ChSeq: A database of chameleon sequences

Protein Sci. 2015 Jul;24(7):1075-86. doi: 10.1002/pro.2689. Epub 2015 Jun 16.

Abstract

Chameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have detected and studied ChSeqs to understand the interplay between local and global interactions in protein structure formation. The different secondary structures adopted by one ChSeq challenge sequence-based secondary structure predictors. With increasing numbers of available Protein Data Bank structures, we here identify a large set of ChSeqs ranging from 6 to 10 residues in length. The homologous ChSeqs discovered highlight the structural plasticity involved in biological function. When compared with previous studies, the set of unrelated ChSeqs found represents an about 20-fold increase in the number of detected sequences, as well as an increase in the longest ChSeq length from 8 to 10 residues. We applied secondary structure predictors on our ChSeqs and found that methods based on a sequence profile outperformed methods based on a single sequence. For the unrelated ChSeqs, the evolutionary information provided by the sequence profile typically allows successful prediction of the prevailing secondary structure adopted in each protein family. Our dataset will facilitate future studies of ChSeqs, as well as interpretations of the interplay between local and nonlocal interactions. A user-friendly web interface for this ChSeq database is available at prodata.swmed.edu/chseq.

Keywords: ChSeq; biological function; chameleon sequence; conformational change; secondary structure; secondary structure prediction; sequence profile; structural plasticity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Databases, Protein
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Folding
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Sequence Homology, Amino Acid
  • Software

Substances

  • Proteins

Associated data

  • PDB/1VL6
  • PDB/1jti
  • PDB/1ova
  • PDB/1p3h
  • PDB/1p3r
  • PDB/1p82
  • PDB/1sol
  • PDB/1svf
  • PDB/1v16
  • PDB/1z9i
  • PDB/2Q0Y
  • PDB/2gya
  • PDB/2jws
  • PDB/2kdm
  • PDB/2kn8
  • PDB/2lcl
  • PDB/2lsw
  • PDB/2mdk
  • PDB/2oug
  • PDB/2q3z
  • PDB/2r1b
  • PDB/2rfe
  • PDB/3S30
  • PDB/3ffn
  • PDB/3id6
  • PDB/3ikk
  • PDB/3l9q
  • PDB/3lru
  • PDB/3ly6
  • PDB/3mw3
  • PDB/3n4p
  • PDB/3q36
  • PDB/3r8s
  • PDB/3rki
  • PDB/4JB9
  • PDB/4gip
  • PDB/4h6z
  • PDB/4hkf
  • PDB/4jb9
  • PDB/4jhw
  • PDB/4jke
  • PDB/4lg1