@article {252, title = {Long Range Correlated Motions of TIM and their Possible Influence on Enzyme Function}, journal = {Biophysical Journal}, volume = {118}, number = {3}, year = {2020}, note = {ISI Document Delivery No.: KK8YX
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Niessen K.A. M.Y., 2017, BIOPHYS J, DOI [10.1016/j.bpj.2016.12.049.3., DOI 10.1016/J.BPJ.2016.12.049.3]
Niessen K, 2019, OPT EXPRESS, V27, P28036, DOI 10.1364/OE.27.028036
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
McKinney, Jeffrey A. Deng, Yanting George, Deepu K. Richard, John Markelz, Andrea G.
64th Annual Meeting of the Biophysical-Society
Feb 15-19, 2020
San Diego, CA
Biophys Soc
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NIH STTRUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [R41 GM125486.1]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.1.

1
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {207A-207A}, type = {Meeting Abstract}, abstract = {

The alpha-beta barrel structure of triosephosphate isomerase (TIM) is possibly the most common among enzymes. In the case of TIM, structural dynamics are known to be essential to function. In particular the stabilization of the binding pocket by a phosphodianion {\textquotedblleft}handle{\textquotedblright} of the substrate and the closing of catalytic site loops 6 and 7 over the substrate. Loop 6 moves by as much as 7 Angstroms with binding. Recently a mutant survey for human TIM (hsTIM) found kcat can change significantly for a single mutation distant from the catalytic site. Crystallographic measurements find no structural change with the mutation, suggesting a dynamical mechanism for the allosteric effect. Here we use Stationary Sample Anisotropic Terahertz Microscopy (SSATM) to measure the long-range intramolecular vibrations and determine if specific vibrations couple the allosteric and catalytic sites. SSATM isolated protein long-range structural vibrations based on the dominant displacement direction [1-4]. We examine if specific vibrational bands are associate with loop 6 and loop 7 flexibility.

}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2019.11.1240}, author = {McKinney, J. A. and Deng, Y. T. and George, D. K. and Richard, J. and Markelz, A. G.} } @proceedings {235, title = {Anisotropic Terahertz Microscopy of Protein Collective Vibrations: Crystal Symmetry and Hydration Dependence}, year = {2019}, note = {ISI Document Delivery No.: BQ4OX
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Legrand L, 2002, ACTA CRYSTALLOGR D, V58, P1564, DOI 10.1107/S0907444902014403
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
McKinney, Jeffrey Deng, Yanting Sharma, Akansha George, D. K. Markelz, A. G.
Irmmw-thz
Proceedings Paper
44th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 01-06, 2019
Paris, FRANCE
Lytid, TYDEX, Swiss Terahertz, Fondat Maison Chimie, CNRS, Lab Physique ENS, Li2S, LUNA, MenloSystems, ENS, PSL Univ Paris, FYLA, ADVANTEST, Springer Nature, Soc Francaise Physique, Sorbonne Univ, Int Soc Infrared Millimeter \& Terahertz Waves, IEEE, GDR NANO THz MIR
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NIHUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [STTR R41 GM125486]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

A stationary sample anisotropic terahertz microscopy technique is used to characterize the intramolecular vibrations for lysozyme. Tetragonal and triclinic crystals are compared. We find excellent reproducibility within a single crystal symmetry group. Several resonant bands are present for both symmetry groups, indicating they originate with the intramolecular vibrations and not crystal lattice phonons. Bands become more pronounced and higher frequency resonant bands begin to emerge with slight dehydration.

