Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings

J Am Chem Soc. 2015 May 20;137(19):6270-8. doi: 10.1021/jacs.5b01289. Epub 2015 May 7.

Abstract

Residual dipolar couplings (RDCs) are important probes in structural biology, but their analysis is often complicated by the determination of an alignment tensor or its associated assumptions. We here apply the maximum entropy principle to derive a tensor-free formalism which allows for direct, dynamic analysis of RDCs and holds the classic tensor formalism as a special case. Specifically, the framework enables us to robustly analyze data regardless of whether a clear separation of internal and overall dynamics is possible. Such a separation is often difficult in the core subjects of current structural biology, which include multidomain and intrinsically disordered proteins as well as nucleic acids. We demonstrate the method is tractable and self-consistent and generalizes to data sets comprised of observations from multiple different alignment conditions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chickens
  • Entropy
  • Escherichia coli / chemistry*
  • Escherichia coli Proteins / chemistry*
  • Membrane Proteins / chemistry*
  • Molecular Dynamics Simulation*
  • Muramidase / chemistry*
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptidylprolyl Isomerase / chemistry*
  • Protein Conformation

Substances

  • Escherichia coli Proteins
  • Membrane Proteins
  • Muramidase
  • Peptidylprolyl Isomerase
  • FkpA protein, E coli