About

Benoit Roux is the MSC PhD Amgen Professor of Biochemistry and Molecular Biology at the University of Chicago, within the Department of Biochemistry & Molecular Biology. He is also a Professor of Neuroscience. His research focuses on biomolecular simulations, emphasizing the implementation of FAIR principles. His work includes studying the mechanisms of ion channels, such as K+ conduction and C-type inactivation, as well as the dynamics of voltage-sensing domains in proteins. Roux's contributions extend to biochemical and biophysical characterizations, the development of genetically encoded sensors, and the regulation of enzyme catalysis through chemical switches. His research aims to deepen understanding of molecular mechanisms underlying cellular functions and to advance computational and experimental approaches in biochemistry and neuroscience.

Research topics

• Computer Science
• Chemistry
• Computational chemistry
• Biology
• Artificial Intelligence
• Genetics
• Pharmacology
• Operating system
• Biophysics
• Physics
• Biochemistry
• Parallel computing
• Statistics
• Computational biology
• Mathematics
• Computer network
• Organic chemistry
• Computational science
• Cell biology

Selected publications

• BPS2026 – Flipping gating polarity in hERG by uncoupling the S4-S5 linker from the inner bundle gate

  Biophysical Journal · 2026-02-01

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  PublisherDOI

• The scientific legacy of Martin Karplus from the perspective of his collaborators

  Biophysical Journal · 2026-04-01

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  PublisherDOI

• Mechanistic Insight into Conformational Control of Enzyme Activity by Genetically Encoded Metal‐Responsive Switches

  ChemBioChem · 2026-04-01

  articleOpen accessCorresponding

  We previously introduced a genetically encoded, metal‐responsive system for reversible control of protein function based on metal chelation by bipyridylalanine (BpyAla) residues. The efficacy of this linking group approach was demonstrated in two structurally and functionally distinct enzymes, Pyrococcus furiosus prolyl oligopeptidase ( Pfu POP) and Photinus pyralis luciferase (Pluc). Here, we investigate the mechanistic basis of this switching in Pfu POP. Fluorescence‐based metal competition assays and molecular dynamics (MD) simulations were conducted to quantify Ni(II) binding affinity and evaluate the structural response to Bpy 2 Ni(II) complex formation. 19 F NMR spectroscopy and MD simulations further indicate that linking group‐controlled conformational changes near the catalytic triad, particularly within the loop containing H592, drive the observed activity modulation upon metal binding. These findings establish that genetically encoded metal‐binding motifs can regulate enzyme function through subtle, localized conformational changes, providing a versatile platform for engineering responsive protein systems in synthetic biology, biosensing, and programmable catalysis.

  PublisherDOI

• Multistate Kinetic Model of the Sodium–Potassium ATPase

  The Journal of Physical Chemistry B · 2025-09-11 · 4 citations

  articleOpen accessSenior authorCorresponding

  ions against their electrochemical potential gradient across the cellular membrane. The function of this ATP-driven ion pump is broadly explained by the schematic Post-Albers alternating-access mechanism. Accordingly, the free energy gained from the phosphorylation/dephosphorylation processes, where the γ-phosphate of ATP is transferred to a conserved Asp located on a cytoplasmic domain of the protein, is used by the enzyme to interconvert between two main conformational states. As a result of experimentally determined structures at atomic resolution, a detailed Post-Albers transport cycle of Na,K-ATPase can comprise more than 20 conformational states of the system. This presents a great opportunity to formulate a detailed multistate kinetic framework model of the transport cycle of the Na,K-ATPase, displaying the thermodynamic and biophysical constraints under which it must operate. Particular attention is given to the effect of coupling to the membrane potential via incremental displacement charges for the microscopic steps of the transport cycle. On the multistate kinetic framework, a simplified continuous model of the transport cycle based on the Smoluchowski equation is formulated, and its consequences on the kinetic efficiency of the turnover rate are explored. These considerations lead to the conjecture that the free energy of the microstates of Na,K-ATPase is optimized for achieving a fast turnover rate when the membrane is depolarized.

  PublisherOA PDFDOI

• Molecular Dynamics-Guided Design and Chemoproteomic Profiling of Covalent Kinase Activity Probes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-18

  preprintOpen access

  Abstract Covalent small molecule activity probes can be powerful tools to interrogate protein function in native cellular environments. The design of family-wide activity probes requires an understanding of the molecular sources of general targeting potential and specificity to enable broad targeting of protein family members. Here, we developed and applied a multifaceted docking and molecular dynamics (MD) simulation pipeline to design and test cell-permeable covalent kinase activity probes from a set of hinge-binding pharmacophores. This computationally-guided approach yielded a new cell-active probe, K60P, which targets around 114 kinases across distinct kinase classes in live cells. Chemoproteomic profiling of this probe and a clinical candidate sharing the same indazole core, KW-2449, identified kinase and non-kinase target profiles that differ from recombinant protein assay profiles, underscoring the utility of native kinase profiling in situ . Biochemical studies with a model target kinase, ABL1, confirmed covalent labeling of the active site lysine across several kinase probes with distinct kinetics, as well as covalent labeling of key tyrosines in trans between ABL1 monomers. Finally, focused proteomics, kinetic modeling, and molecular dynamics simulations revealed that K60P, as well as the comparator probe XO44, preferentially engage with target kinases in their active, DFG-in conformations, which is driven by increasing population of reaction-ready small molecule conformation. These results together establish a computational and kinetic modeling framework for designing covalent activity probes and highlight the balance of target selectivity and kinetic efficiency as a key factor in determining their proteome-wide reactivity. Abstract Figure

