calmodulin alignment of flexible protein structures
Post on 22-Dec-2015
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Calmodulin
Alignment of Flexible Protein Structures
Motivation
•Proteins are flexible. One would like to align proteins modulo the flexibility.
• Hinge and shear protein domain motions (Gerstein, Lesk , Chotia).
Calmodulin complexed with myosin light chain
Troponin C
Rigid Alignment
Proteins are flexible. One would like to align proteins modulo the flexibility.
FlexProt algorithm:
– Flexible structural alignment of hinge-bent proteins without prior knowledge of the flexible hinge regions.
– Simultaneously detects hinge regions and aligns rigid subparts.
– It is insensitive to insertions/deletions.
Immunoglobulin fab fragment - murine T-cell antigen receptor. Immunoglobulin fab fragment (1mcp, chain L) matched with murine T-cell antigen receptor (1tcr, chain B). (A). The best rigid superposition between the two molecules (1mcp; blue). (B). The maximal alignment with one hinge region detected by the program, with 1tcr superimposed on 1mcp (1mcp; blue).
Histocompatibility antigen versus neonatal FC receptor. Histocompatibility antigen, (2clr, chain A), and neonatal FC receptor (3fru, chain A), have two structurally similar domains. (A) Rigid structural alignment (2clr colored blue). Only one domain, on the left side, is aligned. (B) Flexible alignment with two hinges (2clr colored blue). One hinge is detected between the domains, while the second hinge is located inside the MHC antigen-recognition domain.
Class II aminoacyl-tRNA synthetase (aaRS)-like. E. coli threonyl-tRNA synthetase (complexed with its cognate tRNA) (1qf6, chain A), versus histidyl-tRNA synthetase (complexed with histidine, 1adj, chain A). (A) Rigid alignment with respect to the catalytic domain class II aminoacyl-tRNA synthetase (aaRS)-like (1qf6 colored blue). The second domain, anticodon-binding domain of Class II aaRS, is not aligned. (B) Flexible alignment (1qf6 colored blue). Both domains are aligned.
