Joshua Vermaas

  • Program Years: 2011-2016
  • Academic Institution: University of Illinois at Urbana-Champaign
  • Field of Study: Biophysics
  • Academic Advisor: Emad Tajkhorshid
  • Practicum(s):
    National Renewable Energy Laboratory (2012)
    Oak Ridge National Laboratory (2014)
  • Degree(s):
    Ph.D. Biophysics, University of Illinois at Urbana-Champaign, 2016
    B.S. Computational Mathemathics, B.S. Biochemistry, and B.S. Physics, Arizona State University, 2010

Current Status

  • Research Area: Biophysics
  • Contact Information: vermaasjv@ornl.gov

Publications

Vermaas, J. V.; Crowley, M. F.; Beckham, G. T. A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose. ACS Sustain. Chem. Eng. 2019, 7, 19570–19583, DOI: 10.1021/acssuschemeng.9b04648.

Orella, M. J.; Gani, T. Z. H.; Vermaas, J. V.; Stone, M. L.; Anderson, E. M.; Beckham, G. T.; Brushett, F. R.; Román-Leshkov, Y. Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis. ACS Sustain. Chem. Eng. 2019, 7, 18313–18322, DOI: 10.1021/acssuschemeng.9b03534.

Vermaas, J. V.; Dixon, R. A.; Chen, F.; Mansfield, S. D.; Boerjan, W.; Ralph, J.; Crowley, M. F.; Beckham, G. T. Passive Membrane Transport of Lignin-Related Compounds. Proc. Natl. Acad. Sci. 2019, 116, 23117–23123, DOI: 10.1073/pnas.1904643116.

Vermaas, J. V.; Kont, R.; Beckham, G. T.; Crowley, M. F.; Gudmundsson, M.; Sandgren, M.; Ståhlberg, J.; Väljamäe, P.; Knott, B. C. The Dissociation Mechanism of Processive Cellulases. Proc. Natl. Acad. Sci. 2019, 116, 23061–23067, DOI: 10.1073/pnas.1913398116.

Vermaas, J. V.; Dellon, L. D.; Broadbelt, L. J.; Beckham, G. T.; Crowley, M. F. Automated Transformation of Lignin Topologies Into Atomic Structures With LigninBuilder. ACS Sustain. Chem. Eng. 2019, 7, 3443–3453, DOI: 10.1021/acssuschemeng.8b05665.

Zheng, F.; Vermaas, J. V.; Zheng, J.; Wang, Y.; Tu, T.; Wang, X.; Xie, X.; Yao, B.; Beckham, G. T.; Luo, H. Activity and Thermostability of GH5 Endoglucanase Chimeras From Mesophilic and Thermophilic Parents. Appl. Environ. Microbiol. 2019, 85, e02079–e02018, DOI: 10.1128/AEM.02079-18.

Vermaas, J. V.; Petridis, L.; Ralph, J.; Crowley, M. F.; Beckham, G. T. Systematic Parameterization of Lignin for the CHARMM Force Field. Green Chem. 2019, 21, 109–122, DOI:10.1039/C8GC03209B.

Vermaas, J. V.; Bentley, G. J.; Beckham, G. T.; Crowley, M. F. Membrane Permeability of Terpenoids Explored With Molecular Simulation. J. Phys. Chem. B 2018, 122, 10349–10361, DOI: 10.1021/acs.jpcb.8b08688.

Vermaas, J. V.; Rempe, S. B.; Tajkhorshid, E. Electrostatic Lock in the Transport Cycle of the Multidrug Resistance Transporter EmrE. Proc. Natl. Acad. Sci. 2018, 115, E7502– E7511, DOI: 10.1073/pnas.1722399115.

Vermaas, J. V.; Beckham, G. T.; Crowley, M. F. Membrane Permeability of Fatty Acyl Compounds Studied via Molecular Simulation. J. Phys. Chem. B 2017, 121, 11311–11324, DOI: 10.1021/acs.jpcb.7b08233.

Vermaas, J. V.; Pogorelov, T. V.; Tajkhorshid, E. Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems Through Customized in Silico Solvents. J. Phys. Chem. B 2017, 121, 3764–3776, DOI: 10.1021/acs.jpcb.6b11378.

Vermaas, J. V.; Tajkhorshid, E. Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail. Biochemistry 2017, 56, 281–293, DOI: 10.1021/acs.biochem.6b00468.

Mayne, C. G.; Arcario, M. J.; Mahinthichaichan, P.; Baylon, J. L.; Vermaas, J. V.; Navidpour, L.; Wen, P.-C.; Thangapandian, S.; Tajkhorshid, E. The Cellular Membrane as a Mediator for Small Molecule Interaction With Membrane Proteins. Biochim. Biophys. Acta - Biomembr. 2016, 1858, 2290–2304, DOI: 10.1016/j.bbamem.2016.04.016.

