Publications

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2025

Identifying and quantifying membrane interactions of the protein human cis‐prenyltransferase

Duncan M. Boren, Shiri Kredi, Ekaterina Positselskaya, Moshe Giladi, Yoni Haitin, Josh V. Vermaas

Protein Science  ·  24 May 2025  ·  doi:10.1002/pro.70167

Bringing together simulation and experiment, we identify residues involved in protein binding for human cis-prenyltransferase to the membrane.

membrane-protein-interaction small-molecule collaboration healthy

Synthesis, function, and genetic variation of sorgoleone, the major biological nitrification inhibitor in sorghum

Sakiko Okumoto, Bal Maharjan, Nithya Rajan, Jing Xi, Scott R Baerson, …, Michael J. Thomson, Damaris A Odeny, Tadashi Yoshihashi, Josh V Vermaas, Guntur V Subbarao

Crop Science  ·  01 May 2025  ·  doi:10.1002/csc2.70066

Review article on sorgoleone, a natural herbicide made by sorghum.

small-molecule collaboration planty

Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics

Murtaza Barkarar, Daipayan Sarkar, Christopher Hunt, Josh Vermaas

American Chemical Society (ACS)  ·  20 Mar 2025  ·  doi:10.26434/chemrxiv-2024-zj7sn-v2

Dynamics and structural responses to cis-trans isomerization in bacterial lipid bilayers

Saad Raza, Majid Jafari, Troy Sievertsen, Josh Vermaas

American Chemical Society (ACS)  ·  10 Mar 2025  ·  doi:10.26434/chemrxiv-2025-jm423

Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System

Eric J. Young, Henning Kirst, Matthew E. Dwyer, Josh V. Vermaas, Cheryl A. Kerfeld

ACS Synthetic Biology  ·  14 Jan 2025  ·  doi:10.1021/acssynbio.4c00290

Combination of timeseries for light emitted by encapsulated luciferases, which gives us a quantitative estimate for permeability for substrates and products. Turns out open shells missing pentameric capping units are about 50x more permeable.

collaboration microcompartment

2024

Identifying and Quantifying Membrane Interactions of the Protein Human cis-Prenyltransferase

Duncan Boren, Shiri Kredi, Ekaterina Positselskaya, Moshe Giladi, Yoni Haitin, Josh Vermaas

American Chemical Society (ACS)  ·  30 Dec 2024  ·  doi:10.26434/chemrxiv-2024-3gh6x

Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics

Murtaza Barkarar, Daipayan Sarkar, Josh Vermaas

American Chemical Society (ACS)  ·  29 Nov 2024  ·  doi:10.26434/chemrxiv-2024-zj7sn

Electrochemical cofactor recycling of bacterial microcompartments

Markus Sutter, Lisa M. Utschig, Jens Niklas, Sathi Paul, Darren N. Kahan, …, Michaela A. TerAvest, David P. Hickey, Josh V. Vermaas, Corie Y. Ralston, Cheryl A. Kerfeld

Proceedings of the National Academy of Sciences  ·  25 Nov 2024  ·  doi:10.1073/pnas.2414220121

Increasing thermostability of the key photorespiratory enzyme glycerate 3‐kinase by structure‐based recombination

Ludmila V. Roze, Anna Antoniak, Daipayan Sarkar, Aaron H. Liepman, Mauricio Tejera‐Nieves, Josh V. Vermaas, Berkley J. Walker

Plant Biotechnology Journal  ·  17 Nov 2024  ·  doi:10.1111/pbi.14508

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Daipayan Sarkar, Christopher Maffeo, Markus Sutter, Aleksei Aksimentiev, Cheryl A. Kerfeld, Josh V. Vermaas

Proceedings of the National Academy of Sciences  ·  01 Nov 2024  ·  doi:10.1073/pnas.2402277121

Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes

Daipayan Sarkar, Christopher Maffeo, Markus Sutter, Aleksei Aksimentiev, Cheryl Kerfeld, Josh Vermaas

American Chemical Society (ACS)  ·  18 Oct 2024  ·  doi:10.26434/chemrxiv-2024-kbcdf-v2

Adaptative survival of Aspergillus fumigatus to echinocandins arises from cell wall remodeling beyond β−1,3-glucan synthesis inhibition

Malitha C. Dickwella Widanage, Isha Gautam, Daipayan Sarkar, Frederic Mentink-Vigier, Josh V. Vermaas, …, Andrew S. Lipton, Thierry Fontaine, Jean-Paul Latgé, Ping Wang, Tuo Wang

