Retrieving functional pathways of biomolecules from single-particle snapshots

Nat Commun. 2020 Sep 18;11(1):4734. doi: 10.1038/s41467-020-18403-x.

Abstract

A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Calcium Channel Agonists / chemistry*
  • Cryoelectron Microscopy
  • Ligands
  • Macromolecular Substances / chemistry*
  • Molecular Conformation
  • Molecular Dynamics Simulation
  • Ryanodine Receptor Calcium Release Channel / chemistry*
  • Ryanodine Receptor Calcium Release Channel / metabolism

Substances

  • Calcium Channel Agonists
  • Ligands
  • Macromolecular Substances
  • Ryanodine Receptor Calcium Release Channel