@conference {441, title = {Anisotropic Terahertz Microscopy of Lysozyme in Different CrystalLattice Systems}, booktitle = {Biophysical Journal}, year = {2021}, month = {02/2021}, abstract = {

Long-range vibrational modes of proteins at terahertz (THz) frequencies havebeen associated with protein function and allosteric control. The characteriza-tion of these motions has been challenging due to energy overlap with waterabsorption and a large vibrational density of states. Recently it has been demon-strated both experimentally and theoretically that vibrational bands can be iso-lated using stationary sample anisotropic terahertz microscopy (SSTAM) fororiented samples, typically realized using protein crystals [1, 2]. In those earlymeasurements, inhibitor binding contrast was demonstrated for high symmetrytetragonal crystals. While high symmetry crystals are ideal for structural deter-minations, they can limit the types of vibrations observable in the ATM mea-surements. Here we show a survey of ATM measurements of triclinic,monoclinic and tetragonal crystals, demonstrating the unique signaturesobservable for the different symmetry groups, leading to a more completedetermination of the vibrational hot spots that may contribute to enzymatic ef-ficiency. The SSATM spectra indicate the presence of conserved vibrationalmodes near 40 cm-1 and 55 cm-1 for CEWL in triclinic, monoclinic and tetrag-onal lattice systems respectively. For CEWL in the monoclinic lattice system, aprominent band at 20cm1was consistently observed in the SSATM spectrabut not in the triclinic or tetragonal systems. The conserved bands may repre-sent vibrational modes that are unperturbed by crystal contact forces while thedifferences may be related to unique molecular orientation in different crystalsystems.


1.Niessen, K., Y. Deng, and A.G. Markelz,Near-field THz micropo-larimetry.Opt Express, 2019.27(20): p. 28036-28047.

2.Romo, T.D., A.Grossfield, and A.G. MarkelzPersistent Protein Motions in a RuggedEnergy Landscape Revealed by Normal Mode Ensemble Analysis. AcceptedJournal of Chemical Information and Modeling, 2020.

}, doi = {10.1016/j.bpj.2020.11.972}, url = {https://www.cell.com/biophysj/fulltext/S0006-3495(20)31879-8}, author = {McKinney, J. A. and George, D. K. and Deng, Y. and Markelz, A. G.} } @article {329, title = {Near-Field Stationary Sample Terahertz Spectroscopic Polarimetry for Biomolecular Structural Dynamics Determination}, journal = {ACS Photonics}, volume = {8}, year = {2021}, month = {02/2021}, pages = {658-668}, chapter = {658}, abstract = {

THz polarimetry on environmentally sensitive and microscopic samples can provide unique insight into underlying mechanisms of complex phenomena. For example, near-field THz anisotropic absorption successfully isolated protein structural vibrations which are connected to biological function. However, to determine how these vibrations impact function requires high throughput measurements of these complex systems, which is challenged by the need for near field detection, sample environmental control and full polarization variation. Stationary sample anisotropic terahertz spectroscopy (SSATS) and near-field stationary sample anisotropic terahertz microscopy (SSATM) have been proposed using synchronous control of THz and electro optic probe polarizations along an iso-response curve. Here we realize these techniques through robust control and calibration of the THz and NIR polarization states. Both methods rapidly measure the linear dichroism in the far field and near field. Validation measurements using standard birefringent sucrose single crystals found the crystal orientation can be determined by scanning the reference polarization and the synchronous pump{\textendash}probe polarization settings can be optimized to eliminate artifacts. SSATM is then used to determine spectral reproducibility and dehydration effects for a series of chicken egg white lysozyme samples. Reproducible anisotropic absorbance bands are found at about 30, 44, 55, and 62 cm{\textendash}1. These bands initially sharpen with slow dehydration, similar to the increase in resolution achieved in X-ray crystallographic protein structure determination. The SSATM technique confirms the reliability of anisotropic absorption characterization of protein intramolecular vibrations and opens an avenue for rapid determination of how these long-range dynamics affect biological function.