Nature Communications  ·  31 Jul 2024  ·  doi:10.1038/s41467-024-50799-8

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Saad Raza, Daipayan Sarkar, Leanne Jade G. Chan, Joshua Mae, Markus Sutter, Christopher J. Petzold, Cheryl A. Kerfeld, Corie Y. Ralston, Sayan Gupta, Josh V. Vermaas

ACS Omega  ·  18 Jul 2024  ·  doi:10.1021/acsomega.4c02406

Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

Ludmila V. Roze, Anna Antoniak, Daipayan Sarkar, Aaron H. Liepman, Mauricio Tejera-Nieves, Josh V. Vermaas, Berkley J. Walker

Cold Spring Harbor Laboratory  ·  05 May 2024  ·  doi:10.1101/2024.05.02.592181

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Saad Raza, Daipayan Sarkar, Leanne Jade G. Chan, Joshua Mae, Markus Sutter, Christopher J. Petzold, Cheryl A. Kerfeld, Corie Y. Ralston, Sayan Gupta, Josh V. Vermaas

Cold Spring Harbor Laboratory  ·  12 Mar 2024  ·  doi:10.1101/2024.03.12.584231

Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes

Daipayan Sarkar, Christopher Maffeo, Markus Sutter, Aleksei Aksimentiev, Cheryl Kerfeld, Josh Vermaas

American Chemical Society (ACS)  ·  12 Feb 2024  ·  doi:10.26434/chemrxiv-2024-kbcdf

Electron transfer in a crystalline cytochrome with four hemes

William W. Parson, Jingcheng Huang, Martin Kulke, Josh V. Vermaas, David M. Kramer

The Journal of Chemical Physics  ·  09 Feb 2024  ·  doi:10.1063/5.0186958

Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate

Saad Raza, Troy H. Sievertsen, Sakiko Okumoto, Josh V. Vermaas

Phytochemistry  ·  01 Jan 2024  ·  doi:10.1016/j.phytochem.2023.113891

PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid

Martin Kulke, Evan Kurtz, Duncan M. Boren, Dayna M. Olson, Amanda M. Koenig, Susanne Hoffmann-Benning, Josh V. Vermaas

Plant Science  ·  01 Jan 2024  ·  doi:10.1016/j.plantsci.2023.111900

2023

Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator

Vaidyanathan Sethuraman, Josh V. Vermaas, Luna Liang, Arthur J. Ragauskas, Jeremy C. Smith, Loukas Petridis

Biomacromolecules  ·  29 Dec 2023  ·  doi:10.1021/acs.biomac.3c00951

Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II

Gehan A. Ranepura, Junjun Mao, Josh V. Vermaas, Jimin Wang, Christopher J. Gisriel, …, Jose Ortiz-Soto, Md. Raihan Uddin, Muhamed Amin, Gary W. Brudvig, M. R. Gunner

The Journal of Physical Chemistry B  ·  14 Dec 2023  ·  doi:10.1021/acs.jpcb.3c06273

Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content

Daipayan Sarkar, Lintao Bu, Joseph E. Jakes, Jacob K. Zieba, Isaiah D. Kaufman, Michael F. Crowley, Peter N. Ciesielski, Josh V. Vermaas

The Cell Surface  ·  01 Dec 2023  ·  doi:10.1016/j.tcsw.2023.100105

The isoprene‐responsive phosphoproteome provides new insights into the putative signalling pathways and novel roles of isoprene

Sarathi M. Weraduwage, Douglas Whitten, Martin Kulke, Abira Sahu, Josh V. Vermaas, Thomas D. Sharkey

Plant, Cell & Environment  ·  01 Dec 2023  ·  doi:10.1111/pce.14776

An amphipathic helix drives interaction of Fibrillins with plastoglobule lipid droplets

Kiran-Kumar Shivaiah, Duncan M. Boren, Andres Tequia-Herrera, Josh Vermaas, Peter Knut Lundquist

Cold Spring Harbor Laboratory  ·  29 Sep 2023  ·  doi:10.1101/2023.09.28.559984

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Daipayan Sarkar, Hyungro Lee, John W. Vant, Matteo Turilli, Josh V. Vermaas, Shantenu Jha, Abhishek Singharoy

Journal of Chemical Information and Modeling  ·  04 Sep 2023  ·  doi:10.1021/acs.jcim.3c00350

Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate

Saad Raza, Troy Sievertsen, Sakiko Okumoto, Josh Vermaas

American Chemical Society (ACS)  ·  31 Aug 2023  ·  doi:10.26434/chemrxiv-2023-88l2m

Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Martin Kulke, Dayna M. Olson, Jingcheng Huang, David M. Kramer, Josh V. Vermaas

Small  ·  31 Aug 2023  ·  doi:10.1002/smll.202304013

Structural Remodeling of Fungal Cell Wall Promotes Resistance to Echinocandins

Malitha C. Dickwella Widanage, Isha Gautam, Daipayan Sarkar, Frederic Mentink-Vigier, Josh V. Vermaas, Thierry Fontaine, Jean-Paul Latgé, Ping Wang, Tuo Wang

Cold Spring Harbor Laboratory  ·  12 Aug 2023  ·  doi:10.1101/2023.08.09.552708

Nanoscale simulation of the thylakoid membrane response to extreme temperatures

Martin Kulke, Sarathi M. Weraduwage, Thomas D. Sharkey, Josh V. Vermaas

Plant, Cell & Environment  ·  22 May 2023  ·  doi:10.1111/pce.14609

PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid

Martin Kulke, Evan Kurtz, Duncan Boren, Dayna Olson, Amanda Koenig, Susanne Hoffmann-Benning, Josh Vermaas

American Chemical Society (ACS)  ·  17 May 2023  ·  doi:10.26434/chemrxiv-2023-8z8d7

Long Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Martin Kulke, Dayna Olson, Jingcheng Huang, David Kramer, Josh Vermaas

American Chemical Society (ACS)  ·  15 May 2023  ·  doi:10.26434/chemrxiv-2023-4ndh3-v2

Atomistic origins of biomass recalcitrance in organosolv pretreatment

Daipayan Sarkar, Ian J. Santiago, Josh V. Vermaas

Chemical Engineering Science  ·  01 May 2023  ·  doi:10.1016/j.ces.2023.118587

Long Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Martin Kulke, Dayna Olson, Jingcheng Huang, David Kramer, Josh Vermaas

American Chemical Society (ACS)  ·  28 Apr 2023  ·  doi:10.26434/chemrxiv-2023-4ndh3

SARS-CoV2 billion-compound docking

David M. Rogers, Rupesh Agarwal, Josh V. Vermaas, Micholas Dean Smith, Rajitha T. Rajeshwar, …, Ada Sedova, Swen Boehm, Matthew Baker, Jens Glaser, Jeremy C. Smith

Scientific Data  ·  28 Mar 2023  ·  doi:10.1038/s41597-023-01984-9

Nanoscale Simulation of the Thylakoid Membrane Response to Extreme Temperatures

Josh Vermaas V, Martin Kulke, Sarathi Weraduwage M, Thomas Sharkey

Wiley  ·  07 Feb 2023  ·  doi:10.22541/au.167578212.24771627/v1

Characterization of promoter elements of isoprene‐responsive genes and the ability of isoprene to bind START domain transcription factors

Sarathi M. Weraduwage, Abira Sahu, Martin Kulke, Josh V. Vermaas, Thomas D. Sharkey

Plant Direct  ·  31 Jan 2023  ·  doi:10.1002/pld3.483

Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations

Saad Raza, Mykayla Miller, Björn Hamberger, Josh V. Vermaas

The Journal of Physical Chemistry B  ·  30 Jan 2023  ·  doi:10.1021/acs.jpcb.2c07209

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

Daipayan Sarkar, Martin Kulke, Josh V. Vermaas

Biomolecules  ·  05 Jan 2023  ·  doi:10.3390/biom13010107

2022

Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface

Taku Uchiyama, Takayuki Uchihashi, Takuya Ishida, Akihiko Nakamura, Josh V. Vermaas, Michael F. Crowley, Masahiro Samejima, Gregg T. Beckham, Kiyohiko Igarashi

Science Advances  ·  23 Dec 2022  ·  doi:10.1126/sciadv.ade5155

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Josh V. Vermaas, Michael F. Crowley, Gregg T. Beckham

Journal of Biological Chemistry  ·  01 Dec 2022  ·  doi:10.1016/j.jbc.2022.102627

Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations

Saad Raza, Mykayla Miller, Björn Hamberger, Josh Vermaas

American Chemical Society (ACS)  ·  13 Oct 2022  ·  doi:10.26434/chemrxiv-2022-qcg0x

Atomistic Origins of Biomass Recalcitrance in Organosolv Pretreatment

Daipayan Sarkar, Ian Santiago, Josh Vermaas

American Chemical Society (ACS)  ·  23 Sep 2022  ·  doi:10.26434/chemrxiv-2022-9j7zv

Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations

Martin Kulke, Josh V. Vermaas

Journal of Chemical Theory and Computation  ·  21 Sep 2022  ·  doi:10.1021/acs.jctc.2c00327

Lignin Nanoparticle Morphology Depends on Polymer Properties and Solvent Composition: an Experimental and Computational Study

Raisa Carmen Andeme Ela, Saad Raza, Patricia A. Heiden, Josh V. Vermaas, Rebecca G. Ong

ACS Applied Polymer Materials  ·  01 Sep 2022  ·  doi:10.1021/acsapm.2c00854

Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT

S. M. Ayala Mariscal, M. L. Pigazzini, Y. Richter, M. Özel, I. L. Grothaus, …, J. V. Vermaas, L. Colombi Ciacchi, S. Köppen, F. Liu, J. Kirstein

Nature Communications  ·  10 Aug 2022  ·  doi:10.1038/s41467-022-32370-5

Exploring cryo-electron microscopy with molecular dynamics

John W. Vant, Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, Abhishek Singharoy

Biochemical Society Transactions  ·  25 Feb 2022  ·  doi:10.1042/BST20210485

2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

Josh V. Vermaas, Christopher G. Mayne, Eric Shinn, Emad Tajkhorshid

Journal of Chemical Information and Modeling  ·  15 Dec 2021  ·  doi:10.1021/acs.jcim.1c01050

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Daipayan Sarkar, Hyungro Lee, John W. Vant, Matteo Turilli, Josh V. Vermaas, Shantenu Jha, Abhishek Singharoy

Cold Spring Harbor Laboratory  ·  09 Dec 2021  ·  doi:10.1101/2021.12.07.471672

ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome

Alexander T. Baker, Ryan J. Boyd, Daipayan Sarkar, Alicia Teijeira-Crespo, Chun Kit Chan, …, Pierre J. Rizkallah, Taylor S. Cohen, Alan L. Parker, Abhishek Singharoy, Mitesh J. Borad

Science Advances  ·  03 Dec 2021  ·  doi:10.1126/sciadv.abl8213

High-throughput virtual laboratory for drug discovery using massive datasets

Jens Glaser, Josh V Vermaas, David M Rogers, Jeff Larkin, Scott LeGrand, …, Aaron Scheinberg, Andreas F Tillack, Mathialakan Thavappiragasam, Ada Sedova, Oscar Hernandez

The International Journal of High Performance Computing Applications  ·  23 Mar 2021  ·  doi:10.1177/10943420211001565

Supercomputing Pipelines Search for Therapeutics Against COVID-19

Josh Vincent Vermaas, Ada Sedova, Matthew B. Baker, Swen Boehm, David M. Rogers, Jeff Larkin, Jens Glaser, Micholas D. Smith, Oscar Hernandez, Jeremy C. Smith

Computing in Science & Engineering  ·  01 Jan 2021  ·  doi:10.1109/MCSE.2020.3036540

2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

A. Acharya, R. Agarwal, M. B. Baker, J. Baudry, D. Bhowmik, …, V. Q. Vuong, J. Yin, S. Yoo, M. Zahran, L. Zanetti-Polzi

Journal of Chemical Information and Modeling  ·  16 Dec 2020  ·  doi:10.1021/acs.jcim.0c01010

Data-guided Multi-Map variables for ensemble refinement of molecular movies

John W. Vant, Daipayan Sarkar, Ellen Streitwieser, Giacomo Fiorin, Robert Skeel, Josh V. Vermaas, Abhishek Singharoy

The Journal of Chemical Physics  ·  01 Dec 2020  ·  doi:10.1063/5.0022433

Molecular Lignin Solubility and Structure in Organic Solvents

Josh V. Vermaas, Michael F. Crowley, Gregg T. Beckham

ACS Sustainable Chemistry & Engineering  ·  24 Nov 2020  ·  doi:10.1021/acssuschemeng.0c07156

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer

Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, …, Andreas Koch, Stefano Forli, Oscar Hernandez, Jeremy C. Smith, Ada Sedova

Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics  ·  21 Sep 2020  ·  doi:10.1145/3388440.3412472

Mesoscale Reaction–Diffusion Phenomena Governing Lignin‐First Biomass Fractionation

