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The long-term goal of research in the Komives lab is to understand the parameters that govern protein-protein recognition and the mechanisms by which these interactions contribute to biological function. The relative importance of factors such as hydrophobic effects, electrostatic interactions and dynamics are being defined for several different interactions. These parameters are explored by a combination of molecular biological techniques, protein chemistry, surface plasmon resonance, multidimensional NMR, and mass spectrometry. One project aims to discover how thrombomodulin (TM) converts the pro-coagulant activity of thrombin to anti-coagulant activity. The thrombin-TM interaction involves diffusion-controlled association that is highly electrostatically steered. The binding has no favorable enthalpy change, but is instead driven by entropy. In collaboration with the McCammon group, we have obtained evidence from Accelerated Molecular Dynamics that the TM binding site is dynamically coupled to motions at the thrombin active site. We recently were able to obtain beautiful NMR spectra for thrombin, and are now characterizing its dynamics.
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biorxiv(2024)
Daniel J. Brogan,Elena Dalla Benetta, Tianqi Wang,Calvin P. Lin, Fangying Chen, Harry Li, Claire Lin,Elizabeth A. Komives,Omar S. Akbari
biorxiv(2024)
Matthew Mealka, Nicole A Sierra,Diego Avellaneda Matteo,Elene Albekioni, Rachel Khoury, Timothy Mai, Brittany M Conley,Nalani J Coleman, Kaitlyn A Sabo,Elizabeth A Komives,Andrey A Bobkov,Andrew L Cooksy,
Nature communicationsno. 1 (2024): 3785-3785
PROTEIN SCIENCEno. 12 (2023)
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Journal of Biological Chemistryno. 3 (2023): S299-S300
NATURE COMMUNICATIONSno. 1 (2023)
Methods (San Diego, Calif.) (2023): 18-25
Biochemical Society transactionsno. 6 (2023): 2085-2092
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