ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

Aya Narunsky, Sergey Nepomnyachiy, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Protein function involves conformational changes, but often, for a given protein, only some of these conformations are known. The missing conformations could be predicted using the wealth of data in the PDB. Most PDB proteins have multiple structures, and proteins sharing one similar conformation often share others as well. The ConTemplate web server (http://bental.tau.ac.il/contemplate) exploits these observations to suggest conformations for a query protein with at least one known conformation (or model thereof). We demonstrate ConTemplate on a ribose-binding protein that undergoes significant conformational changes upon substrate binding. Querying ConTemplate with the ligand-free (or bound) structure of the protein produces the ligand-bound (or free) conformation with a root-mean-square deviation of 1.7 Å (or 2.2 Å); the models are derived from conformations of other sugar-binding proteins, sharing approximately 30% sequence identity with the query. The calculation also suggests intermediate conformations and a pathway between the bound and free conformations.

Original languageEnglish
Pages (from-to)2162-2170
Number of pages9
JournalStructure
Volume23
Issue number11
DOIs
StatePublished - 3 Nov 2015

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