Dataset Information

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. I. Effect of Solvent Viscosity and Macromolecular Crowding.

ABSTRACT: Protein/solvent interactions largely influence protein dynamics, particularly motions in unfolded and intrinsically disordered proteins (IDPs). Here, we apply triplet-triplet energy transfer (TTET) to investigate the coupling of internal protein motions to solvent motions by determining the effect of solvent viscosity (η) and macromolecular crowding on the rate constants of loop formation (k_c) in several unfolded polypeptide chains including IDPs. The results show that the viscosity dependence of loop formation depends on amino acid sequence, loop length, and co-solute size. Below a critical size (r_c), co-solutes exert a maximum effect, indicating that under these conditions microviscosity experienced by chain motions matches macroviscosity of the solvent. r_c depends on chain stiffness and reflects the length scale of the chain motions, i.e., it is related to the persistence length. Above r_c, the effect of solvent viscosity decreases with increasing co-solute size. For co-solutes typically used to mimic cellular environments, a scaling of k_c ∝ η^-0.1 is observed, suggesting that dynamics in unfolded proteins are only marginally modulated in cells. The effect of solvent viscosity on k_c in the small co-solute limit (below r_c) increases with increasing chain length and chain flexibility. Formation of long and very flexible loops exhibits a k_c ∝ η^-1 viscosity dependence, indicating full solvent coupling. Shorter and less flexible loops show weaker solvent coupling with values as low as k_c ∝ η^{-0.75 ± 0.02}. Coupling of formation of short loops to solvent motions is very little affected by amino acid sequence, but solvent coupling of long-range loop formation is decreased by side chain sterics.

SUBMITTER: Stecher K

PROVIDER: S-EPMC10544011 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Publications

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. I. Effect of Solvent Viscosity and Macromolecular Crowding.

Stecher Karin K Krieger Florian F Schleeger Michael M Kiefhaber Thomas T

The journal of physical chemistry. B 20230918 38

Protein/solvent interactions largely influence protein dynamics, particularly motions in unfolded and intrinsically disordered proteins (IDPs). Here, we apply triplet-triplet energy transfer (TTET) to investigate the coupling of internal protein motions to solvent motions by determining the effect of solvent viscosity (η) and macromolecular crowding on the rate constants of loop formation (<i>k<sub>c</sub></i>) in several unfolded polypeptide chains including IDPs. The results show that the visc ...[more]

PMID: 37722681

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Project description: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 beta-glucosyltransferase, and Ap(4)A 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 A 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.

Project description:Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.

Dataset Information

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. I. Effect of Solvent Viscosity and Macromolecular Crowding.

Publications

Local and Large-Scale Conformational Dynamics in Unfolded Proteins and IDPs. I. Effect of Solvent Viscosity and Macromolecular Crowding.

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