Noah Trebesch

2023 CV • Google Scholar • LinkedIn

Postdoctoral Research Associate
Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
3151 Beckman Institute, 405 N Matthews Ave
Urbana, IL 61801

Education

University of Illinois at Urbana-Champaign, Center for Biophysics and Quantitative Biology (Urbana, IL)

PhD in Biophysics and Computational Biology - December, 2023

University of Minnesota - Twin Cities, College of Science and Engineering (Minneapolis, MN)

BS in Physics (Biological Physics Emphasis) - May, 2014
BS in Computer Science (Computational Science Emphasis) - May, 2014

Research Interests

Structural Elucidation and Thermodynamic Characterization of the Mechanisms of Transporters

Current transporters include NaCT, VcINDY, and LaINDY.
Uses nonequilibrium driven molecular dynamics, molecular dynamics flexible fitting (MDFF), string method with swarms of trajectories (SMwST), bias-exchange umbrella sampling (BEUS), and other advanced computational techniques.
Structural modeling and bioinformatics techniques also utilized.
Provides key insight to biomedical researchers developing drugs targeting transporters and synthetic bioengineers hoping to develop custom biomachines.

Atomistic Modeling, Visualization, and Simulation of Cell-Scale Membrane Structures

Capabilities encapsulated in xMAS (Experimentally-Derived Membrane of Arbitrary Shape) Builder.
Analyzes 3D meshes derived from techniques like electron microscopy to determine placement, orientation, and number of lipid molecules.
Optimizes lipid placement using an MD-based technique, builds atomistic model using a set of lipid conformation libraries, and eliminates complex lipid clashes using an energy minimization simulation technique.
Current application is a Terasaki ramp, a structural motif from endoplasmic reticula with a complex helicoidal structure like that of a parking ramp.
Models allow the interplay between atomic-scale biochemistry and cell-scale biophysics to be probed for the first time.

Presentation Recordings

N. Trebesch, D. B. Sauer, D.-N. Wang, and E. Tajkhorshid. "Mechanistic Insights from Molecular Dynamics Simulations of Large-Scale Conformational Transitions in the INDY Transport Cycle" Biophysical Society 65th Annual Meeting. Virtual (22 Feb 2021).

N. Trebesch and E. Tajkhorshid. "Incorporating Proteins into Geometrically Complex, Cell-Scale Membrane Models." Blue Waters Symposium 2019. Sunriver, OR (5 Jun 2019).

N. Trebesch and E. Tajkhorshid. "Simulation of Geometrically Accurate, Multibillion Atom Cellular Membrane Structures." Blue Waters Symposium 2018. Sunriver, OR (6 Jun 2018).

Publications

(*Equal Contribution)

University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology (Urbana, IL)

N. Trebesch and E. Tajkhorshid. "Structure Reveals Homology in Elevator Transporters." bioRxiv. (2023).
A. Trifan*, D. Gorgun*, M. Salim*, Z. Li*, A. Brace*, M. Zvyagin*, H. Ma*, A. Clyde, D. Clark, D. J. Hardy, T. Burnley, L. Huang, J. McCalpin, M. Emani, H. Yoo, J. Yin, A. Tsaris, V. Subbiah, T. Raza, J. Liu, N. Trebesch, G. Wells, V. Mysore, T. Gibbs, J. Phillips, S. C. Chennubhotla, I. Foster, R. Stevens, A. Anandkumar, V. Vishwanath, J. E. Stone, E. Tajkhorshid, S. A. Harris, and A. Ramanathan. "Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action." International Journal of High-Performance Computing Applications. 36:5-6, 603-623 (2022).
D. B. Sauer, N. Trebesch, J. J. Marden, N. Cocco, J. Song, A. Koide, S. Koide, E. Tajkhorshid, and D.-N. Wang. "Structural basis for the reaction cycle of DASS dicarboxylate transporters." eLife. 9, e61350 (2020).
T. Jiang, P.-C. Wen, N. Trebesch, Z. Zhao, S. Pant, K. Kapoor, M. Shekhar, and E. Tajkhorshid. "Computational Dissection of Membrane Transport at a Microscopic Level." Trends in Biochemical Sciences. 45:3, 202-216 (2020).
P.-C. Wen*, P. Mahinthichaichan*, N. Trebesch, T. Jiang, Z. Zhao, E. Shinn, Y. Wang, M. Shekhar, K. Kapoor, C. K. Chan, and E. Tajkhorshid. "Microscopic View of Lipids and Their Diverse Biological Functions." Current Opinion in Structural Biology. 51, 177-186 (2018).
N. Trebesch, J. V. Vermaas, and E. Tajkhorshid. "Computational Characterization of Molecular Mechanisms of Membrane Transporter Function." Computational Biophysics of Membrane Proteins. C. Domene, Ed. 197-236 (Royal Society of Chemistry, Cambridge, 2016).
J. V. Vermaas, N. Trebesch, C. G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J. L. Baylon, T. Jiang, Y. Wang, M. P. Muller, E. Shinn, Z. Zhao, P.-C. Wen, and E. Tajkhorshid. "Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation." Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B. G. E. Voth, Ed. 578:16 (2016).