Publications

Viral fusion proteins of classes II and III but not of class I sense the lipid composition of host membranes

Chetan S Poojari, Tobias Bommer, Jochen Hub

BioRxiv, 2023

MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress

John Reinhard, Leonhard Starke, Christian Klose, Per Haberkant, Henrik Hammarén, Frank Stein, Ofir Klein, Charlotte Berhorst, Heike Stumpf, James P. Sáenz, Jochen Hub, Maya Schuldiner, Robert Ernst

EMBO Journal. Accepted, 2024

Molecular simulations reveal the free energy landscape and transition state of membrane electroporation

Gari Kasparyan, Jochen Hub

Physical Review Letters. Accepted, 2024

Atomistic ensemble of active SHP2

Massimiliano Anselmi, Jochen Hub

Communications Biology, 2023

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Johanna Linse, Jochen Hub

Communications Chemistry, 2023

Molecular Simulations of Liquid Jet Explosions and Shock Waves Induced by X-Ray Free-Electron Lasers

Leonie Chatzimagas, Jochen Hub

Physical Review Letters, 2023

Hydrophobin Bilayer as Water Impermeable Protein Membrane

Friederike Nolle, Leonhard Starke, Alessandra Griffo, Michael Lienemann, Karin Jacobs, Ralf Seemann, Jean-Baptiste Fleury, Jochen Hub, Hendrik Hähl

Langmuir, 2023

Revealing Allostery in PTPN11 SH2 Domains from MD Simulations

Massimiliano Anselmi, Jochen Hub

Methods in Molecular Biology, 2023

Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy

Jeremy Lapierre, Jochen Hub

Journal of Chemical Information and Modeling, 2023

Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins

Robert Becker, Jochen Hub

Biological Chemistry, 2023

Solvent-Dependent Structural Dynamics in the Ultrafast Photodissociation Reaction of Triiodide Observed with Time-Resolved X-ray Solution Scattering

Amke Nimmrich, Matthijs R. Panman, Oskar Berntsson, Elisa Biasin, Stephan Niebling, Jonas Petersson, Maria Hoernke, Alexander Björling, Emil Gustavsson, Tim B. van Driel, Asmus O. Dohn, Mads Laursen, Diana B. Zederkof, Kensuke Tono, Tetsuo Katayama, Shigeki Owada, Martin M. Nielsen, Jan Davidsson, Jens Uhlig, Jochen Hub, Kristoffer Haldrup, Sebastian Westenhoff

Journal of the American Chemical Society, 2023

Experiment-guided molecular simulations define a heterogeneous structural ensemble for the PTPN11 tandem SH2 domains

Michelangelo Marasco, John Kirkpatrick, Teresa Carlomagno, Jochen Hub, Massimiliano Anselmi

Chemical Science, 2023

Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation

Gari Kasparyan, Jochen Hub

Journal of Chemical Theory and Computation, 2023

Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions

Robert Becker, Jochen Hub

Communications Biology, 2023

Simulated Tempering-Enhanced Umbrella Sampling Improves Convergence of Free Energy Calculations of Drug Membrane Permeation

Carla F. Sousa, Robert Becker, Claus-Michael Lehr, Olga V. Kalinina, Jochen Hub

Journal of Chemical Theory and Computation, 2023

Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein

Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Johanna Linse, Philip Ullmann, Marco Payr, Brice Murciano, Bernd Simon, Jochen Hub, Janosch Hennig

Nucleic Acids Research, 2023

Passive transport of Ca$^{2+}$ ions through lipid bilayers imaged by widefield second harmonic microscopy

Maksim Eremchev, David Roesel, Chetan S Poojari, Aurélien Roux, Jochen Hub, Sylvie Roke

Biophysical Journal, 2023

Structure and ensemble refinement against SAXS data: Combining MD simulations with Bayesian inference or with the maximum entropy principle

Leonie Chatzimagas, Jochen Hub

Methods in Enzymology, 2023

Ion-Induced Transient Potential Fluctuations Facilitate Pore Formation and Cation Transport through Lipid Membranes

