@article {276, title = {Blue Shift of a Molecular Crystal Phonon at the Solid to Liquid Phase Transition}, journal = {Bulletin of the American Physical Society}, volume = {2019}, year = {2019}, author = {Davie, Alex and Vandrevala, Farah and Deng, Yanting and George, D. and Sylvester, Eric D. and Korter, T. and Einarsson, E. and Benedict, Jason B. and Markelz, Andrea} } @proceedings {182, title = {Terahertz Light Fingerprints Biomolecular Dynamics}, year = {2018}, pages = {SW3D. 5}, publisher = {Optical Society of America}, doi = {https://doi.org/10.1364/CLEO_SI.2018.SW3D.5}, author = {Deng, Yanting and Xu, Mengyang and Niessen, Katherine A and George, Deepu Koshy and Markelz, Andrea G} } @article {254, title = {Importance of Protein Vibration Directionality on Function}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
1
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
}, month = {Feb 3}, pages = {353A-353A}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.1916}, author = {Niessen, Katherine A. and Xu, Mengyang and Deng, Yanting and Snell, Edward H. and Markelz, Andrea G.} } @conference {546, title = {Direct Measurements of the Long-Range Collective Vibrations of Photoactive Yellow Protein}, booktitle = {30th Anniversary Symposium of The Protein Society}, year = {2016}, address = {Baltimore MD}, abstract = {

Long-range collective vibrations are thought to be crucial to protein functions. In the case of photoactive protein family, modeling suggests the intramolecular vibrations provide an efficient means of energy relaxation[1], feedback for enhancement of chromophore vibrations that promote structural transitions[2] and can assist in charge energy transfer[3]. As a paradigm of this family, photoactive yellow protein (PYP) is a cytoplasmic photocycling protein related to negative phototactic response to blue light in purple photosynthetic bacteria. PYP has a p-coumaric acid chromophore binding to the cysteine residue via a thioester bond, whose vibrations were found to overlap calculated vibrations of the protein scaffold. Using our unique technique of anisotropic terahertz microscopy(ATM)[4], we measure the intramolecular vibrations for PYP for the first time, including cycling between ground and blue shift (pB) states. Room temperature ATM measurements are performed in the dark and with continuous wave illumination at 488nm, resulting in a steady pB state with approximately 5\% population conversion. In pB state, we find an overall decrease in the strength of resonant band in frequency range of 30-60 cm-1. Our calculated spectra using quasi-harmonic analysis indicate that our measurements are dominated by the protein vibrations, rather than the pCA chromophore, allowing us to characterize how the scaffold dynamics changes with functional states and mutations.

1. Levantino, M., et al. Nat Commun, 2015. 6.

2. Mataga, N., et al. Chem. Phys. Lett., 2002. 352(3-4): p. 220-225.

3. Fokas, A.S., et al. Photosynth. Res., 2014. 122

}, doi = {10.1002/pro.3026}, url = {https://onlinelibrary.wiley.com/doi/10.1002/pro.3026}, author = {Deng, Yanting and Xu, Mengyang and Niessen, Katherine A. and Schmidt, Marius and Markelz, Andrea G.} } @conference {547, title = { The Role of Dynamical Transition in Protein Function: Coupling of Protein Collective Vibrations and Water Dynamics}, booktitle = {30th Anniversary Symposium of The Protein Society}, year = {2016}, address = {Baltimore, MD}, abstract = {

Computational simulations have revealed protein collective vibrations prompt structural rearrangements to accomplish biological function. However, the biological importance of collective vibrations has not been experimentally demonstrated. The attempts have been hampered by the inability to distinguish localized water or side-chain relaxational motions from protein long-range vibrations using conventional techniques. The dynamical transition (DT), extensively observed using X-ray, neutron scattering, NMR and terahertz techniques [1,2], describes a rapid increase in the temperature-dependent dynamics of critically hydrated proteins above \~{}220 K, and has been attributed to thermally activated solvent motions. While some proteins lose function below the specific temperature, others do not. We suggest the difference arises from the nature of the required motions for function. Specifically, functional motions enabled by long-range vibrations will be vulnerable to DT, which require surrounding solvent to be sufficiently mobile. We explored the coupling of protein vibrations to solvent dynamics by applying a recently developed technique, anisotropy terahertz microscopy [3], to directly measure the collective vibrations for lysozyme and investigate the temperature dependence in 150-300 K range. We find long-range intramolecular vibrations occur at 220K and rapidly increase in strength with increasing temperature, consistent with enhanced access above the DT. The results suggest collective vibrations are slaved to DT, and those proteins with function reliant on these motions will cease function below DT.

1. Doster,W., et al. Phys.Rev.Lett., 2010.104(9):098101.

2. Niessen,K., et al. Biophys.Rev., 2015.7,201.

3. Acbas,G., et al. Nat.Commun., 2014.5,3076.

}, doi = {10.1002/pro.3026}, url = {https://onlinelibrary.wiley.com/doi/10.1002/pro.3026}, author = {Xu, Mengyang and Niessen, Katherine and Deng, Yanting and Michki, Nigel and Snell, Edward and Markelz, Andrea} }