}, doi = {10.1021/acsphotonics.0c01876}, url = {https://pubs.acs.org/doi/abs/10.1021/acsphotonics.0c01876}, author = {Deng, Y. and McKinney, J. A. and George, D. K. and Niessen, K. A. and Sharma, A. and Markelz, A.G.} } @article {520, title = {Phonon Kinetics of Fructose at the Melting Transition}, journal = {J. Phys. Chem. C}, volume = {125}, year = {2021}, pages = {12269-12276}, chapter = {12269}, abstract = {

Terahertz time domain spectroscopy (THz TDS) is used to measure the melting kinetics of fructose molecular crystals. Combining single-crystal anisotropy measurements with density functional calculations, we assign the phonon frequencies and interrogate how specific phonons behave with melting. While nearly all the low-frequency phonons continuously red-shift with heating and melting, the lowest-energy phonon polarized along the c-axis blue-shifts at the melting temperature, suggesting an initial structural change immediately before melting. We find that the kinetics follow a 3D growth model with large activation energies, consistent with previous differential scanning calorimetry (DSC) measurements. The large activation energies indicate that multiple H-bonds must break collectively for the transition. The results suggest the generality of the kinetics for molecular crystals and that THz TDS with picosecond resolution could be used to measure ultrafast kinetics.

}, doi = {10.1021/acs.jpcc.1c00610}, author = {A. Davie and F. Vandrevala and S. Dampf and Y. Deng and D. K. George and E. D. Sylvester and T. Korter and E. Einarsson and J. B. Benedict and A. G. Markelz} } @article {253, title = {Evidence of Intramolecular Structural Stabilization in Light Activated State of Orange Carotenoid Protein}, journal = {Biophysical Journal}, volume = {118}, number = {3}, year = {2020}, note = {ISI Document Delivery No.: KK8YX
Times Cited: 0
Cited Reference Count: 0
McKinney, Jeffrey A. Sharma, Akansha Crossen, Kimberly Deng, Yanting George, Deepu K. Lechno-Yossef, Sigal Kerfeld, Cheryl 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]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.

1
2
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {208A-208A}, type = {Meeting Abstract}, abstract = {

Orange carotenoid protein (OCP) controls efficiency of the light harvesting antenna, the phycobilisome (PBS), in diverse cyanobacteria and prevents oxidative damage. It is the only known photoactive protein that uses a carotenoid, canthaxanthin, as its chromophore. The structure of OCP consists of two globular domains, connected by an unstructured loop, that forms a hydrophobic pocket for the carotenoid. In low light, canthaxanthin bound OCP is inactive and appears orange. Illumination by strong light results in an active state that interacts with the PBS to induce fluorescence quenching, a red appearance and conformational changes that include a 12{\r A} shift by canthaxanthin into the N-terminal domain. Terahertz (THz) dynamical transition measurements and anisotropic terahertz microscopy are used to measure the intramolecular structural dynamics in the inactive and active states, which can be induced by photoexcitation or chaotropic salts. The measurements indicate that the active state has a decrease in structural flexibility, which may be related to enhanced interactions with the PBS.

}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2019.11.1245}, author = {McKinney, J. A. and Sharma, A. and Crossen, K. and Deng, Y. and George, D. K. and Lechno-Yossef, S. and Kerfeld, C. and Markelz, A. G.} } @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 {544, title = {Stabilization of Terahertz Vibrational Modes in Illuminated Orange Carotenoid Protein Crystals}, year = {2020}, address = {Buffalo, NY}, abstract = {

