Generating Conformational Transitions Using the Euclidean Distance Matrix

Author

Xiao-Bo Li ; Burkowski, Forbes

Author_Institution

Cheriton Sch. of Comput. Sci., Univ. of Waterloo, Waterloo, ON, Canada

Volume

14

Issue

2

fYear

2015

fDate

Mar-15

Firstpage

203

Lastpage

209

Abstract

Elastic network interpolation (ENI) is an efficient method for generating intermediate conformations between two end protein conformations. Its current formulation uses interatomic distance. We show how this can be generalized to interatomic distances-squared. This generalization is part of an effort to study protein dynamics on the set of positive semidefinite (PSD) matrices, which has a rich mathematical structure. We use lattice structures to test this interpolation scheme, and discuss some limitations observed. We conclude with some suggestions for future research.

Keywords

bond lengths; interpolation; molecular biophysics; molecular configurations; proteins; ENI; Euclidean distance matrix; PSD; conformational transitions; elastic network interpolation; interatomic distance-squared; intermediate conformations; lattice structures; mathematical structure; positive semidefinite matrices; protein conformations; protein dynamics; Equations; Interpolation; Manifolds; Mathematical model; Nanobioscience; Proteins; Yttrium; Conformational transitions; Euclidean distance matrices; Riemannian manifold; positive semidefinite matrices;

fLanguage

English

Journal_Title

NanoBioscience, IEEE Transactions on

Publisher

ieee

ISSN

1536-1241

Type

jour

DOI

10.1109/TNB.2014.2387156

Filename

7012070