%0 Conference Paper %B Biophysical Journal %D 2021 %T Anisotropic Terahertz Microscopy of Lysozyme in Different CrystalLattice Systems %A McKinney, J. A. %A George, D. K. %A Deng, Y. %A Markelz, A. G. %X
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.
%B Biophysical Journal %8 02/2021 %G eng %U https://www.cell.com/biophysj/fulltext/S0006-3495(20)31879-8 %R 10.1016/j.bpj.2020.11.972 %0 Journal Article %J J. Phys. Chem. B %D 2021 %T Functional-State Dependence of Picosecond Protein Dynamics %A George, D. K. %A Chen, J. Y. %A He, Yunfen %A Knab, J. R. %A Markelz, A. G. %XWe examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E1 ∼ 0.1 kJ/mol and E2 ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent–protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.
%B J. Phys. Chem. B %V 125 %P 11134-11140 %G eng %N 40 %& 11134 %R 10.1021/acs.jpcb.1c05018 %0 Journal Article %J ACS Photonics %D 2021 %T Near-Field Stationary Sample Terahertz Spectroscopic Polarimetry for Biomolecular Structural Dynamics Determination %A Deng, Y. %A McKinney, J. A. %A George, D. K. %A Niessen, K. A. %A Sharma, A. %A Markelz, A.G. %XTHz 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–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–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.
%B ACS Photonics %V 8 %P 658-668 %8 02/2021 %G eng %U https://pubs.acs.org/doi/abs/10.1021/acsphotonics.0c01876 %N 2 %& 658 %R 10.1021/acsphotonics.0c01876 %0 Journal Article %J Biophysical Journal %D 2020 %T Evidence of Intramolecular Structural Stabilization in Light Activated State of Orange Carotenoid Protein %A McKinney, J. A. %A Sharma, A. %A Crossen, K. %A Deng, Y. %A George, D. K. %A Lechno-Yossef, S. %A Kerfeld, C. %A Markelz, A. G. %K Biophysics %XOrange 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 12Å 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.
%B Biophysical Journal %V 118 %P 208A-208A %8 Feb %@ 0006-3495 %G English %N 3 %9 Meeting Abstract %M WOS:000513023201290 %R 10.1016/j.bpj.2019.11.1245 %0 Journal Article %J Physical Review B %D 2020 %T Linear dichroism infrared resonance in overdoped, underdoped, and optimally doped cuprate superconductors %A Mukherjee, A. %A Seo, J. %A Arik, M. M. %A Zhang, H. %A Zhang, C. C. %A Kirzhner, T. %A George, D. K. %A Markelz, A. G. %A Armitage, N. P. %A Koren, G. %A Wei, J. Y. T. %A Cerne, J. %K Materials Science %K Physics %XBy measuring the polarization changes in terahertz, infrared, and visible radiation over an extended energy range (3-2330 meV), we observe symmetry breaking in cuprate high-temperature superconductors over wide energy, doping, and temperature ranges. We measure the polarization rotation (Re[theta(F)]) and ellipticity (Im[theta(F)]) of transmitted radiation through thin films as the sample is rotated. We observe a twofold rotational symmetry in theta(F), which is associated with linear dichroism (LD) and occurs when electromagnetic radiation polarized along one direction is absorbed more strongly than radiation polarized in the perpendicular direction. Such polarization anisotropies can be generally associated with symmetry breakings. We measure the amplitude of the LD signal and study its temperature, energy, and doping dependence. The LD signal shows a resonant behavior with a peak in the few hundred meV range, which is coincident with the midinfrared optical feature that has been associated with the formation of the pseudogap state. The strongest LD signal is found in underdoped films, although it is also observed in optimally and overdoped samples. The LD signal is consistent with an electronic nematic order which is decoupled from the crystallographic axes as well as novel magnetoelectric effects.
%B Physical Review B %V 102 %P 6 %8 Aug %@ 2469-9950 %G English %9 Article %M WOS:000562627700004 %] 054520 %R 10.1103/PhysRevB.102.054520 %0 Journal Article %J Biophysical Journal %D 2020 %T Long Range Correlated Motions of TIM and their Possible Influence on Enzyme Function %A McKinney, J. A. %A Deng, Y. T. %A George, D. K. %A Richard, J. %A Markelz, A. G. %K Biophysics %XThe 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 “handle” 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.
