Invited Speaker Australian & New Zealand Society of Magnetic Resonance Conference 2017

Conformational dynamics in molecular recognition and catalysis (#4)

Arthur Palmer 1
  1. Columbia University, New York, NY, United States

NMR spectroscopy and molecular dynamics (MD) simulations are powerful approaches for probing aspects of conformational dynamics in biological macromolecules. Methods that can be utilized to characterize dynamics on picosecond-nanosecond and on microsecond-millisecond time scales will be illustrated by applications to the DNA-repair enzyme AlkB [Ergel, et al., 2014], the enzyme ribonuclease H [Stafford, et al., 2015], and the yeast transcription factor GCN4 [Gill and Palmer, 2015]. In the first example, NMR spin-relaxation measurements establish that the equilibrium distribution of ordered and disordered conformations of the nucleotide recognition element controls order of addition of substrates. In the second example, spin-relaxation measurements and MD simulations as a function of temperature for proteins from psychrotrophic, mesophilic, and thermophilic bacterial species characterize the coupling between conformational dynamics, stability, and function. In the third example, spin-relaxation measurements at five static magnetic fields and MD simulations lead to a two-step selected- and induced-fit mechanism of binding to DNA. Taken together, these cases illustrate the importance of rare, sparsely populated, conformational states in protein function.

 

  1. B. Ergel, M. L. Gill, L. Brown, B. Yu, A. G. Palmer, and J. F. Hunt, Protein dynamics control progression of the catalytic reaction cycle of AlkB, J. Biol. Chem. 289, 29584-29601 (2014).
  2. K. A. Stafford, N. Trbovic, J. A. Butterwick, R. Abel, R. A. Friesner, and A. G. Palmer, Conformational preferences underlying reduced activity of a thermophilic ribonuclease H, J. Mol. Biol. 427, 853–866 (2015).
  3. M. L. Gill, R. A. Byrd, and A. G. Palmer, Phys. Chem. Chem. Phys. 18, 5839-5849 (2015).