Prediction of three dimensional structure of calmodulin

Protein J. 2006 Jan;25(1):57-70. doi: 10.1007/s10930-006-0011-7.

Abstract

Calmodulin (CaM) is an important human protein, which has multiple structures. Numerous researchers studied the CaM structures in the past, and about 50 different structures in complex with fragments derived from CaM-regulated proteins have been discovered. Discovery and analysis of existing and new CaM structures is difficult due to the inherent complexity, i.e. flexibility of 6 loops and a central linker that constitute part of the CaM structure. The extensive interest in CaM structure analysis and discovery calls for a comprehensive study, which based on the accumulated expertise would design a method for prediction and analysis of future and existing CaM structures. It is also important to find the mechanisms by which the protein adjusts its structure with respect to various factors. To this end, this paper analyzes the known CaM structures and finds four factors that influence CaM structure, which include existence of Ca2+ binding, different binding segments, measuring surroundings, and sequence mutation. The degree of influence of specific factors on different structural regions is also investigated. Based on the analysis of the relation between the four factors and the corresponding CaM structure a novel method for prediction of the CaM structure in complex with novel segments, given that the surroundings of the complex, is developed. The developed prediction method is tested on a set aside, newest CaM structure. The prediction results provide useful and accurate information about the structure verifying high quality of the proposed prediction method and performed structural analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Calcium / metabolism
  • Calmodulin / chemistry*
  • Calmodulin / metabolism
  • Databases, Protein
  • Humans
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Structure, Secondary
  • Sequence Alignment

Substances

  • Calmodulin
  • Calcium