  PublisherOA PDFDOI

• Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway

  The Journal of Physical Chemistry B · 2025-06-30 · 2 citations

  articleOpen accessSenior authorCorresponding

  Calculating the binding free energy of small drug-like molecules to a macromolecular receptor is one of the most important applications of molecular dynamics simulations. One computational approach (the "geometrical route") seeks to determine the binding free energy of a ligand by calculating the potential of mean force along a physical path corresponding to the dissociation of the ligand from its receptor. We show here that it is possible to rigorously map the entire ligand-receptor separation process onto a curvilinear separation pathway constructed from the string method and then sample the longitudinal and orthogonal order parameters defined from the Path Collective Variable (PCV) along this pathway to calculate the binding free energy. The theory is illustrated by computing the absolute binding free energy of a glycogen synthase kinase-3 beta (GSK-3β) inhibitor, and the results are compared with the result from a calculation based on the standard alchemical double decoupling approach.

  PublisherOA PDFDOI

• The String Method with Swarms of Trajectories: A Tutorial for Free-Energy Calculations Along a Zero-Drift Pathway

  The Journal of Physical Chemistry B · 2025-06-27 · 3 citations

  articleOpen access

  The objective of this tutorial is to provide a comprehensive overview of the string method and its usage to determine a detailed transition pathway and the free-energy difference between two conformational states of a system. The computational protocol is illustrated in detail by setting out to calculate the free-energy difference between the C7eq and C7ax conformations of the short, terminally blocked peptide, N–acetyl–N′–methylalaninamide. Starting from a rectilinear transition pathway connecting the two conformations in the backbone-torsional subspace, an optimal zero-drift pathway (ZDP) is determined using the string method with a swarm of trajectories. The free-energy change along this path is then estimated using the path-collective variables (PCV) coordinate in the framework of the adaptive biasing force (ABF) importance-sampling algorithm.

  PublisherOA PDFDOI

• Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD

  The Journal of Physical Chemistry B · 2025-08-04 · 4 citations

  articleOpen accessSenior authorCorresponding

  This tutorial examines the application of constant-pH molecular dynamics simulations, a method that addresses the critical problem of modeling systems that can adopt multiple protonation states. While conventional molecular dynamics simulations generally assume fixed protonation states, using a constant-pH technique actively explores dynamic shifts in protonation as the simulation progresses. Once completed, constant-pH simulations can be analyzed to yield titration curves that can be readily compared to experiment.

  PublisherOA PDFDOI

• Structure of the ILT Mutant Shaker K ⁺ Channel and the Mechanism of Voltage Activation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-14

  preprintOpen accessSenior authorCorresponding

  Voltage-gated potassium (Kv) channels play a critical role in cellular excitability and the propagation of the nerve impulse. Despite the extensive amount of information available about Kv channels, the complete process of voltage activation-where a conformational change mediated by voltage-sensor domains (VSD) opens the intracellular gate in response to the depolarization of the membrane potential-has not been fully elucidated. To understand this process, we study the Kv Shaker channel and focus on the ILT mutant (V369I, I372L, S376T) known to display a long-lived closed intermediate state during the activation process. Single particle CryoEM of the ILT mutant reveals a novel conformation of Shaker in which the intracellular gate formed by the S5-S6 helices is in a closed state and the S4 helix in the VSD is in an intermediate state shifted down by ~5Å relative to its position in the fully activated open channel. Additional conformations of the channel generated by Alphafold2 and molecular dynamics simulations are used to map the sequence of intermediate states along the voltage activation process, revealing the nature of the couping between the VSD, the S4-S5 linker, and the S5-S6 intracellular gate. In the final stage of the activation process, as the VSD reaches its fully activated conformation while the gate remains closed, essential interactions between the S4-S5 linker and the intracellular S5-S6 gate are transiently disrupted and reformed when the gate opens, demonstrating that electro-mechanical coupling results from a dynamic shift in population equilibrium between metastable states. These findings provide unprecedented mechanistic insight into how structural rearrangements underlie the voltage activation process in Kv channels, offering broader implications for understanding channelopathies and designing targeted modulators.

  PublisherOA PDFDOI

• Aux origines de la collection ethnographique du musée d’Angoulême : coconstruire une recherche de provenances

  HAL (Le Centre pour la Communication Scientifique Directe) · 2025-10-01

  articleSenior author

  International audience

  Publisher

Recent grants

• Free Energies in Biomolecular Systems: Development and Applications of Theoretical and Computational Approaches

  NSF · $688k · 2009–2013

• Computational Studies of Ion Channels

  NIH · $8.7M · 2001–2024

• NIH Grant U54GM087519

  NIH · $63.6M · 2019

• Free Energies in Biomolecular Systems: Theoretical Development and Application of Computational Approaches

  NSF · $451k · 2005–2008

• Conformational Dynamics of Src-Kinases and Inhibition

  NIH · $5.3M · 2002–2022

Frequent coauthors

• Christophe Chipot

  Centre National de la Recherche Scientifique

  119 shared

• Alexander D. MacKerell

  University of Maryland, Baltimore

  110 shared

• Edward Harder

  Schrodinger (United States)

  68 shared

• Guillaume Lamoureux

  Rutgers Sexual and Reproductive Health and Rights

  62 shared

• Troy W. Whitfield

  Whitehead Institute for Biomedical Research

  56 shared

• Haibo Yu

  University of Wollongong

  52 shared

• Eduardo Perozo

  University of Chicago

  51 shared

• Victor M. Anisimov

  Argonne National Laboratory

  42 shared

Labs

• Benoit RouxPI