A quantum mechanical study on phosphotyrosyl peptide binding to the SH2 domain of p56lck tyrosine kinase with insights into the biochemistry of intracellular signal transduction events

Biophysical Chemistry

Volumn 109, Issue 2, 2004, Pages 295-304

  Pichierri, Fabio ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

Phosphotyrosyl peptide; Quantum mechanical effects; SH2 domain; Signal transduction

Indexed keywords

AMINO ACID DERIVATIVE; PEPTIDE; PHOSPHOTYROSINE; PROTEIN SH2;

ARTICLE; ATOMIC PARTICLE; BINDING AFFINITY; BINDING SITE; BIOCHEMISTRY; ELECTRIC POTENTIAL; EMPIRICISM; ENERGY TRANSFER; HYDROGEN BOND; LIGAND BINDING; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; POLARIZATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; QUANTUM CHEMISTRY; QUANTUM MECHANICS; ROTATION; SIGNAL TRANSDUCTION; SOLVATION; STRUCTURE ANALYSIS; TECHNIQUE;

BINDING SITES; COMPUTATIONAL BIOLOGY; ELECTROSTATICS; HUMANS; HYDROGEN BONDING; LIGANDS; LYMPHOCYTE SPECIFIC PROTEIN TYROSINE KINASE P56(LCK); MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDE FRAGMENTS; PHOSPHOPROTEINS; PHOSPHOTYROSINE; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 1942540506     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2003.12.006     Document Type: Article

References (36)

1. Eyster K.M. Introduction to signal transduction. A primer for untangling the web of intracellular messengers. Biochem. Pharmacol. 55:1998;1921-1938.
2. Krauss G. Biochemistry of Signal Transduction and Regulations. 2001;Wiley-VCH, Weinheim.
3. Hubbard S.R., Till J.H. Protein tyrosine kinase structure and function. Annu. Rev. Biochem. 69:2000;373-398.
4. Pichierri F., Matsuo Y. Mechanism of tyrosine phosphorylation catalyzed by the insulin receptor tyrosine kinase: a semiempirical PM3 study. J. Mol. Struct. (Theochem). 622:2003;257-267.
5. Sadowski I., Stone J.C., Pawson T. A non-catalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol. Cell. Biol. 6:1986;4396-4408.
6. Moran M.F., Koch C.A., Anderson D., Ellis C., England L., Martin G.S., et al. Src homology region 2 domains direct protein-protein interactions in signal transduction. Proc. Natl. Acad. Sci. USA. 87:1990;8622-8626.
7. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
8. Waksman G., Shoelson S.E., Pant N., Cowburn D., Kuriyan J. Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms. Cell. 72:1993;779-790.
9. Bradshow J.M., Grucza R.A., Ladbury J.E., Waksman G. Probing the 'two-pronged plug two-holed socket' model for the mechanism of binding of the Src SH2 domain to phosphotyrosyl peptides: a thermodynamic study. Biochemistry. 37:1998;9083-9090.
10. Grucza R.A., Bradshaw J.M., Mitaxov V., Waksman G. Role of electrostatic interactions in SH2 domain recognition: salt-dependence of tyrosyl- phosphorylated peptide binding to the tandem SH2 domain of the Syk kinase and the single SH2 domain of the Src kinase. Biochemistry. 39:2000;10 072-10 081.
11. lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution. J. Mol. Biol. 256:1996;601-610.
12. Carey P.R., Carriere R.G., Phelps D.J., Schneider H. Charge effects in the active site of papain: resonance Raman and absorption evidence for electron polarization occurring in the acyl group of some acylpapains. Biochemistry. 17:1978;1081-1087.
13. Nolte H.-J., Rosenberry T.L., Neumann E. Effective charge on acetylcholinesterase active sites determined from the ionic strength dependence of association rate constants with cationic ligands. Biochemistry. 19:1980;3705-3711.
14. Simonson T., Archontis G., Karplus M. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation. J. Phys. Chem. B. 103:1999;6142-6156.
15. Dillet V., Van Etten R.L., Bashford D. Stabilization of charges and protonation states in the active site of the protein tyrosine phosphatases: a computational study. J. Phys. Chem. B. 104:2000;11 321-11 333.
16. J.J.P. Stewart, MOPAC2002 (version 1.0), Fujitsu Ltd. (Tokyo).
17. Stewart J.J.P. Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. Int. J. Quantum Chem. 58:1996;133-146.
18. Stewart J.J.P. in: Encyclopedia of Computational Chemistry. 1998;John Wiley and Sons.
19. Thiel W. Perspectives on semiempirical molecular orbital theory. Adv. Chem. Phys. 93:1996;703-757.
20. Dewar M.J.S., Zoebish E.G., Healy E.F., Stewart J.J.P. Development and use of quantum mechanical molecular models. 76 AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107:1985;3902-3909.
21. Stewart J.J.P. J. Comput. Chem. 10:1989;209-220.
22. York D.M., Lee T.-S., Yang W. Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules. Chem. Phys. Lett. 263:1996;297-304.
23. Klamt A., Schüürmann G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc. Perkin Trans. 2:1993;799-805.
24. Kumar S., Nussinov R. Salt bridge stability in monomeric proteins. J. Mol. Biol. 293:1999;1241-1255.
25. Khandogin J., Hu A., York D.M. Electronic structure properties of solvated biomolecules: a quantum approach for macromolecular characterization. J. Comput. Chem. 21:2000;1562-1571.
26. van der Vaart A., Merz K.M. Jr. The role of polarization and charge transfer in the solvation of biomolecules. J. Am. Chem. Soc. 121:1999;9182-9190.
27. Cummins P.L., Titmuss S.J., Jayatilaka D., Bliznyuk A.A., Rendell A.P., Gready J.E. Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules. Chem. Phys. Lett. 352:2002;245-251.
28. Pichierri F., Matsuo Y. Effect of protonation of the N-acetyl neuraminic acid residue of sialyl Lewis X: a molecular orbital study with insights into its binding properties toward the carbohydrate recognition domain of E-selectin. Bioorg. Med. Chem. 10:2002;2751-2757.
29. Pichierri F. Computation of the permanent dipole moment of α-chymotrypsin from semiempirical linear-scaling quantum mechanical methods. J. Mol. Struct. (Theochem). 664-665:2003;197-205.
30. Antosiewicz J., Porschke D. The nature of protein dipole moments: experimental and calculated permanent dipole of α-chymotrypsin. Biochemistry. 28:1989;10 072-10 078.
31. Matsuno K., Paton R.C. Quantum mechanics in the present progressive mode and its significance in biological information processing. Biosystems. 49:1999;229-237.
32. Helms V., Wade R.C. Computational alchemy to calculate absolute protein-ligand binding free energy. J. Am. Chem. Soc. 120:1998;2710-2713.
33. Boresch S., Tettinger F., Leitgeb M., Karplus M. Absolute binding free energies: a quantitative approach to their calculation. J. Phys. Chem. B. 107:2003;9535-9551.
34. Bradshow J.M., Waksman G. Calorimetric examination of high-affinity Src SH2 domain-tyrosyl phoshopeptide binding: dissection of the phosphopeptide sequence specificity and coupling energetics. Biochemistry. 38:1999;5147-5154.
35. Shulz G.E., Schirmer R.H. Principles of Protein Structure. 1979;Springer, New York.
36. Warshel A., Papazyan A. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Curr. Op. Struct. Biol. 8:1998;211-217.