Orange carotenoid protein (OCP) controls efficiency of the phycobilisome (PBS), the light harvesting antenna in cyanobacteria, to prevent oxidative damage. The OCP switches from resting state to photo protective state with intense blue light illumination. Questions persist as to why OCPR interaction increases with the PBS over that with the OCPO. Here we examine the role of long-range intramolecular vibrations within OCP. Using Stationary Sample Anisotropic Terahertz Microscopy (SSATM) we measure changes in the intramolecular vibrations with photo switching. We report the first observation of switching in the intramolecular vibrations with photoexcitation. Results suggest that there is a stiffening of the molecule in the photo protective state. This increase in structural stability may enhance the interaction with the PBS change in OCP interaction with PBS. In low light, carotenoid bound OCP appears orange (OCP o ) and is inactive. Illumination by strong light converts OCP to the active, red (OCPR) state, which interacts with the PBS. A comparison of anisotropic THz microscopy measurements of dark adapted (OCP o ) and illuminated OCP crystals indicate differences in their vibrational modes that may be important for OCP-PBS interactions.

}, doi = {10.1109/IRMMW-THz46771.2020.9370827}, author = {McKinney, J. and Sharma, A. and Deng, Y. and George, D. and Lechno-Yossef, S. and Kerfeld, C. and Markelz, A.} } @proceedings {299, title = {Angular Distortion Removal of THz Anisotropic Dichroism Microscope}, year = {2019}, month = {2019}, pages = {1 - 2}, address = {Paris, France}, abstract = {

We have developed a stationary sample THz anisotropic dichroism microscope as a powerful tool for material characterization. The key innovation is the use of an iso-response curve defined by the terahertz and detection light polarizations. Here we show that following a continuous iso-response curve introduces angular distortion in the spectrum, and this distortion can be eliminated by using a discontinuous iso-response angle pairs avoiding large gradient regions. Employing this additional constraint on the relative polarizations provides a convenient technique for rapid anisotropic terahertz spectroscopy.