Nicholas E. Thornburg, M. Brennan Pecha, David G. Brandner, Michelle L. Reed, Josh V. Vermaas, …, Thomas D. Foust, Bryon S. Donohoe, Yuriy Román‐Leshkov, Peter N. Ciesielski, Gregg T. Beckham

ChemSusChem  ·  08 May 2020  ·  doi:10.1002/cssc.202000558

Advances in Multiscale Modeling of Lignocellulosic Biomass

Peter N. Ciesielski, M. Brennan Pecha, Aaron M. Lattanzi, Vivek S. Bharadwaj, Meagan F. Crowley, Lintao Bu, Josh V. Vermaas, K. Xerxes Steirer, Michael F. Crowley

ACS Sustainable Chemistry & Engineering  ·  13 Feb 2020  ·  doi:10.1021/acssuschemeng.9b07415

2019

A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose

Josh V. Vermaas, Michael F. Crowley, Gregg T. Beckham

ACS Sustainable Chemistry & Engineering  ·  18 Nov 2019  ·  doi:10.1021/acssuschemeng.9b04648

The dissociation mechanism of processive cellulases

Josh V. Vermaas, Riin Kont, Gregg T. Beckham, Michael F. Crowley, Mikael Gudmundsson, Mats Sandgren, Jerry Ståhlberg, Priit Väljamäe, Brandon C. Knott

Proceedings of the National Academy of Sciences  ·  30 Oct 2019  ·  doi:10.1073/pnas.1913398116

Passive membrane transport of lignin-related compounds

Josh V. Vermaas, Richard A. Dixon, Fang Chen, Shawn D. Mansfield, Wout Boerjan, John Ralph, Michael F. Crowley, Gregg T. Beckham

Proceedings of the National Academy of Sciences  ·  28 Oct 2019  ·  doi:10.1073/pnas.1904643116

Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis

Michael J. Orella, Terry Z. H. Gani, Josh V. Vermaas, Michael L. Stone, Eric M. Anderson, Gregg T. Beckham, Fikile R. Brushett, Yuriy Román-Leshkov

ACS Sustainable Chemistry & Engineering  ·  24 Sep 2019  ·  doi:10.1021/acssuschemeng.9b03534

Activity and Thermostability of GH5 Endoglucanase Chimeras from Mesophilic and Thermophilic Parents.

Fei Zheng, Josh V Vermaas, Jie Zheng, Yuan Wang, Tao Tu, Xiaoyu Wang, Xiangming Xie, Bin Yao, Gregg T Beckham, Huiying Luo

Applied and environmental microbiology  ·  20 Feb 2019  ·  pmid:30552196

Systematic parameterization of lignin for the CHARMM force field

Josh V. Vermaas, Loukas Petridis, John Ralph, Michael F. Crowley, Gregg T. Beckham

Green Chemistry  ·  01 Jan 2019  ·  doi:10.1039/C8GC03209B

2018

Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder

Josh V. Vermaas, Lauren D. Dellon, Linda J. Broadbelt, Gregg T. Beckham, Michael F. Crowley

ACS Sustainable Chemistry & Engineering  ·  11 Dec 2018  ·  doi:10.1021/acssuschemeng.8b05665

Membrane Permeability of Terpenoids Explored with Molecular Simulation

Josh V. Vermaas, Gayle J. Bentley, Gregg T. Beckham, Michael F. Crowley

The Journal of Physical Chemistry B  ·  23 Oct 2018  ·  doi:10.1021/acs.jpcb.8b08688

Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE

Josh V. Vermaas, Susan B. Rempe, Emad Tajkhorshid

Proceedings of the National Academy of Sciences  ·  19 Jul 2018  ·  doi:10.1073/pnas.1722399115

2017

Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation

Josh V. Vermaas, Gregg T. Beckham, Michael F. Crowley

The Journal of Physical Chemistry B  ·  01 Nov 2017  ·  doi:10.1021/acs.jpcb.7b08233

Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.

Josh V Vermaas, Taras V Pogorelov, Emad Tajkhorshid

The journal of physical chemistry. B  ·  13 Mar 2017  ·  pmid:28241729

2016

Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail.

