Search Results - "de Groot, Bert L."

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan by Gapsys, Vytautas, Michielssens, Servaas, Seeliger, Daniel, de Groot, Bert L.

“…The prediction of mutation‐induced free‐energy changes in protein thermostability or protein–protein binding is of particular interest in the fields of protein…”
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Lipid-protein interactions modulate the conformational equilibrium of a potassium channel by Gu, Ruo-Xu, de Groot, Bert L.

“…Cell membranes actively participate in the regulation of protein structure and function. In this work, we conduct molecular dynamics simulations to investigate…”
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Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail by Kutzner, Carsten, Grubmüller, Helmut, de Groot, Bert L., Zachariae, Ulrich

“…Presently, most simulations of ion channel function rely upon nonatomistic Brownian dynamics calculations, indirect interpretation of energy maps, or…”
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Central cavity dehydration as a gating mechanism of potassium channels by Gu, Ruo-Xu, de Groot, Bert L.

“…The hydrophobic gating model, in which ion permeation is inhibited by the hydrophobicity, rather than a physical occlusion of the nanopore, functions in…”
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Mechanism of selectivity in aquaporins and aquaglyceroporins by Hub, Jochen S, de Groot, Bert L

“…Aquaporins and aquaglyceroporins form a family of pore proteins that facilitate the efficient and selective flux of small solutes across biological membranes…”
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A molecular mechanism for transthyretin amyloidogenesis by Yee, Ai Woon, Aldeghi, Matteo, Blakeley, Matthew P., Ostermann, Andreas, Mas, Philippe J., Moulin, Martine, de Sanctis, Daniele, Bowler, Matthew W., Mueller-Dieckmann, Christoph, Mitchell, Edward P., Haertlein, Michael, de Groot, Bert L., Boeri Erba, Elisabetta, Forsyth, V. Trevor

“…Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but…”
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Mechanisms of Anion Conduction by Coupled Glutamate Transporters by Machtens, Jan-Philipp, Kortzak, Daniel, Lansche, Christine, Leinenweber, Ariane, Kilian, Petra, Begemann, Birgit, Zachariae, Ulrich, Ewers, David, de Groot, Bert L., Briones, Rodolfo, Fahlke, Christoph

“…Excitatory amino acid transporters (EAATs) are essential for terminating glutamatergic synaptic transmission. They are not only coupled glutamate/Na+/H+/K+…”
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Crystal Structure of an Ammonia-Permeable Aquaporin by Kirscht, Andreas, Kaptan, Shreyas S, Bienert, Gerd Patrick, Chaumont, François, Nissen, Poul, de Groot, Bert L, Kjellbom, Per, Gourdon, Pontus, Johanson, Urban

“…Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane…”
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Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' by Gapsys, Vytautas, de Groot, Bert L

“…A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent…”
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Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches by Gapsys, Vytautas, Yildirim, Ahmet, Aldeghi, Matteo, Khalak, Yuriy, van der Spoel, David, de Groot, Bert L.

“…The accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a considerable challenge in computer-aided drug discovery. Recently,…”
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Conformational transitions upon ligand binding: holo-structure prediction from apo conformations by Seeliger, Daniel, de Groot, Bert L

“…Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of…”
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Crystal structure and functional mechanism of a human antimicrobial membrane channel by Song, Chen, Weichbrodt, Conrad, Salnikov, Evgeniy S., Dynowski, Marek, Forsberg, Björn O., Bechinger, Burkhard, Steinem, Claudia, de Groot, Bert L., Zachariae, Ulrich, Zeth, Kornelius

“…Multicellular organisms fight bacterial and fungal infections by producing peptide-derived broad-spectrum antibiotics. These host-defense peptides compromise…”
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Population Shuffling of Protein Conformations by Smith, Colin A., Ban, David, Pratihar, Supriya, Giller, Karin, Schwiegk, Claudia, de Groot, Bert L., Becker, Stefan, Griesinger, Christian, Lee, Donghan

“…Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of…”
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Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1 by Krivobokova, Tatyana, Briones, Rodolfo, Hub, Jochen S., Munk, Axel, de Groot, Bert L.

“…We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics that maximally correlate…”
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Detection of functional modes in protein dynamics by Hub, Jochen S, de Groot, Bert L

“…Proteins frequently accomplish their biological function by collective atomic motions. Yet the identification of collective motions related to a specific…”
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins by Huang, Jing, Rauscher, Sarah, Nawrocki, Grzegorz, Ran, Ting, Feig, Michael, de Groot, Bert L, Grubmüller, Helmut, MacKerell, Alexander D

“…An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins. The all-atom additive…”
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Binding affinities controlled by shifting conformational equilibria: opportunities and limitations by Michielssens, Servaas, de Groot, Bert L, Grubmüller, Helmut

“…Conformational selection is an established mechanism in molecular recognition. Despite its power to explain binding events, it is hardly used in protein/ligand…”
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Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling by Kopec, Wojciech, Rothberg, Brad S., de Groot, Bert L.

“…Potassium channels are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control channel opening,…”
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More bang for your buck: Improved use of GPU nodes for GROMACS 2018 by Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, Groot, Bert L., Grubmüller, Helmut

“…We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package…”
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Probing the energy landscape of activation gating of the bacterial potassium channel KcsA by Linder, Tobias, de Groot, Bert L, Stary-Weinzinger, Anna

“…The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion…”
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