Sequence-Similar Protein Domain Pairs With Structural or Topological Dissimilarity.

ABSTRACT: For a variety of applications, protein structures are clustered by sequence similarity, and sequence-redundant structures are disregarded. Sequence-similar chains are likely to have similar structures, but significant structural variation, as measured with RMSD, has been documented for sequence-similar chains and found usually to have a functional explanation. Moving two neighboring stretches of backbone through each other may change the chain topology and alter possible folding paths. The size of this motion is compatible to a variation in a flexible loop. We search and find domains with alternate chain topology in CATH4.2 sequence families relatively independent of sequence identity and of structural similarity as measured by RMSD. Structural, topological, and functional representative s

SUBMITTER: Rogen P 

PROVIDER: S-EPMC11809131 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature