Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water

Proteins: Structure, Function and Genetics

Volumn 24, Issue 3, 1996, Pages 304-313

  Berndt, Kurt D ^a,b   Güntert, Peter ^a   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

distance geometry; molecular dynamics simulation; protein structure determination by NMR; structure calculation with DIANA

Indexed keywords

APROTININ;

ARTICLE; CATTLE; COMPUTER PROGRAM; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; APROTININ; CATTLE; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; SOFTWARE; SOLUTIONS; THERMODYNAMICS; TRYPSIN INHIBITORS; WATER;

EID: 0029866846     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199603)24:3<304::AID-PROT3>3.0.CO;2-G     Document Type: Article

References (27)

1. Gũntert, P., Braun, W., Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217:517-530, 1991.
2. Wüthrich, K. "NMR of Proteins and Nucleic Acids." Wiley: New York, 1986.
3. Braun, W., Gō N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186:611-626, 1985.
4. Güntert, P., Wüthrich K Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR, 1:446-456, 1991.
5. Güntert, P., Qian, Y.Q., Otting, G., Müller, M., Gehring, W.J., Wüthrich K. Structure determination of the Antp(C39→S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217:531-540, 1991.
6. Kaptein, R., Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., van Gunsteren, W.F. A protein structure from nuclear magnetic resonance data. Lac repressor headpiece. J. Mol. Biol. 182:179-182, 1985.
7. Brünger, A.T., Clore, G.M., Gronenborn, A.M., Karplus, M. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crarabin. Proc. Natl. Acad. Sci. USA 83: 3801-3805, 1986.
8. Nilges, M., Clore, G.M., Gronenborn, A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry - dynamical simulated annealing calculations. FEBS Lett. 229:317-324, 1988.
9. 1H proximities in solution. Bull. Math. Biol. 46:673-698, 1984.
10. Deisenhofer, J., Steigemann, W. Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1.5 Å resolution. Acta Crystallogr. B31:238-250, 1975.
11. Wlodawer, A., Nachman, J., Gilliland, G.L., Gallagher, W., Woodward, C. Structure of form III crystals of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 198:469-480, 1987.
12. Wlodawer, A., Walter, J., Huber, R., Sjölin, L. Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II. J. Mol. Biol. 180:301-329, 1984.
13. Berndt, K.D., Güntert, P., Orbons, L.P.M., Wüthrich, K. Determination of a high-quality NMR solution structure of the bovine pancreatic trypsin inhibitor (BPTI) and comparison with three crystal structures. J. Mol. Biol. 227: 757-775, 1992.
14. Billeter, M., Schaumann, T., Braun, W., Wüthrich, K. Restrained energy refinement with two different algorithms and force fields of the structure of the α-amylase inhibitor tendamistat determined by NMR in solution. Biopolymers 29:696-706, 1990.
15. Brunne, R.M., Liepinsh, E. Otting, G., Wüthrich, K., van Gunsteren, W.F. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231:1040-1048, 1993.
16. Brunne, R.M., Berndt, K.D., Güntert, P., Wüthrich, K., van Gunsteren, W.F. Structure and dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations. Proteins 23:49-62, 1995.
17. van Gunsteren, W., Berendsen, H.J.C. "Groningen Molecular Simulation (GROMOS) Library Manual." Groningen: Biomos, 1987.
18. Guntert, P., Berndt, K.D., Wüthrich, K. The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J. Biomol. NMR 3:601-606, 1993.
19. Singh, U.C., Weiner, P.K., Caldwell, J.W., Kollman, P.A. "Amber 3.0." San Francisco: University of California, 1986.
20. Berendsen, H.J.C., Grigera, J.R., Straatsma, T.P. The missing term in effective pair potentials. J. Phys. Chem. 91:6269-6271, 1987.
21. Torda, A.E., Scheek, R.M., van Gunsteren, W. Time-dependent distance restraints in molecular dynamics simulations. Chem. Phys. Lett. 157:289-294, 1989.
22. Torda, A.E., Scheek, R.M., van Gunsteren, W. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J. Mol. Biol. 214:223-235, 1990.
23. Xia, T.H. "Software for Determination and Visual Display of NMR Structures of Proteins: The Distance Geometry Program DGPLAY and the Computer Graphics Programs CONFOR and XAM." Zürich: Ph.D. thesis, ETH Nr. 9831, 1992.
24. McLachlan, A.D. Gene duplication in the structural evolution of chymotrypsin. J. Mol. Biol. 128:49-79, 1979.
25. Billeter, M., Kline, A.D., Braun, W., Huber, R., Wüthrich, K. Comparison of the high-resolution structures of the α-amylase inhibitor Tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J. Mol. Biol. 206:677-687, 1989.
26. Richmond, T.J. Solvent-accessible surface area and excluded volume in proteins. J. Mol. Biol. 178:63-89, 1984.
27. Otting, G., Liepinsh, E., Wüthrich, K. Disulfide bond isomerization in BPTI and BP-TI(G36S): An NMR study of correlated mobility in proteins. Biochemistry 32:3571-3582, 1993.