Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
 John Kuszewski,
 Michael Nilges,
 Axel T. Brünger
 … show all 3 hide
Rent the article at a discount
Rent now* Final gross prices may vary according to local VAT.
Get AccessSummary
In this paper, we present a reassessment of the sampling properties of the metric matrix distance geometry algorithm, which is in widespread use in the determination of threedimensional structures from nuclear magnetic resonance (NMR) data. To this end, we compare the conformational space sampled by structures generated with a variety of metric matrix distance geometry protocols. As test systems we use an unconstrained polypeptide, and a small protein (rabbit neutrophil defensin peptide 5) for which only few tertiary distances had been derived from the NMR data, allowing several possible folds of the polypeptide chain. A process called ‘metrization’ in the preparation of a trial distance matrix has a very large effect on the sampling properties of the algorithm. It is shown that, depending on the metrization protocol used, metric matrix distance geometry can have very good sampling properties'indeed, both for the unconstrained model system and the NMRstructure case. We show that the sampling properties are to a great degree determined by the way in which the first few distances are chosen within their bounds. Further, we present a new protocol (‘partial metrization’) that is computationally more efficient but has the same excellent sampling properties. This novel protocol has been implemented in an expanded new release of the program XPLOR with distance geometry capabilities.
 Billeter, M., Havel, T.F. and Wüthrich, K. (1986)J. Comput. Client.,8, 132–141. Braun, W. and Go, N. (1985) J. Mol. Biol., 186,611626.
 Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M. (1983)J. Comp. Chem.,4, 187–217.
 Brünger, A.T. (1991) InTopics in Molecular Biology (Ed., Goodfellow, J.M.) Macmillan Press Ltd., London, pp. 137–178.
 Brünger, A.T. and Karplus, M. (1991)Acc. of Chem. Res.,24, 54–61.
 Brünger, A.T., Clore, G.M., Gronenborn, A. M. and Karplus, M. (1987)Protein Eng.,1, 399–406.
 Brünger, A.T. (1990) XPLOR software manual version 2.1., New Haven, Yale University.
 Clore, G.M. and Gronenborn, A.M. (1991)Science,252, 1390–1399.
 Crippen, G.M. and Havel, T.F. (1988)Distance Geometry and Molecular Conformation, Research Studies Press, Taunton, Somerset, England.
 Dial, R., Glover, F., Karney, D. and Klingman, D. (1979)Networks,9, 215–248.
 Dijkstra, E. W. (1959)Numer. Math.,1, 269–271.
 Dress, A.W.M. and Havel, T.F. (1988)Discrete Appl. Math.,19, 129–144.
 Driscoll, J. R., Gabow, H.N., Shrairman, R. and Tarjan, R. E. (1988)Comm. of the ACM,31, 1343–1354.
 Easthope, P.L. and Havel, T.F. (1989)Bull. Math. Bio.,51, 173–194.
 Ernst, R.R., Bodenhausen, G. and Wokaun, A. (1986)Principles of Nuclear Magnetic Resonance in One and Two Dimensions, Clarendon Press, Oxford.
 Hadwiger, M.A. and Fox, G.E. (1989)J. Biomol. Struct. Dyn.,7, 749–771.
 Hare, D.R. and Reid, B.R. (1986)Biochemistry,25, 5341–5350.
 Havel, T.F., Kuntz, I.D. and Crippen, G.M. (1983)Bull. Math. Bio.,45, 665–720; (1985)errata in Bull. Math. Bio.,47, 157.
 Havel, T.F. and Wüthrich, K. (1984)Bull. Math. Bio.,46, 673–698.
 Havel, T.F. (1990)Biopolymers,29, 1565–1585.
 Hempel, J.C. and Brown, F.K. (1989)J. Am. Chem. Soc.,111, 7323–7327.
 Kuntz, I.D., Crippen, G.M. and Kollman, P.A. (1979)Biopolymers,18, 939–957.
 Levy, R.M., Bassolino, D.A., Kitchen, D.B. and Pardi, A. (1989)Biochemistry,28, 9361–9372.
 Metzler, W.J., Hare, D.R. and Pardi, A. (1989)Biochemistry,28, 7045–7052.
 Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988)FEBS Lett.,229, 317–324.
 Nilges, M., Kuszewski, J. and Brünger, A.T. (1991) InComputational Aspects of the Study of Biological Macromolecules (Ed., Hoch, J.C.) Plenum Press, New York.
 Pardi, A., Hare, D.R., Selsted, M.E., Morrison, R.D., Bassolino, D.A. and Bach, A.C. (1988)J. Mol. Biol.,201, 625–636.
 Powell, M.J.D. (1977)Mathematical Programming,12, 241–254.
 Schlitter, J. (1987)J. Appl. Math. Physics (ZAMP),38, 1–9.
 Tarjan, R.E. (1983)Data Structures and Network Algorithms, Society for Industrial and Applied Mathematics, Philadelphia.
 Thomason, J.F. and Kuntz, I.D. (1989)J. Cell Biochem., Suppl. 13A, no. 37.
 Wüthrich, K., Billeter, M. and Braun, W. (1983)J. Mol. Biol.,169, 949–961.
 Wüthrich, K. (1986)NMR of Proteins and Nucleic Acids, Wiley, New York
 Title
 Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
 Journal

Journal of Biomolecular NMR
Volume 2, Issue 1 , pp 3356
 Cover Date
 19920101
 DOI
 10.1007/BF02192799
 Print ISSN
 09252738
 Online ISSN
 15735001
 Publisher
 Kluwer Academic Publishers
 Additional Links
 Topics
 Keywords

 Distance geometry
 Nuclear magnetic resonance
 Threedimensional structure
 Simulated annealing
 Industry Sectors
 Authors

 John Kuszewski ^{(1)}
 Michael Nilges ^{(1)}
 Axel T. Brünger ^{(1)}
 Author Affiliations

 1. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 06511, New Haven, CT, USA