David Roesel, Maksim Eremchev, Chetan S Poojari, Jochen Hub, Sylvie Roke

Journal of the American Chemical Society, 2022

Predicting solution scattering patterns with explicit-solvent molecular simulations

Leonie Chatzimagas, Jochen Hub

Methods in Enzymology, 2022

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Jill Trewhella, Patrice Vachette, Jan Bierma, Clement Blanchet, Emre Brookes, Srinivas Chakravarthy, Leonie Chatzimagas, Thomas E. Cleveland IV, Nathan Cowieson, Ben Crossett, Anthony P. Duff, Daniel Franke, Frank Gabel, Richard E. Gillilan, Melissa Graewert, Alexander Grishaev, J. Mitchell Guss, Michal Hammel, Jesse Hopkins, Qingqui Huang, Jochen Hub, Greg L. Hura, Thomas C. Irving, Cy Michael Jeffries, Cheol Jeong, Nigel Kirby, Susan Krueger, Anne Martel, Tsutomu Matsui, Na Li, J. Pérez, Lionel Porcar, Thierry Prangé, Ivan Rajkovic, Mattia Rocco, Daniel J. Rosenberg, Timothy M. Ryan, Soenke Seifert, Hiroshi Sekiguchi, Dmitri Svergun, Susana Teixeira, Aurelien Thureau, Thomas M. Weiss, Andrew E. Whitten, Kathleen Wood, Xiaobing Zuo

Acta Crystallography D, 2022

DNA opening during transcription initiation by RNA polymerase II in atomic detail

Jeremy Lapierre, Jochen Hub

Biophysical Journal, 2022

Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap

Alexander E. Yarawsky, Jesse B. Hopkins, Leonie Chatzimagas, Jochen Hub, Andrew B. Herr

Journal of Molecular Biology, 2022

Lipid Droplets Embedded in a Model Cell Membrane Create a Phospholipid Diffusion Barrier

Sevde Puza, Stefanie Caesar, Chetan S Poojari, Michael Jung, Ralf Seemann, Jochen Hub, Bianca Schrul, Jean-Baptiste Fleury

Small, 2022

Free energies of membrane stalk formation from a lipidomics perspective

Chetan S Poojari, Katharina Scherer, Jochen Hub

Nature Communications, 2021

Propensity, free energy contributions and conformation of primary n-alcohols at a water surface

Victor Ekholm, Carl Caleman, Jochen Hub, Malin Wohlert

Physical Chemistry Chemical Physics, 2021

Structure and dynamics of the quaternary hunchback mRNA translation repression complex

Jakub Macošek, Bernd Simon, Johanna Linse, Pravin Kumar Ankush Jagtap, Sophie L Winter, Jaelle Foot, Karine Lapouge, Kathryn Perez, Mandy Rettel, Miloš Ivanović, Pawel Masiewicz, Brice Murciano, Mikhail M Savitski, Inga Loedige, Jochen Hub, Frank Gabel, Janosch Hennig

Nucleic Acids Research, 2021

Three- and four-site models for heavy water: SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW

Johanna Linse, Jochen Hub

The Journal of Chemical Physics, 2021

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Massimiliano Anselmi, Jochen Hub

Proceedings of the National Academy of Sciences, 2021

The structure of Prp2 bound to RNA and ADP-BeF$_3$$^-$ reveals structural features important for RNA unwinding by DEAH-box ATPases

Florian Hamann, Lars C. Zimmerningkat, Robert Becker, Tim B. Garbers, Piotr Neumann, Jochen Hub, Ralf Ficner

Acta Crystallographica Section D, 2021

How arginine derivatives alter the stability of lipid membranes: dissecting the roles of side chains, backbone and termini

Sarah F. Verbeek, Neha Awasthi, Nikolas K. Teiwes, Ingo Mey, Jochen Hub, Andreas Janshoff

European Biophysics Journal, 2021

Interpreting SAXS/WAXS Data with Explicit-Solvent Simulations: A Practical Guide

Markus Hermann, Jochen Hub

Methods in Molecular Biology, 2021

Joint Reaction Coordinate for Computing the Free-Energy Landscape of Pore Nucleation and Pore Expansion in Lipid Membranes

