ArticleStructure (London, England : 1993)2015
Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.
Article in Structure (London, England : 1993), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Conformational changes upon pore blocker removal reveal conductive states of TMEM16A.bioRxiv : the preprint server for biology · 2026Article
- Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT.Nature communications · 2023Article
- Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Molecular mechanism of sugar transport in plants unveiled by structures of glucose/HNature plants · 2021Article
- Labeling Preferences of Diazirines with Protein Biomolecules.Journal of the American Chemical Society · 2021Article
- Single-channel properties of skeletal muscle ryanodine receptor pore ΔCell calcium · 2020Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- MemBlob database and server for identifying transmembrane regions using cryo-EM maps.Bioinformatics (Oxford, England) · 2020Article
- A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology.The Journal of general physiology · 2020Article
- Harmonizing Experimental Data with Modeling to Predict Membrane Protein Insertion in Yeast.Biophysical journal · 2019Article
- Unraveling the structural elements of pH sensitivity and substrate binding in the human zinc transporter SLC39A2 (ZIP2).The Journal of biological chemistry · 2019Article
- A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors.Biophysical journal · 2019Article
- Modeling Membrane Curvature Generation due to Membrane⁻Protein Interactions.Biomolecules · 2018Review
- Substrate-bound outward-open structure of a NaNature communications · 2018Article
- Conformational transitions of the sodium-dependent sugar transporter, vSGLT.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to cytosolic and luminal CaThe Journal of biological chemistry · 2018Article
- Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor.The Journal of biological chemistry · 2017Article
- A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters.Scientific reports · 2017Article
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Authors and funding
5 authors.
Funding
Abstract
The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information.
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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.