head-Gordon M, Replogle ES, Pople JA (2003) Gaussian 03. Gaussian Inc., Wallingford
27. MJS Dewar EG Zoebisch EF Healy JJP Stewart 1985 AM1: a new general purpose quantum mechanical molecular model J Am Chem Soc 107 3902 3909 10.1021/ja00299a024 1:CAS:528:DyaL2MXktFWlsLk%3D
28. WD Cornell P Cieplak CI Bayly IR Gould KM Merz Jr DM Ferguson DC Spellmeyer T Fox JW Caldwell PA Kollman 1995 A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J Am Chem Soc 117 5179 5197 10.1021/ja00124a002 1:CAS:528:DyaK2MXlsFertrc%3D
29. Y Li Y Yang P He Q Yang 2009 QM/MM study of epitope peptides binding to HLA-A*0201: the roles of anchor residues and water Chem Biol Drug Des 74 611 618 10.1111/j.1747-0285.2009.00896.x 1:CAS:528:DC%2BD1MXhsVGku7bK
30. P Zhou J Zou F Tian Z Shang 2009 Fluorine bonding-how does it work in protein-ligand interactions? J Chem Inf Model 49 2344 2355 10.1021/ci9002393 1:CAS:528:DC%2BD1MXhtF2lur7E
31. D Eisenberg AD McLachlan 1986 Solvation energy in protein folding and binding Nature 319 199 203 10.1038/319199a0 1:CAS:528:DyaL28XmsFersg%3D%3D (Pubitemid 16128783)
32. PA Kollman I Massova C Reyes B Kuhn SH Huo L Chong M Lee Y Duan W Wang O Donini P Cieplak J Srinivasan DA Case TE Cheatham 2000 Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc Chem Res 33 889 897 10.1021/ar000033j 1:CAS:528: DC%2BD3cXmvFGiu7g%3D (Pubitemid 32056774)
33. M Retegan A Milet H Jamet 2009 Exploring the binding of inhibitors derived from tetrabromobenzimidazole to the CK2 protein using a QM/MM-PB/SA approach J Chem Inf Model 49 963 971 10.1021/ci8004435 1:CAS:528: DC%2BD1MXktF2gurs%3D
34. K Dubey R Ojha 2011 Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor J Biol Phys 37 69 78 10.1007/s10867-010-9199-z 1:CAS:528:DC%2BC3cXhs1Wms7vI
35. W Rocchia E Alexov B Honig 2001 Extending the applicability of the nonlinear. Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J Phys Chem 105 6507 6514 10.1021/jp010454y 1:CAS:528:DC%2BD3MXktVClsLw%3D (Pubitemid 35339019)
36. MF Sanner AJ Olson JC Spehner 1996 Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 305 320 10.1002/(SICI)1097- 0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y 1:CAS:528:DyaK28XhtlOisro%3D
37. SC Lovell JM Word JS Richardson DC Richardson 2000 The penultimate rotamer library Proteins 40 389 408 10.1002/1097-0134(20000815)40:3<389::AID- PROT50>3.0.CO;2-2 1:CAS:528:DC%2BD3cXlsFCrtLc%3D (Pubitemid 30624447)
38. P Zhou F Tian Z Shang 2009 2D depiction of nonbonding interactions for protein complexes J Comput Chem 30 940 951 10.1002/jcc.21109 1:CAS:528:DC%2BD1MXjvFant70%3D
39. TP Creamer 2000 Side-chain conformational entropy in protein unfolded states Proteins 40 443 450 10.1002/1097-0134(20000815)40:3<443::AID- PROT100>3.0.CO;2-L 1:CAS:528:DC%2BD3cXlsFCrtbo%3D (Pubitemid 30624452)
40. Bader RFW (1990) Atoms in molecules: a quantum theory. UK, Oxford University Press
41. W Wang A Tian NB Wong 2005 Theoretical study on the bromomethane-water 1:2 complexes J Phys Chem A 109 8035 8040 10.1021/jp052557c 1:CAS:528: DC%2BD2MXnvVahtLg%3D (Pubitemid 41367378)
42. AE Reed WeinholdF CuritssLA 1988 Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint Chem Rev 88 889 926 10.1021/cr00088a005
43. C Møller MS Plesset 1934 Note on an approximation treatment for many-electron systems Phys Rev 46 618 622 10.1103/PhysRev.46.618
44. Biegler-Konig F, Schoenbohm J (2002) AIM2000, 2.0 ed. Buro fur Innovative Software, Bielefeld, Germany
45. Glendening ED, Badenhoop JK, Reed AE, Carpente JE, Bohmann JA, Morales CM, Weinhold F (2001) NBO 5.0. Theoretical Chemistry Institute, University of Wisconsin, Madison, WI
46. C Cortes V Vapnik 1995 Support vector networks Mach Learn 20 273 293
47. P Zhou F Tian X Chen Z Shang 2008 Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes Biopolymers (Pept Sci) 90 792 802 10.1002/bip.21091 1:CAS:528:DC%2BD1cXhsV2qtL3I
48. P Zhou X Chen Y Wu Z Shang 2010 Gaussian process: an alternative approach for QSAM modeling of peptides Amino Acids 38 199 212 10.1007/s00726-008-0228-1 1:CAS:528:DC%2BC3cXhtVehtb0%3D
49. P Zhou F Tian F Lv Z Shang 2009 Comprehensive comparison of eight statistical modelling methods used in quantitative structure-retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome J Chromatogr A 1216 3107 3116 10.1016/j.chroma.2009.01.086 1:CAS:528:DC%2BD1MXjsFaitLg%3D
50. CF Matta N Castillo RJ Boyd 2005 Characterization of a closed-shell fluorine-fluorine bonding Interaction in aromatic compounds on the basis of the electron density J Phys Chem A 109 3669 3681 10.1021/jp045044z 1:CAS:528:DC%2BD2MXisleqt74%3D (Pubitemid 40643960)
51. W Nakanishi S Hayashi K Narahara 2008 Atoms-in-molecules dual parameter analysis of weak to strong interactions: behaviors of electronic energy densities versus Laplacian of electron densities at bond critical points J Phys Chem A 112 13593 13599 10.1021/jp8054763 1:CAS:528:DC%2BD1cXhsVWgtL7E
52. Petsalaki E, Stark A, Garcia-Urdiales E, Russell RB (2009) Accurate prediction of peptide binding sites on protein surfaces. 5:e1000335