Sun, C.; Taguchi, A. T.; Vermaas, J. V.; Beal, N. J.; O’Malley, P. J.; Tajkhorshid, E.; Gennis, R. B.; Dikanov, S. A. Q-Band Electron-Nuclear Double Resonance Reveals Out-Of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 From Escherichia coli. Biochemistry 2016, 55, 5714–5725, DOI: 10.1021/acs.biochem.6b00669.

Baylon, J. L.; Vermaas, J. V.; Muller, M. P.; Arcario, M. J.; Pogorelov, T. V.; Tajkhorshid, E. Atomic-Level Description of Protein–Lipid Interactions Using an Accelerated Membrane Model. Biochim. Biophys. Acta - Biomembr. 2016, 1858, 1573–1583, DOI: 10.1016/j.bbamem.2016.02.027.

Vermaas, J. V.; Hardy, D. J.; Stone, J. E.; Tajkhorshid, E.; Kohlmeyer, A. TopoGromacs: Automated Topology Conversion From CHARMM to GROMACS Within VMD. J. Chem. Inf. Model. 2016, 56, 1112–1116, DOI: 10.1021/acs.jcim.6b00103.

Trebesch, N.; Vermaas, J. V.; Tajkhorshid, E. In Comput. Biophys. Membr. Proteins, Domene, C., Ed.; Royal Society of Chemistry: Cambridge, 2016; Chapter 7, pp 197–236, DOI: 10.1039/9781782626695-00197.

Vermaas, J.; Trebesch, N.; Mayne, C.; Thangapandian, S.; Shekhar, M.; Mahinthichaichan, P.; Baylon, J.; Jiang, T.; Wang, Y.; Muller, M.; Shinn, E.; Zhao, Z.; Wen, P.-C.; Tajkhorshid, E. In Methods Enzymol. 2016, pp 373–428, DOI: 10.1016/bs.mie.2016.05.042.

Vermaas, J. V.; Petridis, L.; Qi, X.; Schulz, R.; Lindner, B.; Smith, J. C. Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction. Biotechnol. Biofuels 2015, 8, 217, DOI: 10.1186/s13068-015-0379-8.

Qi, Y.; Cheng, X.; Lee, J.; Vermaas, J. V.; Pogorelov, T. V.; Tajkhorshid, E.; Park, S.; Klauda, J. B.; Im, W. CHARMM-GUI HMMM Builder for Membrane Simulations With the Highly Mobile Membrane-Mimetic Model. Biophys. J. 2015, 109, 2012–2022, DOI: 10.1016/j.bpj.2015.10.008.

Vermaas, J. V.; Baylon, J. L.; Arcario, M. J.; Muller, M. P.; Wu, Z.; Pogorelov, T. V.; Tajkhorshid, E. Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution. J. Membr. Biol. 2015, 248, 563–582, DOI: 10.1007/s00232-015-9806-9.

Vermaas, J. V.; Crowley, M. F.; Beckham, G. T.; Payne, C. M. Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases. J. Phys. Chem. B 2015, 119, 6129–6143, DOI: 10.1021/acs.jpcb.5b00778.

Vermaas, J. V.; Taguchi, A. T.; Dikanov, S. A.; Wraight, C. A.; Tajkhorshid, E. Redox Potential Tuning Through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter Sphaeroides. Biochemistry 2015, 54, 2104–2116, DOI: 10.1021/acs.biochem.5b00033.

Vermaas, J. V.; Tajkhorshid, E. Conformational Heterogeneity of α-Synuclein in Membrane. Biochim. Biophys. Acta - Biomembr. 2014, 1838, 3107–3117, DOI: 10.1016/j.bbamem.2014.08.012.

Pogorelov, T. V.; Vermaas, J. V.; Arcario, M. J.; Tajkhorshid, E. Partitioning of Amino Acids Into a Model Membrane: Capturing the Interface. J. Phys. Chem. B 2014, 118, 1481–1492, DOI: 10.1021/jp4089113.

Vermaas, J. V.; Tajkhorshid, E. A Microscopic View of Phospholipid Insertion Into Biological Membranes. J. Phys. Chem. B 2014, 118, 1754–1764, DOI: 10.1021/jp409854w.

Chamberlin, R. V.; Vermaas, J. V.; Wolf, G. H. Beyond the Boltzmann Factor for Corrections to Scaling in Ferromagnetic Materials and Critical Fluids. Eur. Phys. J. B 2009, 71, 1–6, DOI: 10.1140/epjb/e2009-00278-0.

Awards

Outstanding Honors Student Award, ASU Physics, 2010
Therald Moeller Award, ASU Chemistry & Biochemistry, 2009
Leroy Eyring Award, ASU Chemistry & Biochemistry, 2010
NIH Training Grant Fellowship, NIH, 2010
DOE CSGF Fellow 2011-2016
Sandia National Laboratories Campus Executive Program Fellow, 2014-2016
Director's Postdoctoral Fellowship, NREL, 2016
Wiley Computing in Chemistry Outstanding Postdoc Award, ACS, 2018