ArticleThe journal of physical chemistry. B2012
Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 60 citations in OpenAlex.
- COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.Journal of chemical theory and computation · 2025Article
- COCOMO2: A coarse-grained model for interacting folded and disordered proteins.bioRxiv : the preprint server for biology · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
- Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining.Journal of chemical theory and computation · 2023Article
- On the Effects of Disordered Tails, Supertertiary Structure and Quinary Interactions on the Folding and Function of Protein Domains.Biomolecules · 2022Review
- Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex.Biophysical journal · 2021Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.Journal of molecular biology · 2018Article
- Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.The journal of physical chemistry. B · 2017Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Predicting Molecular Crowding Effects in Ion-RNA Interactions.The journal of physical chemistry. B · 2016Article
- Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.The journal of physical chemistry. B · 2016Article
- The Differential Response of Proteins to Macromolecular Crowding.PLoS computational biology · 2016Article
- Stability of Protein-Specific Hydration Shell on Crowding.Journal of the American Chemical Society · 2016Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Macromolecular crowding is recognized as an important factor influencing folding and conformational dynamics of proteins and nucleic acids. Previous views of crowding have focused on the mostly entropic volume exclusion effect of crowding, but recent studies are indicating the importance of enthalpic effects, in particular, changes in electrostatic interactions due to crowding. Here, temperature replica exchange molecular dynamics simulations of trp-cage and melittin in the presence of explicit protein crowders are presented to further examine the effect of protein crowders on peptide dynamics. The simulations involve a three-component multiscale modeling scheme where the peptides are represented at an atomistic level, the crowder proteins at a coarse-grained level, and the surrounding aqueous solvent as implicit solvent. This scheme optimally balances a physically realistic description for the peptide with computational efficiency. The multiscale simulations were compared with simulations of the same peptides in different dielectric environments with dielectric constants ranging from 5 to 80. It is found that the sampling in the presence of the crowders resembles sampling with reduced dielectric constants between 10 and 40. Furthermore, diverse conformational ensembles are generated in the presence of crowders including partially unfolded states for trp-cage. These findings emphasize the importance of enthalpic interactions over volume exclusion effects in describing the effects of cellular crowding.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.