}, isbn = {978-1-5386-8285-2}, doi = {https://doi.org/10.1109/IRMMW-THz.2019.8873722}, author = {McKinney, J. and Deng, Y. T. and Sharma, A. and George, D. K. and Markelz, A. G.} } @article {248, title = {Deuteration and Inhibitor Binding Dependence of Protein Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 2
Cited References:
Mahajan S, 2015, ARCH BIOCHEM BIOPHYS, V567, P59, DOI 10.1016/j.abb.2014.12.020
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {488A-488A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2633}, author = {Deng, Y. T. and McKinney, J. and Markelz, A.} } @article {251, title = {The Effect of Crystal Contact Forces on the Protein Global Motions}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
McKinney, Jeffrey A. Deng, Yanting George, Deepu Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {489A-489A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2638}, author = {McKinney, J. A. and Deng, Y. T. and George, D. and Markelz, A.} } @article {239, title = {Near-field THz micropolarimetry}, journal = {Optics Express}, volume = {27}, number = {20}, year = {2019}, note = {ISI Document Delivery No.: JB0XT
Times Cited: 1
Cited Reference Count: 31
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Antoniou D, 2011, J PHYS CHEM B, V115, P15147, DOI 10.1021/jp207876k
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Cote Y, 2017, BIOPHYS J, V112, P2575, DOI 10.1016/j.bpj.2017.05.018
Dhillon SS, 2017, J PHYS D APPL PHYS, V50, DOI 10.1088/1361-6463/50/4/043001
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George DK, 2012, J OPT SOC AM B, V29, P1406, DOI 10.1364/JOSAB.29.001406
GRISCHKOWSKY D, 1990, J OPT SOC AM B, V7, P2006, DOI 10.1364/JOSAB.7.002006
Hayes D, 2011, FARADAY DISCUSS, V150, P459, DOI 10.1039/c0fd00030b
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Huang B, 2017, NATURE, V546, P270, DOI 10.1038/nature22391
Jin WC, 2018, NAT COMMUN, V9, DOI 10.1038/s41467-018-07547-6
Lang D, 2018, REV SCI INSTRUM, V89, DOI 10.1063/1.5016281
Markelz A, 2002, PHYS MED BIOL, V47, P3797, DOI 10.1088/0031-9155/47/21/318
Meireles L, 2011, PROTEIN SCI, V20, P1645, DOI 10.1002/pro.711
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Niessen Katherine A, 2015, Biophys Rev, V7, P201, DOI 10.1007/s12551-015-0168-4
Ostroverkhova O, 2006, APPL PHYS LETT, V89, DOI 10.1063/1.2387135
Planken PCM, 2011, J INFRARED MILLIM TE, V32, P975, DOI 10.1007/s10762-011-9824-3
Planken PCM, 2001, J OPT SOC AM B, V18, P313, DOI 10.1364/JOSAB.18.000313
Serita K, 2019, PHOTONICS-BASEL, V6, DOI 10.3390/photonics6010012
Vinh NQ, 2011, J AM CHEM SOC, V133, P8942, DOI 10.1021/ja200566u
You JW, 2018, NANO CONVERG, V5, DOI 10.1186/s40580-018-0158-x
Zhao C, 2017, NAT NANOTECHNOL, V12, P757, DOI [10.1038/NNANO.2017.68, 10.1038/nnano.2017.68]
Niessen, Katherine Deng, Yanting Markelz, A. G.
National Science FoundationNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; U.S. Department of EnergyUnited States Department of Energy (DOE) [DE-SCO016317]; National Institute of General Medical SciencesUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [STTR R41 GM125486]
National Science Foundation (DBI 1556359, MCB 1616529); U.S. Department of Energy DE-SCO016317); National Institute of General Medical Sciences (STTR R41 GM125486).
1
3
9
Optical soc amer
Washington}, month = {Sep}, pages = {28036-28047}, type = {Article}, abstract = {

We introduce a method for rapid determination of anisotropic terahertz absorption with sub micron resolution and high spectral integrity in the terahertz range. The method is ideal for microscopic and environmentally sensitive materials such as 2-D materials and protein crystals where the anisotropic absorption is critical to understanding underlying physics. We introduce the idea of using an iso-response relationship between the THz polarization and electro optic probe polarization to enable stationary sample polarization measurements covering a full 2 pi polarization dependence measurement. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

}, keywords = {binding, conductivity, dynamics, modes, Optics, polarization modulation, Terahertz, time-domain spectroscopy, wse2}, isbn = {1094-4087}, doi = {https://doi.org/10.1364/OE.27.028036}, author = {Niessen, K. and Deng, Y. T. and Markelz, A. G.} } @article {249, title = {Spectral Assignment of Lysozyme Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Romo, Tod Grossfield, Alan Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {564A-564A}, type = {Meeting Abstract}, abstract = {
Global structural vibrations at terahertz (THz) frequencies have been associated with protein function and allosteric control. A chief obstacle to utilizing this control mechanism has been measurement of specific motions. Recently it was shown that while the vibrational density of states, and isotropic absorption spectra are broad and featureless, collective vibrations can be isolated based on their directionality using aligned samples (realized with protein crystals) and anisotropic THz microscopy [1]. However the assignment of resonant bands to specific structural motions was complicated by the high symmetry of the tetragonal crystals used, and the slow experimental method. To structurally map the vibrations of the chicken egg white lysozyme (CEWL) we measure anisotropic absorption of triclinic crystals using our new technique: ideal polarization varying anisotropic THz microscopy (IPV-ATM). The low symmetry triclinic crystals provide absolute protein orientation, and the near field IPV-ATM rapidly measures broadband terahertz linear dichroism of the microcrystals. All measurements were performed at room temperature under 100\% humidity conditions. The unit cell parameters of triclinic lysozyme nitrate crystals, α = 28.5A{\textdegree}, b = 32.7A{\textdegree}, c = 35.1A{\textdegree}, α = 88.2{\textdegree}, β = 108.9{\textdegree}, γ = 111.9{\textdegree}, belonging to the P1 space group, were determined by X-ray diffraction before and after THz measurements. The intramolecular vibrational absorbance of the triclinic crystals has a more complex polarization dependence than the higher symmetry tetragonal crystals, as expected. While the tetragonal crystals have two strong bands at 45cm-1 and 55cm-1, the triclinic crystals have a series of narrow bands between 40 and 60cm-1 and a prominent band at 30cm-1. We compare the measured spectra to normal mode ensemble averaged calculations to assign the observed resonances, and isolating which collective motions impact the catalytic site.
}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.3032}, author = {Deng, Y. T. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A.} } @article {247, title = {Increase in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State}, journal = {Biophysical Journal}, volume = {114}, number = {3}, year = {2018}, note = {ISI Document Delivery No.: GD5RB
Times Cited: 1
Cited Reference Count: 0
Deng, Yanting Luck, Catherine H. Romo, Tod D. Grossfield, Alan M. Bandara, Sepalika Ren, Zhong Yang, Xiaojing Markelz, Andrea G.
62nd Annual Meeting of the Biophysical-Society
Feb 17-21, 2018
San Francisco, CA
Biophys Soc
1