Josh V Vermaas, Emad Tajkhorshid

Biochemistry  ·  20 Dec 2016  ·  pmid:27997124

Computational Characterization of Molecular Mechanisms of Membrane Transporter Function

Noah Trebesch, Josh V. Vermaas, Emad Tajkhorshid

Computational Biophysics of Membrane Proteins  ·  05 Dec 2016  ·  doi:10.1039/9781782626695-00197

The cellular membrane as a mediator for small molecule interaction with membrane proteins

Christopher G. Mayne, Mark J. Arcario, Paween Mahinthichaichan, Javier L. Baylon, Josh V. Vermaas, Latifeh Navidpour, Po-Chao Wen, Sundarapandian Thangapandian, Emad Tajkhorshid

Biochimica et Biophysica Acta (BBA) - Biomembranes  ·  01 Oct 2016  ·  doi:10.1016/j.bbamem.2016.04.016

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo

Chang Sun, Alexander T Taguchi, Josh V Vermaas, Nathan J Beal, Patrick J O’Malley, Emad Tajkhorshid, Robert B Gennis, Sergei A Dikanov

Biochemistry  ·  28 Sep 2016  ·  pmid:27622672

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.

J V Vermaas, N Trebesch, C G Mayne, S Thangapandian, M Shekhar, …, M P Muller, E Shinn, Z Zhao, P-C Wen, E Tajkhorshid

Methods in enzymology  ·  11 Jul 2016  ·  pmid:27497175

Atomic-level description of protein–lipid interactions using an accelerated membrane model

Javier L. Baylon, Josh V. Vermaas, Melanie P. Muller, Mark J. Arcario, Taras V. Pogorelov, Emad Tajkhorshid

Biochimica et Biophysica Acta (BBA) - Biomembranes  ·  01 Jul 2016  ·  doi:10.1016/j.bbamem.2016.02.027

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer

Journal of Chemical Information and Modeling  ·  01 Jun 2016  ·  doi:10.1021/acs.jcim.6b00103

2015

Mechanism of lignin inhibition of enzymatic biomass deconstruction

Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy. C. Smith

Biotechnology for Biofuels  ·  01 Dec 2015  ·  doi:10.1186/s13068-015-0379-8

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

Yifei Qi, Xi Cheng, Jumin Lee, Josh V. Vermaas, Taras V. Pogorelov, Emad Tajkhorshid, Soohyung Park, Jeffery B. Klauda, Wonpil Im

Biophysical Journal  ·  01 Nov 2015  ·  doi:10.1016/j.bpj.2015.10.008

Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution

Josh V. Vermaas, Javier L. Baylon, Mark J. Arcario, Melanie P. Muller, Zhe Wu, Taras V. Pogorelov, Emad Tajkhorshid

The Journal of Membrane Biology  ·  22 May 2015  ·  doi:10.1007/s00232-015-9806-9

Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases

Josh V. Vermaas, Michael F. Crowley, Gregg T. Beckham, Christina M. Payne

The Journal of Physical Chemistry B  ·  02 Apr 2015  ·  doi:10.1021/acs.jpcb.5b00778

Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center ofRhodobacter sphaeroides

Josh V. Vermaas, Alexander T. Taguchi, Sergei A. Dikanov, Colin A. Wraight, Emad Tajkhorshid

Biochemistry  ·  23 Mar 2015  ·  doi:10.1021/acs.biochem.5b00033

Advances in Atomic-Level Simulations of Large-Scale Functional Motions of Membrane Transporters

Emad Tajkhorshid, Mahmoud Moradi, Jing Li, Po-Chao Wen, Sundar Thangapandian, Josh Vermaas

Biophysical Journal  ·  01 Jan 2015  ·  doi:10.1016/j.bpj.2014.11.2032

2014

Conformational heterogeneity of α -synuclein in membrane

Josh V. Vermaas, Emad Tajkhorshid

Biochimica et Biophysica Acta (BBA) - Biomembranes  ·  01 Dec 2014  ·  doi:10.1016/j.bbamem.2014.08.012

Partitioning of Amino Acids into a Model Membrane: Capturing the Interface

Taras V. Pogorelov, Josh V. Vermaas, Mark J. Arcario, Emad Tajkhorshid

The Journal of Physical Chemistry B  ·  30 Jan 2014  ·  doi:10.1021/jp4089113

Characterization of 2- and 3-Methoxy in Ubiquinone Binding and Redox Tuning within the Photosynthetic Reaction Center of Rhodobacter Sphaeroides

Josh V. Vermaas, Alexander T. Taguchi, Colin A. Wraight, Emad Tajkhorshid

Biophysical Journal  ·  01 Jan 2014  ·  doi:10.1016/j.bpj.2013.11.2096

2013

A Microscopic View of Phospholipid Insertion into Biological Membranes

Josh V. Vermaas, Emad Tajkhorshid

The Journal of Physical Chemistry B  ·  16 Dec 2013  ·  doi:10.1021/jp409854w