Abstract
Proteins can be considered molecular machines, and protein 3D-structures are key to the understanding of these machines and to many applications in biotechnology and medicine. We are developing a method to speed up the time consuming process of structure determination significantly. The method closely couples bioinformatics for protein structure prediction with fast experiments (chemical cross-linking, specific proteolysis, mass spectrometry) for structure validation. For a given protein, the method iterates over cycles of bioinformatics and experiments to collect more and more information on the protein structure, finally resulting in an Experimentally Validated Model (EVAM) of the structure.
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References
M. Perutz. Protein Structure — New Approaches to Disease and Therapy. W. H. Freeman and Company, New York, 1992.
C. Branden and J. Tooze. Introduction to Protein Structure. Garland Publishing, New York, 1991.
D. Hoffmann and R. Zimmer. Fluorescence Energy for Elucidating the 3D-Structure of Biological Macromolecules. German Patent Office, PCT/EP99/01008, 10. Feb. 1999.
R. Zimmer and R. Thiele. Fast protein fold recognition and accurate sequence-structure alignment. In R. Hofestädt, T. Lengauer, M. Löffler, and D. Schomburg, editors, German Conference on Bioinformatics (GGB’96), number 1278 in Lecture Notes in Computer Science, pages 137–148. Springer, 1997.
N. Alexandrov, R. Nussinov, and R. Zimmer. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. In L. Hunter and T. E. Klein, editors, Pacific Symposium on Biocomputing’ 96, pages 53–72, Singapore, 1996. World Scientific Publishing Co.
R. Thiele, R. Zimmer, and T. Lengauer. Protein Threading by Recursive Dynamic Programming. J. Mol. Biol., 290(3):757–779, 1999.
K. T. Simons, C. Strauss, and D. Baker. Prospects for Ab Initio Protein Structural Genomics. J. Mol. Biol., 306:1191–1199, 2001.
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. Equation of State Calculations by Fast Computing Machines. J. Chem. Phys., 21(6):1087–1092, 1953.
H. J. C. Berendsen, D.van der Spoel, and R.van Drunen. GROMACS: A Message-Passing Parallel Molecular Dynamics Implementation. Comp. Phys. Gomm., 91:43–56, 1995.
D. Hoffmann and E.-W. Knapp. Folding Pathways of a Helix-Turn-Helix Model Protein. J. Phys. Chem. B, 101:6734–6740, 1997.
D. Hoffmann. A build-up algorithm for protein structure prediction, that considers experimental constraints. To be published.
A. T. Brünger, P. D. Adams, and L. M. Rice. New applications of simulated annealing in X-ray crystallography and solution NMR. Structure, 5:325–336, 1997.
V. Schnaible, S. Wefing, and D. Hoffmann. Protein Chemistry and Bioanalytical Techniques for Protein 3D-Structure Validation. To be published.
S. Wefing. SearchXLinks Manual. caesar, Bonn, Germany, 2001.
D. Fenyö. A Software Tool for the Analysis of Mass Spectrometric Disulfide Mapping Experiments. CABIOS, 13:617–618, 1997.
http://welcome.to/gpmaw
M. M. Young, N. Tang, J. C. Hempel, C. M. Oshiro, E. W. Taylor, I. D. Kuntz, B. W. Gibson, and G. Dollinger. High Throughput Protein Fold Identification by Using Experimental Constraints Derived from Intramolecular Cross-Links and Mass-Spectrometry. Proc. Natl. Acad. Sci. USA, 97:5802–5806, 2000.
A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247:536–540, 1995.
U. Hobohm and C. Sander. Enlarged representative set of protein structures. Prot. Sci., 3:522–524, 1994.
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rogers, O. Kennard, T. Shimanouchi, and M. Tasumi. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535–542, 1977.
N. N. Alexandrov. Sarfing the pdb. Protein Engineering, 9:727–732, 1996.
V. Schnaible, S. Wefing, A. Bücker, S. Wolf-Kümmeth, and D. Hoffmann. Partial Reduction and Two Step Modification of Proteins for Identification of Disulfide Bridges. In Proceedings of the 49th ASMS Conference, Chicago, USA, 2001. In press.
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Hoffmann, D., Schnaible, V., Wefing, S., Albrecht, M., Hanisch, D., Zimmer, R. (2002). A New Method for the Fast Solution of Protein-3D-Structures, Combining Experiments and Bioinformatics. In: Hoffmann, KH. (eds) Coupling of Biological and Electronic Systems. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56177-1_6
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DOI: https://doi.org/10.1007/978-3-642-56177-1_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-62851-1
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