Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

• Published in: Physics of life reviews Vol. 10; no. 1; pp. 1 - 26
• Main Author: Micheletti, Cristian
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.03.2013
• Subjects: Animals; Databases, Protein; Humans; Molecular Dynamics Simulation; PDZ Domains; Peptide Hydrolases - chemistry; Peptide Hydrolases - metabolism; Proteins - chemistry; Proteins - metabolism; Structural Homology, Protein; Structure-Activity Relationship
• ISSN: 1571-0645; 1873-1457; 1873-1457
• DOI: 10.1016/j.plrev.2012.10.009

The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure–function relationship.