A residue level visualization of how protein structures change with time for transmembrane (TM) helices, fast folding proteins and elements of secondary structure will be found by two dimensional infrared spectroscopy (2D IR) a new, powerful method of structural biology. Isotopic labeling of peptides and proteins enhances the spatial resolution of 2D IR and extends it to larger peptides. Weak bonds involved at the helix-helix interfaces of TM sections of Glycophorin A will be accessed to obtain the motions of groups in the interface regions and discover how they stabilize helix-helix interactions in TM proteins. 2D IR exposes lipid fluctuations in terms of spatial arrangements across the membrane. 2D IR of hydrophobic effects, polarity, hydrogen bonding and other weak interactions between buried residues enlighten the mechanisms and structural basis of helix association. The 2D IR with multiple IR frequencies, accesses the hydrophobic interface, correlations between fluctuations at different spatial locations and the N-H/N-D exchange in transmembrane helices. Protein subdomains that fold independently are important tools for solving the folding problem. 2D IR on fast non-exponential folders will permit access to the real time evolution of secondary structure and challenge all atom molecular dynamics of the villin headpiece from the actin-bundling protein villin, which is implicated in the epithelium of the gut and kidney. The folding pathway will be accessed by 2D IR of isotope labeled helices and hydrophobic core. On-pathway intermediates in the redox protein, cytochrome-c, will be examined with novel temperature induced pH jumps. A description of the folding of designed peptides will be sought by 2D IR to visualize how they assemble and strengthen relations to theory. The research involves membrane proteins which are vital components of the cell physiology: they include cell-surface receptors, ion channels, transporters and redox proteins. Integral membrane proteins account for nearly one-quarter of all coding sequences in higher organisms, and more than half of all commercial drugs target this class of proteins. Despite this, study of their 3D structures and their dynamics remains limited. Protein folding is highly relevant because it is a key step in the conversion of genetic information into biological function of all types and therefore its control is an essential part of understanding human health. *

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM012592-45S1
Application #
7932592
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Smith, Ward
Project Start
2009-09-30
Project End
2010-08-31
Budget Start
2009-09-30
Budget End
2010-08-31
Support Year
45
Fiscal Year
2009
Total Cost
$115,250
Indirect Cost
Name
University of Pennsylvania
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Chuntonov, Lev; Pazos, Ileana M; Ma, Jianqiang et al. (2015) Kinetics of exchange between zero-, one-, and two-hydrogen-bonded states of methyl and ethyl acetate in methanol. J Phys Chem B 119:4512-20
Ghosh, Ayanjeet; Tucker, Matthew J; Gai, Feng (2014) 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations. J Phys Chem B 118:7799-805
Ma, Jianqiang; Pazos, Ileana M; Gai, Feng (2014) Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Proc Natl Acad Sci U S A 111:8476-81
Ghosh, Ayanjeet; Wang, Jun; Moroz, Yurii S et al. (2014) 2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel. J Chem Phys 140:235105
Pazos, Ileana M; Ghosh, Ayanjeet; Tucker, Matthew J et al. (2014) Ester carbonyl vibration as a sensitive probe of protein local electric field. Angew Chem Int Ed Engl 53:6080-4
Ma, Jianqiang; Komatsu, Hiroaki; Kim, Yung Sam et al. (2013) Intrinsic structural heterogeneity and long-term maturation of amyloid ? peptide fibrils. ACS Chem Neurosci 4:1236-43
Singh, Prabhat K; Kuroda, Daniel G; Hochstrasser, Robin M (2013) An ion's perspective on the molecular motions of nanoconfined water: a two-dimensional infrared spectroscopy study. J Phys Chem B 117:9775-84
Kuroda, Daniel G; Abdo, Mohannad; Chuntonov, Lev et al. (2013) Vibrational dynamics of a non-degenerate ultrafast rotor: the (C12,C13)-oxalate ion. J Chem Phys 139:164514
Kuroda, Daniel G; Bauman, Joseph D; Challa, J Reddy et al. (2013) Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nat Chem 5:174-81
Chuntonov, Lev; Kuroda, Daniel G; Ghosh, Ayanjeet et al. (2013) Quantum Beats and Coherence Decay in Degenerate States Split by Solvation. J Phys Chem Lett 4:1866-1871

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