The formation and deposition of amyloid fibrils is associated with more than 20 neurodegenerative diseases. These include Alzheimer's, Parkinson's, Huntington's diseases, and the transmissible spongiform encephalopathies and type II diabetes. Oligomeric or other prefibrillar precursors of the fibrils are believed to be the main toxic species, but the mechanism of cell and tissue damage in amyloid-related diseases is not well understood. Improvement of our knowledge of the structure, kinetics of amyloidogenic polypeptides, and of their toxicity is essential for the development of effective treatments of amyloid disorders. Coherent multidimensional optical techniques provide novel probes into the fibril fluctuating structure through the response of molecular vibrational and electronic motions to sequences of carefully timed and shaped femtosecond laser pulses ranging from the infrared to the ultraviolet. Simulation techniques aimed at the design and interpretation of these multidimensional optical signals will be developed. Chirality-induced signals obtained by optimizing the pulse polarization configurations and shapes enhance the resolution and reveal fine details. Cross-peak patterns between side-chain vibrations or electronic excitations of aromatic side-chains with the protein backbone protein/membrane interfaces will be predicted in two-dimensional (2D) UV. Strategies for disentangling multidimensional spectra, enhancing the resolution, and amplifying desired features will be developed. The optical response will be used to characterize small oligomers and their kinetics in the formation of fibrils. Discrimination by their size and structure is of fundamental importance for understanding the molecular factors that affect their formation. It has been suggested that the interactions of amyloidogenic polypeptides with the cell membrane can accelerate fibril formation and are involved in the toxicity of oligomers or protofibrils. Amyloid peptides aggregate on the lipid surface penetrate into membranes and alter their permeability, which may contribute to cell damage. The nonlinear optical probes developed in this program can directly monitor how the formation of fibrils on a membrane damages the bilayer's integrity. Interface-specific even-order optical techniques will be designed to study aggregates of amyloidogenic polypeptides on membranes and identify spectroscopic signatures of their toxicity.

Public Health Relevance

The structure, kinetics, and aggregation mechanism of misfolded proteins which form amyloid fibrils and are associated with several human diseases will be investigated through their response to sequences of ultrashort infrared and UV optical pulses. Surface specific technique will be applied for probing the toxicity of fibrils on membranes. Simulation techniques for probing the binding, fluctuations, and motions of biomolecular complexes will be developed.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Smith, Ward
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Irvine
Schools of Arts and Sciences
United States
Zip Code
Zhang, Yu; Hua, Weijie; Bennett, Kochise et al. (2016) Nonlinear Spectroscopy of Core and Valence Excitations Using Short X-Ray Pulses: Simulation Challenges. Top Curr Chem 368:273-345
Batignani, G; Fumero, G; Mukamel, S et al. (2015) Energy flow between spectral components in 2D broadband stimulated Raman spectroscopy. Phys Chem Chem Phys 17:10454-61
Agarwalla, Bijay Kumar; Ando, Hideo; Dorfman, Konstantin E et al. (2015) Stochastic Liouville equations for femtosecond stimulated Raman spectroscopy. J Chem Phys 142:024115
Zhang, Yu; Biggs, Jason D; Mukamel, Shaul (2015) Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X-ray Spectroscopy: A Simulation Study. Chemphyschem 16:2006-14
Bennett, Kochise; Kowalewski, Markus; Mukamel, Shaul (2015) Probing electronic and vibrational dynamics in molecules by time-resolved photoelectron, Auger-electron, and X-ray photon scattering spectroscopy. Faraday Discuss 177:405-28
Nenov, Artur; Segarra-Martí, Javier; Giussani, Angelo et al. (2015) Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations. Faraday Discuss 177:345-62
Saurabh, Prasoon; Mukamel, Shaul (2014) Communication: atomic force detection of single-molecule nonlinear optical vibrational spectroscopy. J Chem Phys 140:161107
Dorfman, Konstantin E; Mukamel, Shaul (2014) Multidimensional spectroscopy with entangled light: loop vs ladder delay scanning protocols. New J Phys 16:
Zhang, Yu; Biggs, Jason D; Hua, Weijie et al. (2014) Three-dimensional attosecond resonant stimulated X-ray Raman spectroscopy of electronic excitations in core-ionized glycine. Phys Chem Chem Phys 16:24323-31
Zhang, Yu; Biggs, Jason D; Mukamel, Shaul (2014) Understanding Excitation Energy Transfer in Metalloporphyrin Heterodimers with Different Linkers, Bonding Structures and Geometries through Stimulated X-Ray Raman Spectroscopy. J Mod Opt 61:558-567

Showing the most recent 10 out of 140 publications