Jochen Hub

Journal of Chemical Theory and Computation, 2021

Observing the Structural Evolution in the Photodissociation of Diiodomethane with Femtosecond Solution X-Ray Scattering

Matthijs R. Panman, Elisa Biasin, Oskar Berntsson, Markus Hermann, Stephan Niebling, Ashley J. Hughes, Joachim Kübel, Kalina Atkovska, Emil Gustavsson, Amke Nimmrich, Asmus O. Dohn, Mads Laursen, Diana B. Zederkof, Alireza Honarfar, Kensuke Tono, Tetsuo Katayama, Shigeki Owada, Tim B. van Driel, Kasper Kjaer, Martin M. Nielsen, Jan Davidsson, Jens Uhlig, Kristoffer Haldrup, Jochen Hub, Sebastian Westenhoff

Physical Review Letters, 2020

An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase

Massimiliano Anselmi, Jochen Hub

Scientific Reports, 2020

Cooperative Effects of an Antifungal Moiety and DMSO on Pore Formation over Lipid Membranes Revealed by Free Energy Calculations

Gari Kasparyan, Chetan S Poojari, Róg, Tomasz, Jochen Hub

The Journal of Physical Chemistry B, 2020

Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase

Massimiliano Anselmi, Paolo Calligari, Jochen Hub, Marco Tartaglia, Gianfranco Bocchinfuso, Lorenzo Stella

Journal of Chemical Information and Modeling, 2020

Computer simulations of protein–membrane systems

Jennifer Loschwitz, Olujide O. Olubiyi, Jochen Hub, Birgit Strodel, Chetan S Poojari

Progress in Molecular Biology and Translational Science, 2020

Small-Angle X-ray Scattering Curves of Detergent Micelles: Effects of Asymmetry, Shape Fluctuations, Disorder, and Atomic Details

Miloš Ivanović, Markus Hermann, Maciej Wójcik, Javier Pérez, Jochen Hub

The Journal of Physical Chemistry Letters, 2020

SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy

Markus Hermann, Jochen Hub

Journal of Chemical Theory and Computation, 2019

Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations

Po-chia Chen, Roman Shevchuk, Felix M. Strnad, Charlotte Lorenz, Lukas Karge, Ralph Gilles, Andreas M. Stadler, Janosch Hennig, Jochen Hub

Journal of Chemical Theory and Computation, 2019

Free-Energy Calculations of Pore Formation in Lipid Membranes

Neha Awasthi, Jochen Hub

Biomembrane Simulations, 2019

Steroid–steroid interactions in biological membranes: Cholesterol and cortisone

Adree Khondker, Jochen Hub, Maikel C. Rheinstädter

Chemistry and Physics of Lipids, 2019

Molecular Mechanism of Polycation-Induced Pore Formation in Biomembranes

Neha Awasthi, Wojciech Kopec, Natalia Wilkosz, Dorota Jamróz, Jochen Hub, Maria Zatorska, Rafał Petka, Maria Nowakowska, Mariusz Kepczynski

ACS Biomaterials Science & Engineering, 2018

Quantifying the influence of the ion cloud on SAXS profiles of charged proteins

Miloš Ivanović, Linda K. Bruetzel, Roman Shevchuk, Jan Lipfert, Jochen Hub

Physical Chemistry Chemical Physics, 2018

Rationalizing Steroid Interactions with Lipid Membranes: Conformations, Partitioning, and Kinetics

Kalina Atkovska, Johannes Klingler, Johannes Oberwinkler, Sandro Keller, Jochen Hub

ACS Central Science, 2018

Merging In-Solution X-ray and Neutron Scattering Data Allows Fine Structural Analysis of Membrane–Protein Detergent Complexes

Gaëtan Dias Mirandela, Giulia Tamburrino, Miloš Ivanović, Felix M. Strnad, Olwyn Byron, Tim Rasmussen, Paul A. Hoskisson, Jochen Hub, Ulrich Zachariae, Frank Gabel, Arnaud Javelle

The Journal of Physical Chemistry Letters, 2018

Assigning crystallographic electron densities with free energy calculations—The case of the fluoride channel Fluc

