molecular
biological
physics
John Portman
Associate Professor
Physics
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Our research is in the general area of molecular biological physics. Conformational flexibility and dynamics of protein molecues is often the key connection between the structure of a protein and its biological function. We are developing analytical and computational approaches to understand the mechanisms controlling large-scale (main-chain) structural changes in proteins. Examples include protein folding, allostery, and conformational changes induced from interactions with molecular surfaces.

We use a variety of theoretical concepts from statistical mechanics of phase transitions, soft condensed matter physics, and physical chemistry. We aim to bridge the gap between analytical theory, simulation, and experimental measurements to understand structure, dynamics and function of biomolecules. For students, this effort provides truly interdisciplinary research experience at the interface between physics, chemistry, and biology.

Double-click on the image to see a prediction of the folding/unfolding route (lambda-repressor). The color of each residue represents the degree of order from red (delocalized density) to blue (localized density).

Selected Publications

  • Conformational flexibility and the mechanisms of allosteric transitions in topologically simlar proteins, Swarnendu Tripathi and John J. Portman, J. Chem. Phys. 135, 075104 (2011).
  • Inherrent flexibility determines the transition mechanisms of the EF-hands of Calmodulin, Swarnendu Tripathi and John J. Portman, Proc. Natl. Acad. Sci. USA 106, 2104--2109 (2009).
  • Capillarity-like growth of protein folding nuclei, Xianghong Qi and John J. Portman, Proc. Natl. Acad. Sci. USA 105, 11164--11169 (2008).
  • Inherent flexibility and protein function: the open/closed conformational transition of the N-terminal domain of calmodulin, Swarnendu Tripathi and John J. Portman, J. Chem. Phys. 128, 205104 (2008).
  • Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates, Xianghong Qi and John J. Portman, Proc. Natl. Acad. Sci. USA 104, 10841--10846 (2007).
  • Speeding Molecular Recognition by Using the Folding Funnel: The Fly-casting Mechanism', Benjamin Shoemaker, John J. Portman, and Peter G. Wolynes, Proc. Natl. Acad. Sci. USA 97, 8868--8873 (2000).
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John J. Portman,106 SRL, Kent State University, Kent, OH 44242-0001
Phone: (330) 672-9518Fax: (330) 672-2959
jportman@kent.edu