Why ligand cross-reactivity is high within peptide recognition domain families? A case study on human c-Src SH3 domain

Journal of Theoretical Biology

Volumn 340, Issue , 2014, Pages 30-37

  He, Ping ^a   Wu, Wei ^a   Wang, Hai Dong ^a   Liao, Ke Long ^a   Zhang, Wei ^a   Lv, Feng Lin ^b   Yang, Kang ^a  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

^b CHONGQING UNIVERSITY   (China)

Author keywords

Atomic cross nonbonded interaction analysis; C Src SH3 domain; Ligand cross reactivity; Peptide recognition domain

Indexed keywords

PROTEIN KINASE P60; PROTEIN SH3;

EUKARYOTE; LIGAND; MOLECULAR ANALYSIS; PANEL DATA; PEPTIDE; PHYSICOCHEMICAL PROPERTY; PROTEIN;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CROSS REACTION; HUMAN; LIGAND BINDING; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PEPTIDE RECOGNITION DOMAIN; PHYSICAL CHEMISTRY; POINT MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SH3 DOMAIN; STRUCTURE ANALYSIS;

ATOMIC CROSS-NONBONDED INTERACTION ANALYSIS; C-SRC SH3 DOMAIN; LIGAND CROSS-REACTIVITY; PEPTIDE RECOGNITION DOMAIN;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MOLECULAR SEQUENCE DATA; PEPTIDES; POINT MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS PP60(C-SRC); SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; SRC HOMOLOGY DOMAINS; STATIC ELECTRICITY;

EID: 84884711542     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2013.08.026     Document Type: Article

References (36)

1. Basdevant N., Borgis D., Ha-Duong T. A coarse-grained protein-protein potential derived from an all-atom force field. Journal of Physical Chemistry B 2007, 11:9390-9399.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Research 2000, 28:235-242.
3. Boulesteix A.L., Strimmer K. Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Briefings in Bioinformatics 2007, 8:32-44.
4. Brian K.K. SH3 domains come of age. FEBS Letters 2012, 586:2606-2608.
5. Casares S., Ab E., Eshuis H., Lopez-Mayorga O., van Nuland N.A., Conejero-Lara F. The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3. BMC Structural Biology 2007, 7:22.
6. Cesareni G., Panni S., Nardelli G., Castagnoli L. Can we infer peptide recognition specificity mediated by SH3 domains?. FEBS Letters 2002, 513:38-44.
7. Chen J.R., Chang B.H., Allen J.E., Stiffler M.A., MacBeath G. Predicting PDZ domain-peptide interactions from primary sequences. Nature Biotechnology 2008, 26:1041-1045.
8. Duan Y., Wu C., Chowdhury S., Lee M.C., Xiong G. A point-charge force field for molecular mechanics simulations of proteins. Journal of Computational Chemistry 2003, 24:1999-2012.
9. Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature 1986, 319:199-203.
10. Feng S., Chen J.K., Yu H., Simon J.A., Schreiber S.L. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 1994, 266:1241-1247.
11. 2!. Journal of Molecular Graphics and Modelling 2002, 20:269-276.
12. He P., Wu W., Wang H.D., Yang K., Liao K.L., Zhang W. Toward quantitative characterization of the binding profile between the human amphiphysin-1 SH3 domain and its peptide ligands. Amino Acids 2010, 38:1209-1218.
13. He P., Wu W., Yang K., Jing T., Liao K.L., Zhang W., Wang H.D., Hua X. Exploring the activity space of peptides binding to diverse SH3 domains using principal property descriptors derived from amino acid rotamers. Biopolymers 2011, 96:288-301.
14. Hou T., Chen K., McLaughlin W.A., Lu B., Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Computational Biology 2006, 2:46-55.
15. Hou T., Zhang W., Case D.A., Wang W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. Journal of Molecular Biology 2008, 376:1201-1214.
16. Hou T., Li N., Li Y., Wang W. Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Journal of Proteome Research 2012, 11:2982-2995.
17. Larson S.M., Davidson A.R. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Science 2000, 9:2170-2180.
18. Krivov G.G., Shapovalov M.V., Dunbrack R.L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77:778-795.
19. Kuriyan J., Cowburn D. Modular peptide recognition domains in eukaryotic signaling. Annual Review of Biophysics and Biomolecular Structure 1997, 26:259-288.
20. McDonald C.B., Seldeen K.L., Deegan B.J., Farooq A. Structural basis of the differential binding of the SH3 domains of Grb2 adaptor to the guanine nucleotide exchange factor Sos1. Archives of Biochemistry and Biophysics 2008, 479:52-62.
21. Nguyen J.T., Turck C.W., Cohen F.E., Zuckermann R.N., Lim W.A. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science 1998, 282:2088-2092.
22. Nguyen J.T., Porter M., Amoui M., Miller W.T., Zuckermann R.N., Lim W.A. Improving SH3 domain ligand selectivity using a non-natural scaffold. Chemistry and Biology 2000, 7:463-473.
23. Onufriev A., Bashford D., Case D.A. Effective Born radii in the generalized Born approximation: the importance of being perfect. Journal of Computational Chemistry 2002, 23:1297-1304.
24. Petsalaki E., Russell R.B. Peptide-mediated interactions in biological systems: new discoveries and applications. Current Opinion in Biotechnology 2008, 19:344-350.
25. Petsalaki E., Stark A., García-Urdiales E., Russell R.B. Accurate prediction of peptide binding sites on protein surfaces. PLoS Computational Biology 2009, 5:e1000335.
26. Rickles R.J., Botfield M.C., Zhou X.M., Henry P.A., Brugge J.S., Zoller M.J. Phage display selection of ligand residues important for Src homology 3 domain binding specificity. Proceedings of National Academy of Sciences of the United States of America 1995, 92:10909-10913.
27. Sanner M.F., Olson A.J., Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996, 38:305-320.
28. Stiffler M.A., Chen J.R., Grantcharova V.P., Lei Y., Fuchs D., Allen J.E., Zaslavskaia L.A., MacBeath G. PDZ domain binding selectivity is optimized across the mouse proteome. Science 2007, 317:364-369.
29. Tian F., Yang L., Lv F., Yang Q., Zhou P. In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach. Amino Acids 2009, 36:535-554.
30. Velthuis A.J., Sakalis P.A., Fowler D.A., Bagowski C.P. Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One 2011, 24:e16047.
31. Wang J., Morin P., Wang W., Kollman P.A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. Journal of the American Chemical Society 2001, 123:5221-5230.
32. Yip K.Y., Utz L., Sitwell S., Hu X., Sidhu S.S., Turk B.E., Gerstein M., Kim P.M. Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. BMC Biology 2011, 9:53.
33. Yu H., Chen J.K., Feng S., Dalgarno D.C., Brauer A.W., Schreiber S.L. Structural basis for the binding of proline-rich peptides to SH3 domains. Cell 1994, 76:933-945.
34. Zhou P., Tian F., Li Z. A structure-based, quantitative structure-activity relationship approach for predicting HLA-A*0201-restricted cytotoxic T lymphocyte epitopes. Chemical Biology and Drug Design 2007, 69:56-67.
35. Zhou P., Tian F., Chen X., Shang Z. Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes. Biopolymers (Peptide Science) 2008, 90:792-802.
36. Zhou P., Wang C., Ren Y., Yang C., Tian F. Computational peptidology: a new and promising approach to therapeutic peptide design. Current Medicinal Chemistry 2013, 20:1985-1996.