Igor Ariz-Extreme, Jochen Hub

PLOS ONE, 2018

Metastable Prepores in Tension-Free Lipid Bilayers

Christina L. Ting, Neha Awasthi, Marcus Müller, Jochen Hub

Physical Review Letters, 2018

Temperature-Dependent Atomic Models of Detergent Micelles Refined against Small-Angle X-Ray Scattering Data

Miloš Ivanović, Linda K. Bruetzel, Jan Lipfert, Jochen Hub

Angewandte Chemie International Edition, 2018

Interpreting solution X-ray scattering data using molecular simulations

Jochen Hub

Current Opinion in Structural Biology, 2017

A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion

P. Guardado-Calvo, Kalina Atkovska, S. A. Jeffers, N. Grau, M. Backovic, J. Pérez-Vargas, S. M. de Boer, M. A. Tortorici, G. Pehau-Arnaudet, J. Lepault, P. England, P. J. Rottier, B. J. Bosch, Jochen Hub, F. A. Rey

Science, 2017

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

Roman Shevchuk, Jochen Hub

PLOS Computational Biology, 2017

Energetics and mechanism of anion permeation across formate-nitrite transporters

Kalina Atkovska, Jochen Hub

Scientific Reports, 2017

Probing a Continuous Polar Defect: A Reaction Coordinate for Pore Formation in Lipid Membranes

Jochen Hub, Neha Awasthi

Journal of Chemical Theory and Computation, 2017

Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM

Igor Ariz-Extreme, Jochen Hub

The Journal of Physical Chemistry B, 2017

Disentangling polydispersity in the PCNA−p15PAF complex, a disordered, transient and multivalent macromolecular assembly

Tiago N. Cordeiro, Po-chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J. Blanco, Jochen Hub, Ramon Crehuet, Pau Bernadó

Nucleic Acids Research, 2016

Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs

Naomi Nitschke, Kalina Atkovska, Jochen Hub

The Journal of Chemical Physics, 2016

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Levin Brinkmann, Jochen Hub

Proceedings of the National Academy of Sciences, 2016

Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects

Neha Awasthi, Jochen Hub

Journal of Chemical Theory and Computation, 2016

The Lipid Bilayer Provides a Site for Cortisone Crystallization at High Cortisone Concentrations

Richard J. Alsop, Adree Khondker, Jochen Hub, Maikel C. Rheinstädter

Scientific Reports, 2016

Structural Properties of Protein–Detergent Complexes from SAXS and MD Simulations

Po-chia Chen, Jochen Hub

The Journal of Physical Chemistry Letters, 2015

Quantifying Lateral Inhomogeneity of Cholesterol-Containing Membranes

Celsa Díaz-Tejada, Igor Ariz-Extreme, Neha Awasthi, Jochen Hub

The Journal of Physical Chemistry Letters, 2015

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics

Levin Brinkmann, Jochen Hub

The Journal of Chemical Physics, 2015

Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics

Po-chia Chen, Jochen Hub

Biophysical Journal, 2015

MemGen: a general web server for the setup of lipid membrane simulation systems

Chris Knight, Jochen Hub

Bioinformatics, 2015

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

Chris Knight, Jochen Hub

Nucleic Acids Research, 2015

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

Po-chia Chen, Jochen Hub

Biophysical Journal, 2014

CO$_2$ and O$_2$ Distribution in Rubisco Suggests the Small Subunit Functions as a CO$_2$ Reservoir

Michiel van Lun, Jochen Hub, David van der Spoel, Inger Andersson

Journal of the American Chemical Society, 2014

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

Florian Zocher, David van der Spoel, Peter Pohl, Jochen Hub

Biophysical Journal, 2013

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

Jochen Hub, Bert L. de Groot, Helmut Grubmüller, Gerrit Groenhof

Journal of Chemical Theory and Computation, 2013

Thermodynamics of hydronium and hydroxide surface solvation

Jochen Hub, Maarten G. Wolf, Carl Caleman, Paul J. van Maaren, Gerrit Groenhof, David van der Spoel

