Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations

Protein Science

Volumn 8, Issue 1, 1999, Pages 25-34

  Frimurer, Thomas M ^a   Peters, Günther H ^b   Sørensen, Morten Dahl ^b,c   Led, Jens Jørgen ^b   Olsen, Ole Hvilsted ^a  

^a NOVO NORDISK A S   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c LEO PHARMA A S   (Denmark)

Author keywords

Adiabatic mapping; Conformational change; Essential dynamics; Free energy simulations; Kunitz type inhibitor 3(VI)

Indexed keywords

COLLAGEN TYPE 6; ISOLEUCINE; THREONINE; TRYPSIN; TRYPTOPHAN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; ENERGY TRANSFER; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

EID: 0032924055     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.1.25     Document Type: Article

References (51)

1. Amadei A, Linssen AMB, Berendsen HJC. 1993. Essential dynamics of proteins. Proteins Struct Funct Genet 17:412-425.
2. Arnoux B, Mérigeau K, Saludian P, Norris F, Norris K, Bjørn S, Olsen O, Petersen L, Ducruix A. 1995. The 1.6 Å structure of Kunitz-type domain from the α3 chain of human type VI collagen. J. Mol Biol 246:609-617.
3. Asakura T, Williamsson M, Magn L. 1993. Empirical comparisons of models for chemical-shift calculation in proteins. J Magn Reson Ser B 101:63-71.
4. Berndt KD, Güenter P, Orbons LPM, Wüthrich K. 1992. Determination of a high-quality structure of the bovine pancreatic trypsin inhibitor and comparison with tree crystal structures. J. Mol Biol 227:757-775.
5. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rogers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer based archival file for macromolecular structure. J Mol Biol 112:535-542.
6. Boresch S, Archontis G, Karplus M. 1994. Free energy simulations: The meaning of the individual contributions from a component analysis. Proteins Struct Funct Genet 20:25-33.
7. Boresch S, Karplus M. 1995. The meaning of component analysis: Decomposition of the free energy in terms of specific interactions. J Mol Biol 254:801-807.
8. Brooks BR, Bruccoleri RE, Olafsen BD, States DJ, Swaminthan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
9. Brooks CL III, Karplus M, Pettitt BMA. 1988. Theoretical perspective of dynamics, structure and thermodynamics. Proteins Adv Chem Phys 71.
10. Case DA, Karplus M. 1979. Dynamics of ligand binding to heme proteins. J Mol Biol 132:343-368.
11. CHARMM Molecular Modeling Software Package, Release 3.3. 1992. Waltham, Massachusetts: Molecular Simulations Inc.
12. Chu ML, Zhang R, Pan TC, Stokes D, Conway D, Kuo HJ, Glanville R, Meyer U, Mann K, Deutzmann R, Timpl R. 1990. Mosaic structure of globular domains in the human type VI collagen α3 chain: Similarity to Von Willebrand factor, fibronectin, actin, salivary proteins and aprotinin type protease inhibitors. EMBO J 9:385-393.
13. Derewenda U, Swenson L, Wei Y, Green R, Kobos PM, Joerger R, Haas MJ, Derewenda ZS. 1994. Conformational lability of lipases observed in the absence of an oil-water interface: Crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar. J Lip Res 35:524-534.
14. 1 substrate interactions. Proteins Struct Funct Genet 17:1661-175.
15. Fersht AR. 1988. Relationships between apparent binding energies measured in site-directed mutagenesis experiments and energetics of binding and catalysis. Biochemistry 27:1577-1580.
16. Fleischman SH, Brooks CL. 1987. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes. J Chem Phys 87:3029-3037.
17. Fleischman SH, Zichi D. 1991. A. Free energy simulations of methane solvation. A study of integrand convergence properties using thermodynamic integration. J Chem Phys 88:2617-2622.
18. Gilquin B, Perahia D, Dive V. 1993. A free-energy study of a bacterial collagenase inhibitor. Int J Pept Protein Res 43:384-392.
19. Goldsack DE. 1976. Relation of the hydrophobicity index to the thermal stability of homologous proteins. Biopolymers 9:247-252.
20. Heald SL, Tilton RF, Hammond LJ, Lee A, Bayney RM, Kamarck ME, Ramabhadran TV, Dreyer RN, Davis G, Unterbech A, Tamburini PP. 1991. Sequential NMR resonance assignment and structure determination of the Kunitz-type inhibitor domain of the Alzheimer's β-amyloid precursor protein. Biochemistry 30:10467-10478.
21. Hodel A, Simonson T, Fox AO, Brünger AT. 1993. Conformational substrates and uncertainty in macro-molecular free energy calculations. J Phys Chem 97:3409-3417.
22. Jørgensen WL, Chandrasdkhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulation liquid water. J Chem Phys 79:926-935.
