S curve, a graphic representation of protein secondary structure sequence and its applications

Biopolymers. 2000 Jun;53(7):539-49. doi: 10.1002/(SICI)1097-0282(200006)53:7<539::AID-BIP2>3.0.CO;2-2.

Abstract

A secondary structure sequence is a symbolic string composed of three kinds of letters, indicating the helix, strand, and coil (including turns), respectively. A graphic representation for this abstract symbolic sequence is proposed here, called the S curve. The S curve is the unique representation for a given secondary structure sequence in the sense that the sequence and the S curve can be uniquely determined from the other. Therefore, the S curve contains all the information that the secondary structure sequence contains. Different geometrical properties of the S curve are studied in details, which reflect the basic characteristics of the secondary structure sequences. The S curves are used to display, analyze, and compare the secondary structure sequences. Detailed application examples are presented. One advantage of the S curve methodology is that the main patterns of a given secondary structure sequence can be grasped quickly in a perceivable form. This is particularly useful in the cases in which longer sequences are involved and structures of proteins are unknown.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Models, Molecular*
  • Models, Theoretical*
  • Molecular Sequence Data
  • Peptides / chemistry
  • Protein Structure, Secondary*
  • Proteins / chemistry*

Substances

  • Peptides
  • Proteins