7
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {522A-522A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2017.11.2854}, author = {Deng, Y. T. and Luck, C. H. and Romo, T. D. and Grossfield, A. M. and Bandara, S. and Ren, Z. and Yang, X. J. and Markelz, A. G.} } @article {256, title = {Escaping the Water Cage: Protein Intramolecular Vibrations and the Dynamical Transition}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {ISI Document Delivery No.: EW3DR
Times Cited: 0
Cited Reference Count: 0
Xu, Mengyang Niessen, Katherine A. Deng, Yanting Michki, Nigel S. Markelz, Andrea G.
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]
This work was supported by NSF (DBI 1556359 and MCB 1616529), and DOE DE-SC0016317.

7
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {318A-318A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.1723}, author = {Xu, M. Y. and Niessen, K. A. and Deng, Y. T. and Michki, N. S. and Markelz, A. G.} } @article {250, title = {Orange Carotenoid Protein Picosecond Dynamics Changes with Photo and Chemical Activation}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {ISI Document Delivery No.: EW3DS
Times Cited: 0
Cited Reference Count: 3
Cited References:
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Wilson A, 2006, PLANT CELL, V18, P992, DOI 10.1105/tpc.105.040121
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Deng, Yanting Xu, Mengyang Liu, Haijun Blankenship, Robert E. Markelz, Andrea G.
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
Liu, Haijun/0000-0003-0537-0302

14
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {441A-441A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.2355}, author = {Deng, Y. T. and Xu, M. Y. and Liu, H. J. and Blankenship, R. E. and Markelz, A. G.} } @proceedings {246, title = {Anisotropic Absorption Measurements Reveal Protein Dynamical Transition in Intramolecular Vibrations}, year = {2016}, note = {ISI Document Delivery No.: BG7KC
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Niessen K., 2015, BIOPHYSICAL REV
PETHIG R, 1995, PROTEIN SOLVENT INTE, P265
RUPLEY JA, 1991, ADV PROTEIN CHEM, V41, P37
Xu, Mengyang Niessen, Katherine Michki, Nigel Deng, Yanting Snell, Edward Markelz, A. G.
Irmmw-thz
Proceedings Paper
41st International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 25-30, 2016
Copenhagen, DENMARK
DTU, IEEE, QMC Instruments, Danish Ctr Laser Infrastructure, DTU Fotonik, Dept Photon Engn, ARL, Carl Sberg Fdn, AF Off Sci Res, Tech Univ Denmark, IEEE Microwave Theory \& Tech Soc, Azpect Photon, Ekspla, Hubner HF Syst Engn, I2S, Laser Quantum, Menlo Syst, Neaspec, Springer, TeraView, Virginia Diodes
Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

Modeling has predicted that intramolecular structural vibrations enables proteins to access functionally important structural change. We show that the vibrational density of states and the isotropic absorption in the terahertz range are only weakly dependent on the protein functional state for several bench marking proteins. At the same time the direction of motions changes dramatically with functional state and with a resulting impact on the anisotropic absorption. Our anisotropic THz microscopy (ATM) measurements confirm this sensitivity. Here we apply the technique to the question of whether the protein dynamical transition (DT) is important to protein function. We find a strong anisotropic resonance at 70 cm(-1) rapidly increases in strength at temperatures above the DT. As these intramolecular vibrations enable protein structure to change conformation, the results suggest function will cease below DT for those proteins that require large scale conformational change.

}, isbn = {978-1-4673-8485-8}, doi = {10.1109/IRMMW-THz.2016.7758347}, author = {Xu, M. Y. and Niessen, K. and Michki, N. and Deng, Y. T. and Snell, E. and Markelz, A. G.} }