Structural analysis, identification, and design of calcium-binding sites in proteins.

Published

Journal Article

Assigning proteins with functions based on the 3-D structure requires high-speed techniques to make a systematic survey of protein structures. Calcium regulates many biological systems by binding numerous proteins in different biological environments. Despite the great diversity in the composition of ligand residues and bond angles and lengths of calcium-binding sites, our structural analysis of 11 calcium-binding sites in different classes of proteins has shown that common local structural parameters can be used to identify and design calcium-binding proteins. Natural calcium-binding sites in both EF-hand proteins and non-EF-hand proteins can be described with the smallest deviation from the geometry of an ideal pentagonal bipyramid. Further, two different magnesium-binding sites in parvalbumin and calbindin(D9K) can also be identified using an octahedral geometry. Using the established method, we have designed de novo calcium-binding sites into the scaffold of non-calcium-binding proteins CD2 and Rop. Our results suggest that it is possible to identify calcium- and magnesium-binding sites in proteins and design de novo metal-binding sites.

Full Text

Duke Authors

Cited Authors

  • Yang, W; Lee, H-W; Hellinga, H; Yang, JJ

Published Date

  • May 2002

Published In

Volume / Issue

  • 47 / 3

Start / End Page

  • 344 - 356

PubMed ID

  • 11948788

Pubmed Central ID

  • 11948788

Electronic International Standard Serial Number (EISSN)

  • 1097-0134

International Standard Serial Number (ISSN)

  • 0887-3585

Digital Object Identifier (DOI)

  • 10.1002/prot.10093

Language

  • eng