Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

Background: The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results: Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin
• Keywords: BMCBI 2010, Business, Comparative Molecular Dynamics, Dynamic Motions, Protein