Investigation of Glucose Binding Sites on Insulin

Proteins: Structure, Function and Genetics

Volumn 55, Issue 3, 2004, Pages 568-581

  Zoete, Vincent ^a,b   Meuwly, Markus ^a,b   Karplus, Martin ^a,c  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b UNIVERSITY OF BASEL   (Switzerland)

^c HARVARD UNIVERSITY   (United States)

Author keywords

D glucose; Insulin; MCSS; Molecular docking; Molecular dynamics; Normal modes; Scoring; SEED

Indexed keywords

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; COMPUTER PROGRAM; COMPUTER SIMULATION; CORRELATION ANALYSIS; DIELECTRIC CONSTANT; GLUCOSE METABOLISM; INSULIN METABOLISM; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOTION; PRIORITY JOURNAL; SCORING SYSTEM;

BINDING SITES; COMPUTER SIMULATION; GLUCOSE; INSULIN; MODELS, MOLECULAR; MOTION; SOFTWARE;

EID: 2442535181     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20071     Document Type: Article

References (31)

1. De Meyts P, Whittaker J. Structural biology of insulin and IGF1 receptors: implications for drug design. Nat Rev Drug Discov 2002;1:769-783.
2. Weiss MA, Nakagawa SH, Jia W, Xu B, Hua QX, Chu YC, Wang RY, Katsoyannis PG. Protein structure and the spandrels of San Marco: insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability. Biochemistry 2002;41: 809-819.
3. Ludvigsen S, Olsen HB, Kaarsholm NC. A structural switch in a mutant insulin exposes key residues for receptor binding. J Mol Biol 1998;279:1-7.
4. Weiss MA, Nguyen DT, Khait I, Inouye K, Frank BH, Beckage M, O'Shea E, Shoelson SE, Karplus M, Neuringer LJ. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics. Biochemistry 1989;28:9855-9873.
5. Hua QX, Weiss MA. Comparative 2D NMR studies of human insulin and des-pentapeptide insulin: sequential resonance assignment and implications for protein dynamics and receptor recognition. Biochemistry 1991;30:5505-5515.
6. Falconi M, Bozzi M, Paci M, Raudino A, Purrello R, Cambria A, Sette M, Cambria MT. Spectroscopic and molecular dynamics simulation studies of the interaction of insulin with glucose. Int J Biol Macromol 2001;29:161-168.
7. Miranker A, Karplus M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 1991;11:29-34.
8. Majeux N, Scarsi M, Apostokalis J, Ehrhardt C, Caflisch A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins 1999;37:88-105.
9. Majeux N, Scarsi M, Caflisch A. Efficient electrostatic solvation model for protein-fragment docking. Proteins 2001;42:256-268.
10. Sirockin F, Sich C, Improta S, Schaefer M, Saudek V, Froloff N, Karplus M, Dejaegere A. Structure activity relationship by NMR and by computer: a comparative study. J Am Chem Soc 2002;124: 11073-11084.
11. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr Biol Crystallogr 2002;58:899-907.
12. Baker EN, Blundell TL, Cutfield JF, Cutfield SM, Dodson EJ, Dodson GG, Hodgkin DM, Hubbard RE, Isaacs NW, Reynolds CD, et al. The structure of 2Zn pig insulin crystals at 1.5 Å resolution. Philos Trans R Soc Lond B Biol Sci 1988;319:369-456.
13. Brunger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins 1988;4:148-156.
14. Brooks BR, Bruccoleri R, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J Comput Chem 1983;4: 187-217.
15. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem 1998; B102:3586-3616.
16. Caflisch A, Schramm HJ, Karplus M. Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach. J Comput Aided Mol Des 2000;14:161-179.
17. Schaefer M, Zoete V, Karplus M. Fully automated, efficient procedure for predicting the binding mode of small ligands. 2004. Submitted for publication.
18. Zoete V, Michielin O, Karplus M. Protein-ligand binding free energy estimation using continuum electrostatics. J Comp-Aided Mol Des 2004. In press.
19. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz-J, Gilson MK, Bagheri B, Scott LR, McCammon JA. Electrostatics and diffusion in solution: simulations with the University of Houston Brownian Dynamics program. Comp Phys Comm 1995;91:57-95.
20. Ajay, Murcko MA. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 1995;38:4953-4967.
21. Brooks III CL, Karplus M, Pettitt BM. Protein. A theoretical perspective of dynamics, structure, and thermodynamics, volume 71 of Advances in chemical physics. New York: Wiley-Interscience; 1988. p 38-44.
22. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
23. Brooks III CL, Karplus M. Solvent effects on protein motion and protein effects on solvent motion. J Mol Biol 1989;208:159-181.
24. Brooks III CL, Karplus M. Deformable stochastic boundaries in molecular dynamics. J Chem Phys 1983;79:6312-6325.
25. Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion if a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
26. Tidor B, Karplus M. The contribution of vibrational entropy to molecular association. J Mol Biol 1994;238:405-414.
27. Karplus M, Ichiye T. Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations." J Mol Biol 1996;263:120-122.
28. Zhou Y, Cook M, Karplus M. Protein motions at zero angular momentum: the importance of long range correlations. Biophys J 2000;79:2902-2908.
29. Harte WE, Swaminathan S, Beveridge DL. Molecular dynamics of HIV-1 protease. Proteins 1992;13:175-194.
30. Brooks BR, Janezic D, Karplus M. Harmonic analysis of large systems. I. Methodology. J Comput Chem 1995;16:1522-1542.
31. Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.