}, keywords = {absorption, angular distortion removal, Biomedical measurement, continuous iso-response curve, detection light polarizations, discontinuous iso-response angle pairs, Distortion, light polarisation, material characterization, Microscopy, proteins, rapid anisotropic terahertz spectroscopy, relative polarizations, spectroscopy, stationary sample, terahertz spectroscopy, terahertz wave spectra, THz anisotropic dichroism microscope, vibrations}, isbn = {2162-2035}, doi = {10.1109/IRMMW-THz.2019.8873793}, url = {https://ieeexplore.ieee.org/document/8873793}, author = {Y. Deng and K. Niessen and A. Markelz} } @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 {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} } @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
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Antoniou D, 2011, J PHYS CHEM B, V115, P15147, DOI 10.1021/jp207876k
Bagsican FR, 2017, SCI REP-UK, V7, DOI 10.1038/s41598-017-01883-1
Baxter JB, 2006, J PHYS CHEM B, V110, P25229, DOI 10.1021/jp064399a
BROOKS B, 1985, P NATL ACAD SCI USA, V82, P4995, DOI 10.1073/pnas.82.15.4995
Chen JY, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2748852
Chhowalla M, 2013, NAT CHEM, V5, P263, DOI [10.1038/NCHEM.1589, 10.1038/nchem.1589]
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
Docherty CJ, 2014, ACS NANO, V8, P11147, DOI 10.1021/nn5034746
Ebbinghaus S, 2007, P NATL ACAD SCI USA, V104, P20749, DOI 10.1073/pnas.0709207104
Fan ST, 2014, J PHYS D APPL PHYS, V47, DOI 10.1088/0022-3727/47/37/374009
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
Hirota Y, 2006, OPT EXPRESS, V14, P4486, DOI 10.1364/OE.14.004486
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
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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.} } @conference {306, title = {Protein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence}, booktitle = {APS R63.003}, year = {2019}, month = {03/2019}, url = {https://meetings.aps.org/Meeting/MAR19/Session/R63.3}, author = {Deng, Y. and McKinney, J. and Romo, T. and Grossfield, A. 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.} } @conference {284, title = {Measuring Protein Intramolecular Dynamics with Terahertz Light: Functional Changes and Relevance to Biology}, booktitle = {APS 2018}, volume = {H50.001}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.H50.1}, author = {Xu, M. and Deng, Y. and Luck, C. and Sharma, A. and Markelz, A.} } @conference {285, title = {Rapid Terahertz Dichroism Near Field Microscopy for Biomolecular Intramolecular Vibrational Spectroscopy}, booktitle = {APS 2018}, volume = {A50.008}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.A50.8}, author = {Deng, Y. and Niessen, K. and Markelz, A.} } @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 {224, title = {The 2017 terahertz science and technology roadmap}, journal = {Journal of Physics D-Applied Physics}, volume = {50}, number = {4}, year = {2017}, note = {ISI Document Delivery No.: EI0HL
Times Cited: 541
Cited Reference Count: 209
Cited References:
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[Anonymous], 2013, 178512012 IEEE
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Dhillon, S. S. Vitiello, M. S. Linfield, E. H. Davies, A. G. Hoffmann, Matthias C. Booske, John Paoloni, Claudio Gensch, M. Weightman, P. Williams, G. P. Castro-Camus, E. Cumming, D. R. S. Simoens, F. Escorcia-Carranza, I. Grant, J. Lucyszyn, Stepan Kuwata-Gonokami, Makoto Konishi, Kuniaki Koch, Martin Schmuttenmaer, Charles A. Cocker, Tyler L. Huber, Rupert Markelz, A. G. Taylor, Z. D. Wallace, Vincent P. Zeitler, J. Axel Sibik, Juraj Korter, Timothy M. Ellison, B. Rea, S. Goldsmith, P. Cooper, Ken B. Appleby, Roger Pardo, D. Huggard, P. G. Krozer, V. Shams, Haymen Fice, Martyn Renaud, Cyril Seeds, Alwyn Stoehr, Andreas Naftaly, Mira Ridler, Nick Clarke, Roland Cunningham, John E. Johnston, Michael B.
Huggard, Peter/U-2150-2019; Konishi, Kuniaki/AAN-3624-2020; Zeitler, J. Axel/B-4885-2008; Paoloni, Claudio/AAH-9824-2019; Hoffmann, Matthias C./N-1082-2019; Wallace, Vincent P/A-9320-2012; Johnston, Michael/B-9813-2008; Castro-Camus, Enrique/V-6861-2019; Krozer, Viktor/P-5623-2014; Hoffmann, Matthias C/B-3893-2009; PAOLONI, CLAUDIO/AAA-3211-2020; Gonokami, Makoto/F-3641-2012; Shams, Haymen/H-3754-2012; Ridler, Nick/AAN-9637-2020; Huber, Rupert/N-4126-2018
Konishi, Kuniaki/0000-0003-2389-9787; Zeitler, J. Axel/0000-0002-4958-0582; Hoffmann, Matthias C./0000-0002-3596-9853; Wallace, Vincent P/0000-0003-3814-5400; Johnston, Michael/0000-0002-0301-8033; Krozer, Viktor/0000-0002-2387-1947; Hoffmann, Matthias C/0000-0002-3596-9853; PAOLONI, CLAUDIO/0000-0002-0265-0862; Shams, Haymen/0000-0002-5333-6478; Huber, Rupert/0000-0001-6617-9283; Davies, Alexander/0000-0002-1987-4846; Seeds, Alwyn/0000-0002-5228-627X; Castro-Camus, Enrique/0000-0002-8218-9155; Cunningham, John/0000-0002-1805-9743; Naftaly, Mira/0000-0002-0671-822X; Cumming, David/0000-0002-7838-8362
Engineering and Physical Sciences Research CouncilUK Research \& Innovation (UKRI)Engineering \& Physical Sciences Research Council (EPSRC) [EP/P015883/1, EP/M00306X/1, EP/K023349/1, EP/M017095/1, EP/L026597/1, EP/J017671/1] Funding Source: researchfish; Natural Environment Research CouncilUK Research \& Innovation (UKRI)NERC Natural Environment Research Council [NER/Z/S/2003/00642, NE/L012375/1, NER/Z/S/2000/01292] Funding Source: researchfish; Science and Technology Facilities CouncilUK Research \& Innovation (UKRI)Science \& Technology Facilities Council (STFC) [ST/P002056/1] Funding Source: researchfish; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation; Div Of Biological InfrastructureNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation; Div Of Molecular and Cellular BioscienceNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1616529] Funding Source: National Science Foundation
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1361-6463}, month = {Feb}, pages = {49}, type = {Review}, abstract = {

