Principal component method for assessing structural heterogeneity across multiple alignment media.
The recent availability of residual dipolar coupling measurements in a variety of different alignment media raises the question to what extent biomolecular structure and dynamics are differentially affected by their presence. A computational method is presented that allows the sensitive assessment of such changes using dipolar couplings measured in six or more alignment media. The method is based on a principal component analysis of the covariance matrix of the dipolar couplings. It does not require a priori structural or dynamic information nor knowledge of the alignment tensors and their orientations. In the absence of experimental errors, the covariance matrix has at most five nonzero eigenvalues if the structure and dynamics of the biomolecule is the same in all media. In contrast, differential structural and dynamic changes lead to additional nonzero eigenvalues. Characteristic features of the eigenvalue distribution in the absence and presence of noise are discussed using dipolar coupling data calculated from conformational ensembles taken from a molecular dynamics trajectory of native ubiquitin.
Hus
Jean-Christophe
JC
Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA.
Brüschweiler
Rafael
R
D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D006860:Hydrogen Bonding; D008432:Mathematical Computing; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry*
D011506:Proteins; D025801:Ubiquitin