ArticleProceedings of the National Academy of Sciences of the United States of America2020
Dynamical control by water at a molecular level in protein dimer association and dissociation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 59 citations in OpenAlex.
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- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Ligand Gaussian accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.bioRxiv : the preprint server for biology · 2024Article
- Cooperative Membrane Binding of HIV-1 Matrix Proteins.The journal of physical chemistry. B · 2024Article
- Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation.Biophysical journal · 2024Article
- Computational Approach to Elucidating Insulin-Protamine Binding Interactions and Dynamics in Insulin NPH Formulations.ACS omega · 2024Article
- Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding.Biophysical journal · 2024Article
- Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding.Global challenges (Hoboken, NJ) · 2023Article
- Predicting Biomolecular Binding Kinetics: A Review.Journal of chemical theory and computation · 2023Review
- Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.Journal of chemical theory and computation · 2023Article
- Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.Scientific reports · 2022Article
- Counteractive Effects of Choline Geranate (CAGE) ILs and Ethanol on Insulin's Stability-A Leap Forward towards Oral Insulin Formulation.Molecules (Basel, Switzerland) · 2022Article
- Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.Journal of chemical theory and computation · 2022Article
- Progress in Simulation Studies of Insulin Structure and Function.Frontiers in endocrinology · 2022Review
- Challenges and frontiers of computational modelling of biomolecular recognition.QRB discovery · 2022Article
- Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.The journal of physical chemistry. B · 2021Article
- In Silico Identification and Validation of Organic Triazole Based Ligands as Potential Inhibitory Drug Compounds of SARS-CoV-2 Main Protease.Molecules (Basel, Switzerland) · 2021Article
- Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity.The journal of physical chemistry. B · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Water, often termed as the "lubricant of life," is expected to play an active role in navigating protein dissociation-association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1-2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance R
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