Similar chemistry, but different bond preferences in inter versus intra-protein interactions

Proteins: Structure, Function and Genetics

Volumn 72, Issue 2, 2008, Pages 741-753

  Cohen, Mati ^a   Reichmann, Dana ^a   Neuvirth, Hani ^a   Schreiber, Gideon ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Interaction geometry; Interface symmetry; Protein complex database; Protein packing; Protein protein interface

Indexed keywords

HETERODIMER; HOMODIMER; PROTEIN;

ARTICLE; HYDROGEN BOND; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION;

DIMERIZATION; HYDROGEN BONDING; PROTEIN FOLDING; PROTEINS;

EID: 46449113031     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21960     Document Type: Article

References (66)

1. Deremble C, Lavery R. Macromollecullar recognition. Curr Opin Struct Biol 2005;15:171-175.
2. Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
3. Janin J. Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci 2005;14:278-283.
4. Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Protein Struct Funct Bioinformatics 2005;60:150-169.
5. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
6. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
7. Block P, Paern J, Hullermeier E, Sanschagrin P, Sotriffer CA, Klebe G. Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Protein Struct Funct Bioinformatics 2006;65:607-622.
8. Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Protein Struct Funct Bioinformatics 2003;53:708-719.
9. Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
10. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 1996;260:604-620.
11. Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003;325:377-387.
12. McCoy AJ, Chandana Epa V, Colman PM. Electrostatic complementarity at protein/protein interfaces. J Mol Biol 1997;268:570-584.
13. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 1996;31:127-152.
14. Tsai CJ, Xu D, Nussinov R. Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. Protein Sci 1997;6:1793-1805.
15. 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.
16. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
17. Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
18. Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999;285:1735-1747.
19. Forrest LR, Honig B. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Protein Struct Funct Bioinformatics 2005;61:296-309.
20. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 1999;285:1711-1733.
21. Baker EN, Hubbard RE. Hydrogen-bonding in globular-proteins. Prog Biophys Mol Biol 1984;44:97-179.
22. Brunger AT, Karplus M. Polar hydrogen positions in proteins - empirical energy placement and neutron-diffraction comparison. Protein Struct Funct Genet 1988;4:148-156.
23. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
24. Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Protein Struct Funct Bioinformatics 2005;61:6-20.
25. Fischer TB, Arunachalam KV, Bailey D, Mangual V, Bakhru S, Russo R, Huang D, Paczkowski M, Lalchandani V, Ramachandra C, Ellison B, Galer S, Shapley J, Fuentes E, Tsai J. The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics 2003;19:1453-1454.
26. Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally non-redundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004;13:1043-1055.
27. Kim WK, Henschel A, Winter C, Schroeder M. The many faces of protein-protein interactions: a compendium of interface geometry. PLoS Comput Biol 2006;2:e124.
28. Larsen TA, Olson AJ, Goodsell DS. Morphology of protein-protein interfaces. Structure 1998;6:421-427.
29. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
30. Teyra J, Doms A, Schroeder M, Pisabarro MT. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics 2006;7:104.
31. Morozov AV, Kortemme T, Tsemekhman K, Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci USA 2004;101:6946-6951.
32. Xu D, Tsai CJ, Nussinov R. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng Des Sel 1997;10:999-1012.
33. Jiang L, Lai LH. CH center dot center dot center dot O hydrogen bonds at protein-protein interfaces. J Biol Chem 2002;277:37732-37740.
34. Derewenda ZS, Lee L, Derewenda U. The occurrence of C-H. . .O hydrogen bonds in proteins. J Mol Biol 1995;252:248-262.