Science and technologies based on terahertz frequency electromagnetic radiation (100 GHz-30 THz) have developed rapidly over the last 30 years. For most of the 20th Century, terahertz radiation, then referred to as sub-millimeter wave or far-infrared radiation, was mainly utilized by astronomers and some spectroscopists. Following the development of laser based terahertz time-domain spectroscopy in the 1980s and 1990s the field of THz science and technology expanded rapidly, to the extent that it now touches many areas from fundamental science to {\textquoteright}real world{\textquoteright} applications. For example THz radiation is being used to optimize materials for new solar cells, and may also be a key technology for the next generation of airport security scanners. While the field was emerging it was possible to keep track of all new developments, however now the field has grown so much that it is increasingly difficult to follow the diverse range of new discoveries and applications that are appearing. At this point in time, when the field of THz science and technology is moving from an emerging to a more established and interdisciplinary field, it is apt to present a roadmap to help identify the breadth and future directions of the field. The aim of this roadmap is to present a snapshot of the present state of THz science and technology in 2017, and provide an opinion on the challenges and opportunities that the future holds. To be able to achieve this aim, we have invited a group of international experts to write 18 sections that cover most of the key areas of THz science and technology. We hope that The 2017 Roadmap on THz science and technology will prove to be a useful resource by providing a wide ranging introduction to the capabilities of THz radiation for those outside or just entering the field as well as providing perspective and breadth for those who are well established. We also feel that this review should serve as a useful guide for government and funding agencies.

}, keywords = {ex-vivo, generation, metal wave-guides, near-field, performance, photoconductive emitters, Physics, quantum-cascade lasers, radiation, semiconductors, Terahertz, thz, time-domain spectroscopy}, isbn = {0022-3727}, doi = {https://doi.org/10.1088/1361-6463/50/4/043001}, author = {Dhillon, S. S. and Vitiello, M. S. and Linfield, E. H. and Davies, A. G. and Hoffmann, M. C. and Booske, J. and Paoloni, C. and Gensch, M. and Weightman, P. and Williams, G. P. and Castro-Camus, E. and Cumming, D. R. S. and Simoens, F. and Escorcia-Carranza, I. and Grant, J. and Lucyszyn, S. and Kuwata-Gonokami, M. and Konishi, K. and Koch, M. and Schmuttenmaer, C. A. and Cocker, T. L. and Huber, R. and Markelz, A. G. and Taylor, Z. D. and Wallace, V. P. and Zeitler, J. A. and Sibik, J. and Korter, T. M. and Ellison, B. and Rea, S. and Goldsmith, P. and Cooper, K. B. and Appleby, R. and Pardo, D. and Huggard, P. G. and Krozer, V. and Shams, H. and Fice, M. and Renaud, C. and Seeds, A. and Stohr, A. and Naftaly, M. and Ridler, N. and Clarke, R. and Cunningham, J. E. and Johnston, M. B.} } @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.} } @conference {288, title = {Global Picosecond Structural Dynamics of Orange Carotenoid Protein in Photo/Chemical Activated Signaling States}, booktitle = {APS 2017 S4.002}, year = {2017}, month = {03/2017}, url = {http://meetings.aps.org/link/BAPS.2017.MAR.S4.2}, author = {Deng, Y. and Xu, M. and Liu, H. and Blankenship, R. and Markelz, A.} } @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.} } @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:
King JD, 2014, FEBS LETT, V588, P4561, DOI 10.1016/j.febslet.2014.10.024
Wilson A, 2006, PLANT CELL, V18, P992, DOI 10.1105/tpc.105.040121
Wilson A, 2008, P NATL ACAD SCI USA, V105, P12075, DOI 10.1073/pnas.0804636105
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.} } @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} }