ArticlePhysical chemistry chemical physics : PCCP2011
Exploring the free-energy landscapes of biological systems with steered molecular dynamics.
Article in Physical chemistry chemical physics : PCCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
- Uncovering the interactions between PME and PMEI at the gene and protein levels: Implications for the design of specific PMEI.Journal of molecular modeling · 2023Article
- Measuring pico-Newton Forces with Lipid Anchors as Force Sensors in Molecular Dynamics Simulations.The journal of physical chemistry. B · 2023Article
- Aquaglyceroporin AQP7's affinity for its substrate glycerol: Have we reached convergence in the computed values of glycerol-aquaglyceroporin affinity?RSC advances · 2022Article
- Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.ACS chemical neuroscience · 2018Article
- Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles.The journal of physical chemistry. B · 2015Article
- Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods.Scientific reports · 2015Article
- Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.Journal of chemical theory and computation · 2015Article
- Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin.Biophysical chemistry · 2015Article
- Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach.Molecular membrane biology · 2015Article
- Interaction between functionalized gold nanoparticles in physiological saline.Physical chemistry chemical physics : PCCP · 2014Article
- Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF.Biochimica et biophysica acta · 2013Article
- Glycerol inhibits water permeation through Plasmodium falciparum aquaglyceroporin.Journal of structural biology · 2013Article
- Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z.Journal of molecular modeling · 2012Article
- Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel.Biophysical chemistry · 2012Article
- Insights into Ligand-Protein Binding from Local Mechanical Response.Journal of chemical theory and computation · 2011Article
- Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.Biophysical chemistryArticle
- 1,3-Propanediol binds inside the water-conducting pore of aquaporin 4: Does this efficacious inhibitor have sufficient potency?Journal of systems and integrative neuroscienceArticle
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.
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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.