Protein Tertiary Structure Modeling
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Insights into the 3D?structure of a protein have proven useful during experiment design. Experimentally elucidated structures are often not available, but comparative protein modeling provides a viable alternative in many cases. This unit presents comparative protein modeling and how to use the highly sophisticated but easy?to?use free software available on the Internet.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Glossary
- Accessing SwissModel Programs and Documentation
- ExPDB Database
- Formatting a First Approach Modeling Request
- Viewing SwissModel Results
- Examples of SwissModel Requests
- Commentary
- Literature Cited
- Figures
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Figure 2.8.1 Submitting a First Approach modeling request to the SwissModel server. View Image -
Figure 2.8.2 Message sent when the server starts to build the model. The unique process identification (AAAa002Of) is added in the subject of all subsequent e‐mails. This is useful when several modeling requests are treated concurrently. View Image -
Figure 2.8.3 First part of the modeling log file, containing a summary of the template identification process (see text). View Image -
Figure 2.8.4 Second part of the modeling log file, containing a summary of action taken during the modeling procedure (see text). View Image -
Figure 2.8.5 Submitting a First Approach modeling request to the SwissModel server with specific EXPDB templates. View Image -
Figure 2.8.6 Log file for the optimise mode when modeling templates are specified. View Image -
Figure 2.8.7 Amino acid sequence of the SwissProt entry Q21735 in FASTA format. View Image -
Figure 2.8.8 Results of a template search for the SwissProt entry Q21735. View Image -
Figure 2.8.9 Alignment between Q21735 and the best template identified. View Image -
Figure 2.8.10 (A ) Automatic alignment between Q21735 and its modeling template (1OUNA) as shown within SPDBV. (B ) Complete alignment, shown for clarity. View Image -
Figure 2.8.11 Log file for the optimise mode with default alignment. View Image -
Figure 2.8.12 (A ) Manually refined alignment between Q21735 and its modeling template (1OUNA) as shown within SPDBV. (B ) Complete alignment, shown for clarity. View Image -
Figure 2.8.13 Partial Log file for the optimise mode with manually optimised alignment. View Image -
Figure 2.8.14 Loop from Ile110 to Ans133 rebuilt with the default alignment. (A ) Backbone representation where Cα are emphasized with bigger atoms. Hydrogen bonds are drawn as dotted lines. (B ) Ribbon representation of the same loop. (C and D ) Same region rebuilt after manual optimisation of the alignment. The H‐bonding pattern is more regular, which makes a longer β‐sheet. View Image -
Figure 2.8.15 Typical example of a Log file for a model that failed because a long loop had to be rebuilt (between THR83 and THR94). As no suitable solution was found after several attempts to gain more flexibility using ever increasing number of residues, the modeling procedure stopped. In most cases, the only way of addressing this problem is to move the gap location in SPDBV, and resubmit an “optimise mode” modeling request. View Image -
Figure 2.8.16 Twice the amino acid sequence of the SwissProt entry Q21735 separated by a semicolon. This allows for dimer modeling. View Image
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Literature Cited
| Literature Cited | |
| Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410. | |
| Bairoch, A. and Apweiler, R. 1999. The SwissProt protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res. 27:49‐54. | |
| Chothia, C. and Lesk, A.M. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823‐826 | |
| Guex, N. and Peitsch, M.C. 1997. SwissModel and SwissPdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714‐2723. | |
| Guex, N., Diemand, A., and Peitsch, M.C. 1999. Protein modeling for all. Trends Biochem. Sci. 24:364‐367. | |
| Harrison, R.W., Chatterjee, D., and Weber, I.T. 1995. Analysis of six protein structures predicted by comparative modeling techniques. Proteins Struct. Func. Genet. 23:463‐471. | |
| Hooft, R.W.W., Vriend, G., Sander, C., and Abola, E.E. 1996. Errors in protein structures. Nature 381:272‐272. | |
| Peitsch, M.C. 1997. Large scale protein modeling and model repository. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (T. Gaasterland, P. Karp, K. Karplus, C. Ouzonis, C. Sander, and A. Valencia, eds.) pp.234‐236. AAAI Press, Menlo Park, Calif. | |
| Sánchez, R. and Sali, A. 1998. Large‐scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U.S.A. 95:13597‐13602. | |
| Tilton, R.F., Dewan, J.C., and Petsko, G.A. 1992. Effects of temperature on protein structure and dynamics: X‐ray crystallographic studies of the protein ribonuclease‐A at nine different temperatures from 98 to 320 K. Biochemistry 31:2469‐2481. | |
| van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., and Tinoni, I.G. 1996. In Biomolecular Simulation: The GROMOS96 Manual and User Guide. Vdf Hochschulverlag ETH, Zurich (http://igc.ethz.ch/gromos/). |
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