A new approach to the design of a sequence with the highest affinity for a molecular surface

We describe an algorithm to design the primary structures for peptides which must have the strongest binding to a given molecular surface. This problem cannot be solved by a direct combinatorial sorting, because of an enormous number of possible primary and spatial structures. The approach to solve...

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Bibliographic Details
Published in:Protein engineering 1992-10, Vol.5 (7), p.625-628
Main Authors: Reva, B.A., Finkelstein, A.V.
Format: Article
Language:English
Subjects:
Algorithms
Binding Sites
Biological and medical sciences
Biotechnology
Computer-Aided Design
drug design
dynamic programming
Fundamental and applied biological sciences. Psychology
Methods. Procedures. Technologies
Models, Chemical
Peptides - chemistry
Peptides - metabolism
Protein engineering
specificity of binding
surface binding
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Summary:We describe an algorithm to design the primary structures for peptides which must have the strongest binding to a given molecular surface. This problem cannot be solved by a direct combinatorial sorting, because of an enormous number of possible primary and spatial structures. The approach to solve this problem is to describe a state of each residue by two variables: (i) amino acid type and (ii) 3-D coordinate, and to minimize binding energy over all these variables simultaneously. For short chains which have no long-range interactions within themselves, this minimization can be done easily and efficiently by dynamic programming. We also discuss the problem of how to estimate specificity of binding and how to deduce a sequence with maximal specificity for a given surface. We show that this sequence can be deduced by the same algorithm after some modification of energetic parameters.
ISSN:1741-0126
0269-2139
1741-0134
1460-213X
DOI:10.1093/protein/5.7.625