@article{Conformational:2830,
      recid = {2830},
      author = {Feng, Chi-Jui},
      title = {Protein Conformational Variation Studied by Amide I  Infrared Spectroscopy and Computational Spectroscopy},
      publisher = {University of Chicago},
      school = {Ph.D.},
      address = {2021-03},
      pages = {461},
      abstract = {Protein structure-function relationship has been rethought  over the past decades to account for conformational  variation and its functional role. Coupled-folding and  binding process in biomolecular recognition is a  manifestation of such conformational disorder and  heterogeneous conformational ensemble. The ensemble nature  and the coupled dynamics nature between protein-water  interactions, conformational fluctuations, and  folding/binding events require high structural and temporal  resolution, which create major experimental challenges. To  address these challenges, this thesis presents a combined  experimental and computational approach using  two-dimensional infrared (2D IR) spectroscopy and  computational spectroscopy. 2D IR spectroscopy offers  sub-picosecond temporal resolution to probe protein  structural variation. Site-specific structural information  can be achieved by introducing isotope-labeling on selected  amide groups, and computational spectroscopy that  translates protein structures into an IR spectrum.

To  validate this approach, peptide-water interactions are  studied on dialanine using 2D IR spectroscopy, and  computational IR spectra predicted from molecular dynamics  simulations. Amide I frequency fluctuation and vibrational  energy relaxation is found to have the common origin of  effective fluctuating forces due to water hydrogen bond  dynamics. A chemical exchange process is also observed  experimentally on the order of tens of ps, and is predicted  to be coupled peptide-water motions through computational  analysis.

The idea of estimating conformational ensemble  from isotope-labeled IR spectroscopy is tested on  trialanine, which is well-characterized for its  conformational variation. A Bayesian ensemble refinement  scheme is developed for direct characterization of  conformational ensemble against experimental IR  spectroscopy. Isotope-edited 2D IR spectroscopy is found to  provide a stringent constraint on the conformational  distribution, and it returns consistent ensembles across  different force fields and water models. The dominant  factor influencing the quality of the ensemble refinements  is the systematic frequency uncertainty from spectroscopic  maps, but it can be significantly reduced by incorporating  2D IR spectra in addition to the Fourier-transform IR  spectroscopy. This Bayesian ensemble refinement method with  IR spectroscopy provide an effective approach to determine  complex protein conformational ensemble.

One of the model  systems to understand coupled-folding and binding processes  is association of human insulin monomer. During  association, partially disordered B-chains from each  monomer form an inter-monomer β-sheet in a native dimer  crystal structure. However, the dimer conformational  characterization still needs investigation. Conformational  ensemble of insulin dimer is characterized using  site-specific isotope-edited 2D IR spectroscopy, Markov  State Models (MSMs), and amide I computational  spectroscopy. Isotope-edited IR spectroscopy indicates an  additional spectroscopic species other than the native  dimer, and the distribution of these species can be  influenced by tuning the ionic strength. The MSM predicted  this additional conformation states of twisted dimer that  exhibits a ~55° rotation of the native dimer interface,  resulting in shifting the β-sheet registry and reorganizing  its sidechain packing. Computational spectroscopy of the  twisted dimer consistently accounts for the additional  spectroscopic species. The presence of twisted  conformations suggests a potential kinetic intermediate  along the homodimer association and/or multi-pathway  nature. This study provides additional insight on the  conformational distribution of dimer and establishes a  refined molecular picture of describing coupled folding and  binding process in insulin monomer association.},
      url = {http://knowledge.uchicago.edu/record/2830},
      doi = {https://doi.org/10.6082/uchicago.2830},
}