Interpreting correlated motions using normal mode analysis.
With the increased popularity of normal mode analyses in structural biology, it is important to carefully consider how to best utilize the results for gaining biological insights without over interpretation. The discussion in this article argues that for the purpose of identifying correlated motions in biomolecules, a case separate from concomitant conformational changes of structural motifs, it is generally important to use a large number of normal modes. This is illustrated through three increasingly complex examples. The simplest case includes two bilinearly coupled harmonic oscillators and serves as a straightforward problem where the important considerations are explicit and transparent. The argument is then generalized to include a system of N-coupled harmonic oscillators and finally to a realistic biomolecule. Although a small number of normal modes are useful for probing structural flexibility, it is clear that a much larger number of modes are required for properly investigating correlated motions in biomolecules.
Van Wynsberghe
Adam W
AW
Graduate Program in Biophysics, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA.
Cui
Qiang
Q
D000465:Algorithms; D020816:Amino Acid Motifs; D003461:Crystallography; D030562:Databases, Protein; D007477:Ions; D008024:Ligands; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D015394:Molecular Structure; D009991:Oscillometry; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D007477:Ions; D008024:Ligands; D011506:Proteins