A proline to glycine mutation in the Lck SH3-domain affects conformational sampling and increases ligand binding affinity

FEBS Letters

Volumn 581, Issue 8, 2007, Pages 1555-1560

  Bauer, Finn ^a   Sticht, Heinrich ^a  

^a Institut für Biochemie   (Germany)

Author keywords

Conformational sampling; Lck; Ligand affinity; Molecular dynamics; SH3 domain

Indexed keywords

GLYCINE; PROLINE; PROTEIN KINASE LCK; PROTEIN SH3;

ARTICLE; BINDING AFFINITY; CONFORMATION; FLUORESCENCE; GENE MUTATION; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; SIMULATION; WILD TYPE;

ANIMALS; GLYCINE; HUMANS; LIGANDS; LYMPHOCYTE SPECIFIC PROTEIN TYROSINE KINASE P56(LCK); MUTATION; PROLINE; PROTEIN CONFORMATION; SRC HOMOLOGY DOMAINS;

EID: 34047156098     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.03.012     Document Type: Article

References (35)

1. Morton C.J., and Campbell I.D. SH3 domains. Molecular 'Velcro'. Curr. Biol. 4 (1994) 615-617
2. Lim W.A., Richards F.M., and Fox R.O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372 (1994) 375-379
3. Feng S., Chen J.K., Yu H., Simon J.A., and Schreiber S.L. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 266 (1994) 1241-1247
4. Feng S., Kasahara C., Rickles R.J., and Schreiber S.L. Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands. Proc. Natl. Acad. Sci. USA 92 (1995) 12408-12415
5. Pisabarro M.T., and Serrano L. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain. Biochemistry 35 (1996) 10634-10640
6. Pisabarro M.T., Serrano L., and Wilmanns M. Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions. J. Mol. Biol. 281 (1998) 513-521
7. Ghose R., Shekhtman A., Goger M.J., Ji H., and Cowburn D. A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat. Struct. Biol. 8 (2001) 998-1004
8. Bauer F., Schweimer K., Meiselbach H., Hoffmann S., Rosch P., and Sticht H. Structural characterization of Lyn-SH3 domain in complex with a herpesviral protein reveals an extended recognition motif that enhances binding affinity. Protein Sci. 14 (2005) 2487-2498
9. Tran T., Hoffmann S., Wiesehan K., Jonas E., Luge C., Aladag A., and Willbold D. Insights into human Lck SH3 domain binding specificity: different binding modes of artificial and native ligands. Biochemistry 44 (2005) 15042-15052
10. Schmidt H., Hoffmann S., Tran T., Stoldt M., Stangler T., Wiesehan K., and Willbold D. Solution structure of a Hck SH3 domain ligand complex reveals novel interaction modes. J. Mol. Biol. 365 (2007) 1517-1532
11. Schweimer K., Hoffmann S., Bauer F., Friedrich U., Kardinal C., Feller S.M., Biesinger B., and Sticht H. Structural investigation of the binding of a herpesviral protein to the SH3 domain of tyrosine kinase Lck. Biochemistry 41 (2002) 5120-5130
12. Arold S., O'Brien R., Franken P., Strub M.P., Hoh F., Dumas C., and Ladbury J.E. RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef. Biochemistry 37 (1998) 14683-14691
13. Chakrabartty A., Doig A.J., and Baldwin R.L. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. USA 90 (1993) 11332-11336
14. Bauer F., Hofinger E., Hoffmann S., Rosch P., Schweimer K., and Sticht H. Characterization of Lck-binding elements in the herpesviral regulatory Tip protein. Biochemistry 43 (2004) 14932-14939
15. Dayie K.T., and Wagner G. Relaxation-rate measurements for 15N-1H groups with pulsed-field gradients and preservation of coherence pathways. J. Magn. Reson. 111 (1994) 121-126
16. Pearlman D.A., et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91 (1995) 1-41
17. Cheatham III T.E., Cieplak P., and Kollman P.A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16 (1999) 845-862
18. Cornell W.D., et al. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
19. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
20. Darden T.A., York D.M., and Pedersen L.G. Particle mesh Ewald. An N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
21. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
22. Koradi R., Billeter M., and Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph 14 (1996) 51-55 29-32
23. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph 14 (1996) 33-38 27-38
24. Brünger A.T. XPLOR, Version 3.1. A System for X-ray Crystallography and NMR (1992), Yale University Press, New Haven, CT
25. Goodman J.L., Pagel M.D., and Stone M.J. Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters. J. Mol. Biol. 295 (2000) 963-978
26. Engh R.A., et al. Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design. Structure 4 (1996) 1353-1362
27. Prade L., Engh R.A., Girod A., Kinzel V., Huber R., and Bossemeyer D. Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential. Structure 5 (1997) 1627-1637
28. Brzozowski A.M., et al. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 389 (1997) 753-758
29. Urzhumtsev A., et al. A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure 5 (1997) 601-612
30. Davis A., and Teague S. Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis. Angew. Chem., Int. Ed. Engl. 38 (1999) 736-749
31. Fritz T.A., Tondi D., Finer-Moore J.S., Costi M.P., and Stroud R.M. Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase. Chem. Biol. 8 (2001) 981-995
32. Rauh D., Klebe G., and Stubbs M.T. Understanding protein-ligand interactions: the price of protein flexibility. J. Mol. Biol. 335 (2004) 1325-1341
33. Perryman A.L., Lin J.H., and McCammon J.A. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci. 13 (2004) 1108-1123
34. Wartha F., Horn A.H.C., Meiselbach H., and Sticht H. Molecular dynamics simulations of HIV-1 protease suggest different mechanisms contributing to drug resistance. J. Chem. Theory Comput. 1 (2005) 315-324
35. Meiselbach H., Horn A.H., Harrer T., and Sticht H. Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations. J. Mol. Model 13 (2007) 297-304