The Ultrafast Laser Resource at the University of Pennsylvania is founding the technoogies for multidimensional infrared spectroscopy in biological and biomedical research including drug design. The components of the laboratory are an integrated multifaceted attack on advancing two dimensional infrared methods. Each TR&D is dynamically evolving at the cutting edge of infrared technology, they are mutually supportive. The utility of 2D IR in biomedical applications is increasing substantially. Just within the last year a protein structure has been determined by 2D IR. TR&D's #1 focuses on phototriggered states, the technology combines optical and infrared methods to obtain 2D IR structural-time dependent information during nonequilibrium dynamical processes. The TR&D #2 concerns dual frequency 2D IR which combines into a two dimensional spectrum the excitation of two modes having widely separated frequencies of proteins and proton channels. TR&D#3 involves a specialization on structure determination, to build on previous studies using 2D IR, by improvements in the methodology that are specifically geared towards the equilibrium dynamics of structures of proteins on time scales that have not been achieved by other structural methods. Six DBF's are included: (1)The M2 proton channel of the Influenza A virus: properties of channel water (W.F. DeGrado, UCSF).(2)The structure and dynamics of amyloid A40 fibrils and their formation kinetics (P. Abelson, Upend) (3) Phototriggering of conformational change (A.B. Smith, Upend)) (4) Pushing the Structural Resolution Limit of Linear and Nonlinear Infrared Spectroscopies (F. Gai, Upend) (5) Radical pair dynamics by optically triggered - IR probe spectroscopy (S. Vinogradov, Upend) (6) Spectroscopy and dynamics of HlV-1 RT/inhibitor complexes probed by 2D IR methods and MD simulations (E. Arnold, Rutgers). The proposal also includes seven Collaborative and Service projects on (1) Nitrile and Azide probes (Brewer) (2) Protonated histidines (Londergan) (3) Amyloid fluorescence (Petersson)(4) Blood coagulation (Knshnaswamy) (5) Kinases models (Sarkar)(6)Amyloid kinetics (Dai) (7) Oxygen microscopy (Vinogradov), The Resource provides training for users, and the work is widely disseminated.

Public Health Relevance

The resource employs driving biomedical projects, collaborative and service projects to explore and advance new methods of structure determination with ultrafast infared pulses which are applied in these research projects to expose mechanisms of action of the influenza A virus and HIV AIDS drugs acting on reverse transcriptase, the folding and misfolding of amyloid proteins and of dysregulaed blood coagulation

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1-BCMB-N (40))
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Friedman, Fred K
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University of Pennsylvania
Schools of Arts and Sciences
United States
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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
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
Eisenberg, Azaria Solomon; Juszczak, Laura J (2014) The broken ring: reduced aromaticity in Lys-Trp cations and high pH tautomer correlates with lower quantum yield and shorter lifetimes. J Phys Chem B 118:7059-69
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
Courter, Joel R; Abdo, Mohannad; Brown, Stephen P et al. (2014) The design and synthesis of alanine-rich *-helical peptides constrained by an S,S-tetrazine photochemical trigger: a fragment union approach. J Org Chem 79:759-68
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
Chuntonov, Lev; Kumar, Revati; Kuroda, Daniel G (2014) Non-linear infrared spectroscopy of the water bending mode: direct experimental evidence of hydration shell reorganization? Phys Chem Chem Phys 16:13172-81
Chuntonov, Lev; Ma, Jianqiang (2013) Quantum process tomography quantifies coherence transfer dynamics in vibrational exciton. J Phys Chem B 117:13631-8
Capraro, Benjamin R; Shi, Zheng; Wu, Tingting et al. (2013) Kinetics of endophilin N-BAR domain dimerization and membrane interactions. J Biol Chem 288:12533-43
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

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