23. Joseph-McCarthy D, Petsko GA, Karplus M. 1995. Use of a minimum perturbation approach to predict TIM mutant structures. Protein Eng 8: 1103-1115.
24. Kitaguchi N, Takahashi Y, Tokushima Y, Shiojiri S, Ito H. 1988. Nature 331:530-532.
25. Kollman PA. 1993. Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417.
26. Mark AE, van Gunsteren WF. 1994. Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. J Mol Biol 240:167-176.
27. Mazor M, Pettitt BM. 1991. Convergence of the chemical potential in aqueous simulations. Mol Simul 6:1-4.
28. McCammon JA, Straatsma TP. 1992. Alchemical free energy simulation. Ann Rev Phys Chem 43:407-416.
29. Mitchell MJ, McCammon JA. 1991. A. Free energy difference calculations by thermodynamic integration-difficulties in obtaining a precise value. J Comp Chem 12:271-275.
30. Northrup SH, Pear MR, Lee CY, McCammon JA, Karplus M. 1982. Dynamical theory of activated processes in globular proteins. Dynamical theory of activated processes in globular proteins. Proc Nat Acad Sci USA 79:4035-4039.
31. Otting G, Liepinsh E, Wüthrich K. 1993. Disulfide bond isomerization in BPTI and BPTI(G36S): NMR study of correlated mobility in proteins. Biochemistry 32:3571-3582.
32. Pearlman DA. 1993. Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations. J Comp Phys 98:8946-8957.
33. Pearlman DA. 1994. Free energy derivatives: A new method for probing the convergence problem in free energy calculations. J Comp Chem 15:105-123.
34. Pearlman DA, Kollman PA. 1991. The overlooked bond-stretching contributions. J Chem Phys 94:4532-4545.
35. Peters GH, van Aalten DMF, Edholm O, Toxvaerd S, Bywater R. 1996. Dynamics of proteins in different solvent systems: Analysis of essential motion in lipases. Biophys J 71:2245-2255.
36. Philippopoulos M, Xiang Y, Lim C. 1995. Identifying the mechanism of protein loop closure: A molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution. Protein Eng 8:565-573.
37. Ryckaert J-P, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the Cartesian equation of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 23:327-335.
38. Shi Y-Y, Mark AE, Wang C, Huang F, Berendsen HJC, van Gunsteren WF. 1993. Can the stability of protein mutants be predicted by free energy calculations? Protein Eng 6:289-295.
39. Shih HH-L, Brady J, Karplus M. 1985. Structure of proteins with single-site mutations: A minimum perturbation approach. Proc Natl Acad Sci USA 82:1697-1700.
40. Sørensen MD, Bjørn S, Norris K, Olsen O, Petersen L, James LT, Led JJ. 1997. Solution structure and backbone dynamics of the human α3-chain type VI collagen C-terminal Kunitz domain. Biochemistry 36:10439-10450.
41. Sørensen MD, Kristensen SM, Bjørn S, Norris K, Olsen O, Led JJ. 1996. Elucidation of the origin of multiple conformations of the human α3-chain type VI collagen C-terminal Kunitz domain: The reorientation of the Trp21 ring. J Biomol NMR 8:391-403.
42. Straatsma TP, McCammon JA. 1991. Multiconfiguration thermodynamic integration. J Chem Phys 95:1175-1188.
43. Young HD. 1962. Statistical treatment of experimental data. New York: McGraw-Hill.
44. van Aalten DMF, Amadei A, Linssen ABM, Eijsink VGH, Vriend G. 1995. The essential dynamics of thermolysin-conformation of the hingebending motion and comparison of simulations in vacuum and water. Proteins Struct Funct Genet 22:45-54.
45. van Gunsteren WF, Beutler TC, Fraternali F, King PM, Mark AE, Smith PE. 1993. Computation of free energy in practice: Choice of approximations and accuracy limiting factors. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, eds. Computer simulations in biological systems. Leiden, The Netherlands: Escon Science Publishers.
46. Vriend G. 1990. WHAT IF: A molecular modelling and drug design program. J Mol Graph 8:52-56.
47. Wade CR, Davies ME, Luty BA, Madura DJ, McCammon JA. 1993. Gating of the active site of tripose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J 64:9-15.
48. Wade CR, Luty BA, Demchuk E, Madura DJ, Davies ME, Brigges JM, McCammon JA. 1994. Simulation of enzyme-substrate encounter with gated active-sites. Nature Struct Biol 1:63-67.
49. Wade CR, McCammon A. 1992. Binding of an antiviral agent to a sensitive and a resistant human thinovirus. Computer studies with sampling of amino acid side-chain conformations. J Mol Biol 225:679-696.
50. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S Jr, Weiner P. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106:765-784.
51. Zweckstetter M, Czisch M, Mayer U, Chu M-L, Zinth W, Timpl R, Holak TA. 1996. Structure 4:195-209.