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Calculating three‐dimensional changes in protein structure due to amino‐acid substitutions: The variable region of immunoglobulins
Author(s) -
Snow Mark E.,
Amzel L. Mario
Publication year - 1986
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340010310
Subject(s) - amino acid , protein structure , amino acid residue , chemistry , fragment (logic) , perturbation (astronomy) , sequence (biology) , antibody , variable (mathematics) , peptide sequence , computational biology , crystallography , algorithm , mathematics , physics , biology , biochemistry , genetics , mathematical analysis , gene , quantum mechanics
A procedure (coupled perturbation procedure, CPP) is introduced as a specific method for calculating the detailed three‐dimensional structure of a protein molecule which has a nummber of amino‐acid substitutions relative to some previously determined “parent” protein structure. The accuracy of the procedure is tested by calculating the conformation of a region of the human immunoglobulin fragment Fab Kol based on the analogous region of the human immunoglobulin fragment Fab New. Both structures have previously been determined crystallographically. The calculated model is accurate to the extent that both of the sequence differences in the region are modeled correctly and that conformational changes in a number of nearby residues are correctly identified. CPP is shown to give better results than other commonly used modeling procedures when applied to the same problem.