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CO$_2$ and O$_2$ Distribution in Rubisco Suggests the Small Subunit Functions as a CO$_2$ Reservoir
Protein–gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two …
Michiel van Lun, Jochen S. Hub, David van der Spoel, Inger Andersson
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CO$_2$ and O$_2$ Distribution in Rubisco Suggests the Small Subunit Functions as a CO$_2$ Reservoir
Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes
The permeability of lipid membranes for metabolic molecules or drugs is routinely estimated from the solute’s oil/water partition …
Florian Zocher, David van der Spoel, Peter Pohl, Jochen S. Hub
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Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally …
Jochen S. Hub, Bert L. de Groot, Helmut Grubmüller, Gerrit Groenhof
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Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
Thermodynamics of hydronium and hydroxide surface solvation
The concentration of hydronium and hydroxide at the water–air interface has been debated for a long time. Recent evidence from a range …
Jochen S. Hub, Maarten G. Wolf, Carl Caleman, Paul J. van Maaren, Gerrit Groenhof, David van der Spoel
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Thermodynamics of hydronium and hydroxide surface solvation
Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1
We introduce an approach based on the recently introduced functional mode analysis to identify collective modes of internal dynamics …
Tatyana Krivobokova, Rodolfo Briones, Jochen S. Hub, Axel Munk, Bert L. de Groot
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Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1
Organic molecules on the surface of water droplets – an energetic perspective
The solubility of organic molecules is a well established property, founded on decades of measurements, the results of which have been …
Jochen S. Hub, Carl Caleman, David van der Spoel
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Organic molecules on the surface of water droplets – an energetic perspective
Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes
Cholesterol plays an important role in maintaining the correct fluidity and rigidity of the plasma membrane of all animal cells, and …
Christian L. Wennberg, David van der Spoel, Jochen S. Hub
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Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and …
Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel
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Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
Time-resolved wide-angle x-ray scattering (TR-WAXS) is an emerging biophysical method which probes protein conformational changes with …
Erik Malmerberg, Ziad Omran, Jochen S. Hub, Xuewen Li, Gergely Katona, Sebastian Westenhoff, Linda C. Johansson, Magnus Andersson, Marco Cammarata, Michael Wulff, David van der Spoel, Jan Davidsson, Alexandre Specht, Richard Neutze
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Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
Atomistic simulation of ion solvation in water explains surface preference of halides
Water is a demanding partner. It strongly attracts ions, yet some halide anions—chloride, bromide, and iodide—are expelled to the …
Carl Caleman, Jochen S. Hub, Paul J. van Maaren, David van der Spoel
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Atomistic simulation of ion solvation in water explains surface preference of halides