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A new method for modeling large-scale rearrangements of protein domains

✍ Scribed by Vladimir Maiorov; Ruben Abagyan

Publisher: John Wiley and Sons
Year: 1997
Tongue: English
Weight: 353 KB
Volume: 27
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(199703)27:3<410::aid-prot9>3.0.co;2-g

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✦ Synopsis

A method for modeling largescale rearrangements of protein domains connected by a single-or a double-stranded linker is proposed. Multidomain proteins may undergo substantial domain displacements, while their intradomain structure remains essentially unchanged. The method allows automatic identification of an interdomain linker and builds an all-atom model of a protein structure in internal coordinates. Torsion angles belonging to the interdomain linkers and side chains potentially able to form domain interfaces are set free while all remaining torsions, bond lengths, and bond angles are fixed. Large-scale sampling of the reduced torsion conformational subspace is effected with the ''biased probability Monte Carlo-minimization'' method [

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