35. Kumar S, Nussinov R. Salt bridge stability in monomeric proteins. J Mol Biol 1999;293:1241-1255.
36. Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995;63:31-65.
37. Kumar S, Nussinov R. Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J 2002;83:1595-1612.
38. Sagarik K, Chaiyapongs S. Structures and stability of salt-bridge in aqueous solution. Biophys Chem 2005;117:119-140.
39. Barlow DJ, Thornton JM. Ion-pairs in proteins. J Mol Biol 1983;168:867-885.
40. Chelli R, Gervasio FL, Procacci P, Schettino V. Stacking and T-shape competition in aromatic-aromatic amino acid interactions. J Am Chem Soc 2002;124:6133-6143.
41. Misura KMS, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction\. J Mol Biol 2004;342:651-664.
42. Meyer EA, Castellano RK, Diederich F. Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed Engl 2003;42:1210-1250.
43. Vaupel S, Brutschy B, Tarakeshwar P, Kim KS. Characterization of weak NH-pi intermolecular interactions of ammonia with various substituted pi-systems. J Am Chem Soc 2006;128:5416-5426.
44. Rodham DA, Suzuki S, Suenram RD, Lovas FJ, Dasgupta S, Goddard WA, Blake GA. Hydrogen-bonding in the benzene ammonia dimer. Nature 1993;362:735-737.
45. Takahashi O, Kohno Y, Iwasaki S, Saito K, Iwaoka M, Tomoda S, Umezawa Y, Tsuboyama S, Nishio M. Hydrogen-bond-like nature of the CH/pi interaction as evidenced by crystallographic database analyses and ab initio molecular orbital calculations. Bull Chem Soc Jpn 2001;74:2421-2430.
46. Jiang L, Gao Y, Mao FL, Liu ZJ, Lai LH. Potential of mean force for protein-protein interaction studies. Protein Struct Funct Genet 2002;46:190-196.
47. Seeliger D, de Groot BL. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Protein Struct Funct Bioinformatics 2007;68:595-601.
48. Sarkhel S, Desiraju GR. N-H⋯O, O-H⋯O, and C-H⋯O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition. Protein Struct Funct Bioinformatics 2004;54:247-259.
49. Tsai CJ, Xu D, Nussinov R. Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. Protein Sci 1997;6:1793-1805.
50. McGaughey GB, Gagne M, Rappe AK. pi-Stacking interactions. Alive and well in proteins. J Biol Chem 1998;273:15458-15463.
51. Brocchieri L, Karlin S. Geometry of interplanar residue contacts in protein structures. Proc Natl Acad Sci USA 1994;91:9297-9301.
52. Pierce AC, Sandretto KL, Bemis GW. Kinase inhibitors and the case for CH⋯O hydrogen bonds in protein-ligand binding. Protein Struct Funct Bioinformatics 2002;49:567-576.
53. Brandl M, Weiss MS, Jabs A, Suhnel J, Hilgenfeld R. C-H center dot center dot center dot pi-interactions in proteins. J Mol Biol 2001;307:357-377.
54. Ringer AL, Figgs MS, Sinnokrot MO, Sherrill CD. Aliphatic C-H/pi interactions: methane-benzene, methane-phenol, and methane-indole complexes. J Phys Chem A 2006;110:10822-10828.
55. Gallivan JP, Dougherty DA. Cation-pi interactions in structural biology. Proc Natl Acad Sci USA 1999;96:9459-9464.
56. Mintseris J, Weng ZP. Atomic contact vectors in protein-protein recognition. Protein Struct Funct Genet 2003;53:629-639.
57. Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
58. Ansari S, Helms V. Statistical analysis of predominantly transient protein-protein interfaces. Protein Struct Funct Bioinformatics 2005;61:344-355.
59. Gerstein M, Chothia C. Packing at the protein-water interface. Proc Natl Acad Sci USA 1996;93:10167-10172.
60. Kabsch W, Sander C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
61. Boas FE, Harbury PB. Potential energy functions for protein design. Curr Opin Struc Biol 2007;17:199-204.
62. Haliloglu T, Keskin O, Ma BY, Nussinov R. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J 2005;88:1552-1559.
63. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
64. Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 2004;56:93-101.
65. Reichmann D, Cohen M, Abramovich R, Dym O, Lim D, Strynadka NC, Schreiber G. Binding hot spots in the TEM1-BLIP interface in light of its modular architecture. J Mol Biol 2007;365:663-679.
66. Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G. The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 2007;17:67-76.