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.
Highlights
A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms
The primary goals of this paper are as follows: (i) demonstrate that energy landscapes associated with complex biological function can be extracted from experimental data, and corroborated by molecular simulations, (ii) elucidate the conformational paths associated with complex biological function in all-atoms detail, including possible routes for transitions between different landscapes, (iii) establish that motions associated with functional paths on energy landscapes can be significantly different from those inferred by discrete clustering methods, (iv) outline the new biological insights gained by studying the continuous conformational changes associated with function, and (v) render the algorithms used in this paper widely accessible
The 791,956 cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1) molecules analyzed in this study comprised about the same number of molecules in equilibrium with a thermal bath with and without ligands (Ca2+, ATP, and caffeine) prior to cryofreezing[22]
Summary
A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Macromolecules undergo continuous conformational changes, a subset of which are functionally important. A macromolecule with N atoms has (3N-6) degrees of conformational freedom. Barring exceptions such as intrinsically disordered proteins, biological function involves coordinated changes in structural blocks, e.g., an alpha helix, or an entire molecular domain. The number and nature of the degrees of freedom exercised during unperturbed function, and the conformational coordinates relevant to function must be extracted from the data. The energy of each observed conformational state can be determined from the number of times it has been sighted, through the so-called inverse-Boltzmann relation between the statistical weight and the energy of the state[1,2,3] (see “Methods”). The majority of experimentally determined energy landscapes have involved one conformational coordinate[14,15], have been compromised by low spatial resolution[16,17], and/or limited by the inability to account for the multiple energy landscapes associated with the vast variety of biological functions involving ligands and cofactors[17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