Chemical Science, 2013

Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

Tatyana Krivobokova, Rodolfo Briones, Jochen Hub, Axel Munk, Bert L. de Groot

Biophysical Journal, 2012

Organic molecules on the surface of water droplets – an energetic perspective

Jochen Hub, Carl Caleman, David van der Spoel

Physical Chemistry Chemical Physics, 2012

Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

Christian L. Wennberg, David van der Spoel, Jochen Hub

Journal of the American Chemical Society, 2012

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen Hub, Luciano T. Costa, David van der Spoel

Journal of Chemical Theory and Computation, 2011

Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

Erik Malmerberg, Ziad Omran, Jochen 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

Biophysical Journal, 2011

Comment on “Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory”

Jochen Hub, Bert L. de Groot

The Journal of Physical Chemistry B, 2011

Atomistic simulation of ion solvation in water explains surface preference of halides

Carl Caleman, Jochen Hub, Paul J. van Maaren, David van der Spoel

Proceedings of the National Academy of Sciences, 2011

A Decade of Debate: Significance of CO$_2$ Permeation through Membrane Channels still Controversial

Bert L. de Groot, Jochen Hub

ChemPhysChem, 2011

Voltage-Regulated Water Flux through Aquaporin Channels In Silico

Jochen Hub, Camilo Aponte-Santamaría, Helmut Grubmüller, Bert L. de Groot

Biophysical Journal, 2010

g_wham — A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Jochen Hub, Bert L. de Groot, David van der Spoel

Journal of Chemical Theory and Computation, 2010

Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes

Jochen Hub, Fritz K. Winkler, Mike Merrick, Bert L. de Groot

Journal of the American Chemical Society, 2010

Dynamics and energetics of solute permeation through the $\textit{Plasmodium falciparum}$ aquaglyceroporin

Camilo Aponte-Santamaría, Jochen Hub, Bert L. de Groot

Physical Chemistry Chemical Physics, 2010

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

Jochen Hub, Marcus B. Kubitzki, Bert L. de Groot

PLOS Computational Biology, 2010

Detection of Functional Modes in Protein Dynamics

Jochen Hub, Bert L. de Groot

PLOS Computational Biology, 2009

Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations?

Jochen Hub, Helmut Grubmüller, Bert L. de Groot

Handbook of Experimental Pharmacology, Aquaporins, 2008

g_permute: Permutation-reduced phase space density compaction

F. Reinhard, O.F. Lange, Jochen Hub, J. Haas, H. Grubmüller

Computer Physics Communications, 2008

Not Only Enthalpy: Large Entropy Contribution to Ion Permeation Barriers in Single-File Channels

Guillem Portella, Jochen Hub, Martin D. Vesper, Bert L. de Groot

Biophysical Journal, 2008

Mechanism of selectivity in aquaporins and aquaglyceroporins

Jochen Hub, Bert L. de Groot

Proceedings of the National Academy of Sciences, 2008

Is TEA an inhibitor for human Aquaporin-1?

E. Matthias Müller, Jochen Hub, Helmut Grubmüller, Bert L. de Groot

Pflügers Archiv - European Journal of Physiology, 2008

Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments

Jochen Hub, Tim Salditt, Maikel C. Rheinstädter, Bert L. de Groot

Biophysical Journal, 2007

Molecular Anatomy of a Trafficking Organelle

Shigeo Takamori, Matthew Holt, Katinka Stenius, Edward A. Lemke, Mads Grønborg, Dietmar Riedel, Henning Urlaub, Stephan Schenck, Britta Brügger, Philippe Ringler, Shirley A. Müller, Burkhard Rammner, Frauke Gräter, Jochen Hub, Bert L. de Groot, Gottfried Mieskes, Yoshinori Moriyama, Jürgen Klingauf, Helmut Grubmüller, John Heuser, Felix Wieland, Reinhard Jahn

Cell, 2006

Does CO$_2$ Permeate through Aquaporin-1?

Jochen Hub, Bert L. de Groot

Biophysical Journal, 2006

Dynamics and Criticality of Correlated Electrons and Quantum Gases

C. Lavalle, M. Rigol, Jochen Hub, A. Muramatsu

High Performance Computing in Science and Engineering' 04, 2004

Preprints

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