Physics of Proteins I: Structure, Dynamics & Evolution

FOCUS · MAR-B60 · ID: 3980491

Presentations

  • ORAL · Invited

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    Publication: Li, H. and Ma, A., "Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation", Nature Communications, vol. 16, 786 (2025).
    Ma, A. and Li, H., "Reaction coordinates are optimal channels of energy flow", Annual Review of Physical Chemistry, vol. 76, 153 (2025).
    Wu, S., Li, H. and Ma., A., "Exact reaction coordinates for flap opening in HIV-1 protease", PNAS, vol. 119, e2214906119 (2022).

    Presenters

    • Ao Ma

      • University of Illinois at Chicago
      • University of Illinois Chicago

    Authors

    • Ao Ma

      • University of Illinois at Chicago
      • University of Illinois Chicago

    • Huiyu Li

      • University of Illinois at Chicago

    • Kenneth K Tsui

      • University of Illinois at Chicago

    View abstract →

  • ORAL

    –

    Publication: Planned paper: Developing an experimental method for detection of proton transfer during protein function.

    Presenters

    • Aihua Xie

      • Oklahoma State University-Stillwater

    Authors

    • Aihua Xie

      • Oklahoma State University-Stillwater

    • Wouter D Hoff

      • Oklahoma State University-Stillwater

    • Mohammad Hadidi

      • Oklahoma State University

    • Rosalie Dohmen

      • Oklahoma State University

    • Amber D Dohmen

      • Oklahoma State University

    • Muluken Ergudo

      • Oklahoma State University

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  • ORAL · Invited

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    Publication: Matange K, Marland E, Frenkel-Pinter M, & Williams LD (2025) Biological polymers: Evolution, function, and significance. Acc Chem Res.
    Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV, & Williams LD (2021) Water and life: The medium is the message. J Mol Evol 1-10.
    Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, & Williams LD (2020) Root of the tree: The significance, evolution, and origins of the ribosome. Chem Rev 120: 4848-4878.
    Runnels CM, Lanier KA, Williams JK, Bowman JC, Petrov AS, Hud NV, & Williams LD (2018) Folding, assembly, and persistence: The essential nature and origins of biopolymers. J Mol Evol 86: 598-610.
    Bernier CR, Petrov AS, Kovacs NA, Penev PI, & Williams LD (2018) Translation: The universal structural core of life. Mol Biol Evol 35: 2065-2076.
    Lanier KA, Petrov AS, & Williams LD (2017) The central symbiosis of molecular biology: Molecules in mutualism. J Mol Evol 85: 8-13.
    Kovacs NA, Petrov AS, Lanier KA, & Williams LD (2017) Frozen in time: The history of proteins. Mol Biol Evol 34: 1252-1260.
    Petrov AS, Gulen B, Norris AM, Kovacs NA, Bernier CR, Lanier KA, Fox GE, Harvey SC, Wartell RM, Hud NV, & Williams LD (2015) History of the ribosome and the origin of translation. Proc Natl Acad Sci USA 112: 15396-15401.
    Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, & Williams LD (2014) Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci USA 111: 10251-10256.
    Hsiao C, Mohan S, Kalahar BK, & Williams LD (2009) Peeling the onion: Ribosomes are ancient molecular fossils. Mol Biol Evol 26: 2415-2425.

    Presenters

    • Loren D Williams

      • Georgia Tech

    Authors

    • Loren D Williams

      • Georgia Tech

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  • ORAL

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    Publication: A. Fakharzadeh, C. Goolsby, E. Tajkhorshid, and M. Moradi, "Thermodynamic and kinetic char- acterization of protein conformational dynamics within a Riemannian diffusion formalism." (Under review at J. Phys. Chem. A).
    A. Fakharzadeh, J. Losey, C. Goolsby, E. Tajkhorshid, and M. Moradi, "Along-the-path Markov
    models for state transition in membrane transporters." (Ready for submission).

    Presenters

    • Ashkan Fakharzadeh

      • UNIVERSITY OF ILLINOIS URBANA - CHAMPAIGN

    Authors

    • Ashkan Fakharzadeh

      • UNIVERSITY OF ILLINOIS URBANA - CHAMPAIGN

    • Mahmoud Moradi

      • University of Arkansas

    • Emad Tajkhorshid

      • UNIVERSITY OF ILLINOIS URBANA - CHAMPAIGN

    View abstract →

  • ORAL

    –

    Publication: H. Li, A. Ma, Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation. Nature Communications 16 (2025)

    Presenters

    • Huiyu Li

      • University of Illinois at Chicago

    Authors

    • Huiyu Li

      • University of Illinois at Chicago

    • Ao Ma

      • University of Illinois at Chicago
      • University of Illinois Chicago

    View abstract →