Abstract
Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approach for modeling crowding effects, which enables an atomistic representation of “test” proteins. Here this approach is applied to study how crowding affects the equilibria and transition rates between open and closed conformations of seven proteins: yeast protein disulfide isomerase (yPDI), adenylate kinase (AdK), orotidine phosphate decarboxylase (ODCase), Trp repressor (TrpR), hemoglobin, DNA β-glucosyltransferase, and Ap4A hydrolase. For each protein, molecular dynamics simulations of the open and closed states are separately run. Representative open and closed conformations are then used to calculate the crowding-induced changes in chemical potential for the two states. The difference in chemical-potential change between the two states finally predicts the effects of crowding on the population ratio of the two states. Crowding is found to reduce the open population to various extents. In the presence of crowders with a 15 Å radius and occupying 35% of volume, the open-to-closed population ratios of yPDI, AdK, ODCase and TrpR are reduced by 79%, 78%, 62% and 55%, respectively. The reductions for the remaining three proteins are 20–44%. As expected, the four proteins experiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration). Larger proteins also tend to experience stronger crowding effects than smaller ones [e.g., comparing yPDI (480 residues) and TrpR (98 residues)]. The potentials of mean force along the open-closed reaction coordinate of apo and ligand-bound ODCase are altered by crowding, suggesting that transition rates are also affected. These quantitative results and qualitative trends will serve as valuable guides for expected crowding effects on protein conformation changes inside cells.
Highlights
It is increasingly recognized that protein dynamics serves the critical link between structure and function [1,2,3,4,5,6]
An important manifestation of protein dynamics is the sampling of alternative conformations
We find crowding to reduce the open-to-closed population ratios to various extents; the potentials of mean force (PMFs) along the open-closed reaction coordinate of apo and ligand-bound orotidine phosphate decarboxylase (ODCase), and the transition rates, are affected
Summary
It is increasingly recognized that protein dynamics serves the critical link between structure and function [1,2,3,4,5,6]. Structures of the same proteins at different functional states are becoming available These structures provide atomistic details of conformational changes. One expects that macromolecular crowding will significantly modify the energy landscapes of conformational changes, favoring more compact structures over more open ones [18]. Such effects of crowding have been scrutinized experimentally (see [18] for a recent review). Molecular dynamics simulations have been carried out to investigate the energy landscapes of a number of proteins under crowding, in the context of either conformational change [19] or folding-unfolding transition [20,21,22]. Conformations from this simulation are used to calculate the change in
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
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
