The mechanism by which a protein folds to its native, biologically active structure is one of the major unsolved problems of modern structural biology, with important practical consequences for rational protein design, protein structure prediction and folding related disease states. The central objective of this proposal is to characterize the molecular dynamics and mechanisms of early events in protein folding. Fundamentally new approaches to the rapid initiation and characterization of folding reactions are required to fulfill this objective. The viability of such an approach has been established in experiments using a laser-induced temperature jump and time-resolved infrared spectroscopy. Thus, for the first time, it is possible to initiate and follow the kinetics of protein folding or unfolding on a time scale of 50 ps,or some 107 times faster than conventional (rapid mixing) kinetics studies. The organizing question of this work is what are the dynamics and mechanisms of secondary structure formation in an isolated peptide and in a protein, and what is the role of secondary structure formation in guiding the folding process and stabilizing early intermediates. Specifically, new methods for the rapid initiation of protein folding will be developed, using a laser-induced, impulsive macroscopic perturbation of temperature of pH. Time-resolved infrared spectroscopy will be used as a structure specific probe of the dynamics of protein folding intermediates. The amide and sidechain vibrations of peptides and proteins, together with isotopic labeling will be used to identify specific structures in static and time-resolved infrared spectra. A hierarchy of problems will be investigated. Starting with a series of de novo peptides, the dynamics and mechanism of helix, turn and sheet formation will be investigated. The rate of nucleation and propagation, and the role of local interactions (electrostatic, salt bridges, end capping) will be explored. Second, the dynamics and mechanism of folding of fragments of the fast folding core of apomyoglobin will be explored. The influence of local interactions is again the focus, particularly the formation of reverse turns and helices, and their relative roles in the folding reactions of small peptides. Finally, the folding dynamics of two proteins, apomyoglobin (globular helical protein) and CspA (fast-folding beta-barrel) will be investigated. A key focus of this work is to establish the role of local and nonlocal (intrachain) interactions in shaping the energy landscape, hence the dynamics of protein folding.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular and Cellular Biophysics Study Section (BBCA)
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Wehrle, Janna P
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Los Alamos National Lab
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Los Alamos
United States
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Dyer, R Brian; Eller, Micah W (2018) Dynamics of hemagglutinin-mediated membrane fusion. Proc Natl Acad Sci U S A 115:8655-8657
Nagarajan, Sureshbabu; Xiao, Shifeng; Raleigh, Daniel P et al. (2018) Heterogeneity in the Folding of Villin Headpiece Subdomain HP36. J Phys Chem B :
Zhao, Jing; Su, Hanquan; Vansuch, Gregory E et al. (2018) Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase Transition. ACS Nano :
Siaw, Hew Ming Helen; Raghunath, Gokul; Dyer, R Brian (2018) Peripheral Protein Unfolding Drives Membrane Bending. Langmuir 34:8400-8407
Su, Hanquan; Liu, Zheng; Liu, Yang et al. (2018) Light-Responsive Polymer Particles as Force Clamps for the Mechanical Unfolding of Target Molecules. Nano Lett 18:2630-2636
Reid, Keon A; Davis, Caitlin M; Dyer, R Brian et al. (2018) Binding, folding and insertion of a ?-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing. Biochim Biophys Acta Biomembr 1860:792-800
Davis, Caitlin M; Reddish, Michael J; Dyer, R Brian (2017) Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics. Spectrochim Acta A Mol Biomol Spectrosc 178:185-191
Zanetti-Polzi, Laura; Davis, Caitlin M; Gruebele, Martin et al. (2017) Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett 591:3265-3275
Jeong, Ban-Seok; Dyer, R Brian (2017) Proton Transport Mechanism of M2 Proton Channel Studied by Laser-Induced pH Jump. J Am Chem Soc 139:6621-6628
Davis, Caitlin M; Dyer, R Brian (2016) The Role of Electrostatic Interactions in Folding of ?-Proteins. J Am Chem Soc 138:1456-64

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