ArticleJournal of chemical theory and computation2017
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
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- GraphDeep-hERG: Graph Neural Network PharmacoAnalytics for Assessing hERG-Related Cardiotoxicity.Pharmaceutical research · 2025Article
- Mycobactin analogue interacting with siderophore efflux-pump protein: insights from molecular dynamics simulations and whole-cell assays.Frontiers in antibiotics · 2024Article
- Computational insights into ligand-induced G protein and β-arrestin signaling of the dopamine D1 receptor.Journal of computer-aided molecular design · 2023Article
- Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations.Journal of computer-aided molecular design · 2023Article
- Million-atom molecular dynamics simulations reveal the interfacial interactions and assembly of plant PSII-LHCII supercomplex.RSC advances · 2023Article
- Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations.Journal of chemical theory and computation · 2021Article
- Article
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies.Journal of chemical information and modeling · 2019Article
- Novel compounds that specifically bind and modulate MscL: insights into channel gating mechanisms.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.Journal of chemical information and modeling · 2019Article
- A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.International journal of molecular sciences · 2018Article
- Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.Journal of chemical information and modeling · 2017Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here, we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows: (1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. (2) The highly different accessibilities in the membrane and water regions are addressed with a two-step, two-probe grid-labeling procedure. (3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe good agreement with the experimental results.
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