%B Biophysical Journal %V 118 %P 207A-207A %8 Feb %@ 0006-3495 %G English %9 Meeting Abstract %M WOS:000513023201285 %R 10.1016/j.bpj.2019.11.1240 %0 Journal Article %J Biophysical Journal %D 2020 %T Is the Protein Dynamical Transition useful? %A Sharma, A. %A George, D. K. %A Crossen, K. %A McKinney, J. %A Kerfeld, C. %A Markelz, A. %B Biophysical Journal %V 118 %G eng %N 3 %& 521a %R 10.1016/j.bpj.2019.11.2866 %0 Conference Proceedings %B 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves %D 2019 %T Anisotropic Terahertz Microscopy of Protein Collective Vibrations: Crystal Symmetry and Hydration Dependence %A McKinney, J. %A Deng, Y. T. %A Sharma, A. %A George, D. K. %A Markelz, A. G. %XA 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.
%B 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves %S International Conference on Infrared Millimeter and Terahertz Waves %I Ieee %C New York %@ 978-1-5386-8285-2 %G English %M WOS:000591783800033 %R https://doi.org/10.1109/IRMMW-THz.2019.8873722 %0 Journal Article %J arXiv:1906.00893 %D 2019 %T Photo Switching of Protein Dynamical Collectivity %A Xu, M. %A George, D. K. %A Jimenez, R. %A Markelz, A. G. %B arXiv:1906.00893 %G eng %U https://arxiv.org/abs/1906.00893 %0 Conference Proceedings %B 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves %D 2019 %T Stationary Sample Anisotropic THz Spectroscopy using Discretely Tunable THz Sources %A LaFave, T., Jr. %A George, D. K. %A Markelz, A. G. %A McNee, Ian %A Kozlov, Vladimir %A Schunemann, Peter %XWe demonstrate anisotropic THz spectroscopy of sucrose using newly developed compact discretely tunable THz sources for turn-key spectroscopic systems.
%B 2019 44th International Conference on Infrared, Millimeter, and Terahertz Waves %S International Conference on Infrared Millimeter and Terahertz Waves %@ 978-1-5386-8285-2 %G eng %M WOS:000591783800538 %R https://doi.org/10.1109/IRMMW-THz.2019.8874234 %0 Conference Proceedings %B Conference on Next-Generation Spectroscopic Technologies XII %D 2019 %T Tunable Compact Narrow Band THz Sources for Frequency Domain THz Anisotropic Spectroscopy %A George, D. K. %A LaFave, T. J. %A Markelz, A. G. %A McNee, I. %A Tekavec, P. %A Kozlov, V. %A Schunemann, P. %? Spie, %? Univ Buffalo, Dept Phys Buffalo N. Y. U. S. A. %? Microtech Instruments, Eugene O. R. U. S. A. %? Bae Syst, P. O. B. Nashua N. H. U. S. A. %K anisotropy %K biomolecules %K femtosecond %K optical rectification %K orientation patterned gallium phosphide %K Terahertz %K THz generation %XWe demonstrate frequency domain THz anisotropy signature detection for protein crystal models using newly developed compact tunable narrow band THz sources based on Orientation Patterned Gallium Phosphide for turn-key spectroscopic systems.
%B Conference on Next-Generation Spectroscopic Technologies XII %S Proceedings of SPIE %I Spie-Int Soc Optical Engineering %C Baltimore, MD %V 10983 %8 Apr 15-17 %@ 978-1-5106-2632-4 %G English %M WOS:000484438200016 %1 BELLINGHAM %2 2019 %( Next-generation spectroscopic technologies xii %R https://doi.org/10.1117/12.2519878 %0 Conference Paper %B APS S23-002 %D 2019 %T Tunable narrow band sources for anisotropic THz spectroscopy %A George, D. K. %A McNee, I. %A Tekavec, P. %A Kozlov, V. %A Schunemann, P. %A Markelz, A. G. %B APS S23-002 %8 02/2019 %G eng %U https://meetings.aps.org/Meeting/MAR19/Session/S23.2 %0 Conference Proceedings %B Nonlinear Frequency Generation and Conversion: Materials and Devices Xviii %D 2019 %T Tunable narrowband THz generation in orientation patterned gallium phosphide for THz anisotropy identification %A McNee, I. %A Tekavec, P. %A Kozlov, V. %A Markelz, A. G. %A George, D. K. %A Schunemann, P. %E Schunemann, P. G. %E Schepler, K. L. %K anisotropy %K biomolecules %K femtosecond %K optical rectification %K orientation patterned gallium phosphide %K Terahertz %K THz generation %XWe demonstrate tunable narrowband THz generation by optical rectification of a femtosecond pulse in Orientation Patterned Gallium Phosphide. Center frequencies of 0.9 - 3.8 THz with average power up to 15 mu W were achieved using a 1.064 mu m fiber laser for the pump laser. Biomolecular characterization for an early application of this system is also shown in this work by anisotropic spectroscopic signature detection of molecular crystals in the THz region.
%B Nonlinear Frequency Generation and Conversion: Materials and Devices Xviii %S Proceedings of SPIE %I Spie-Int Soc Optical Engineering %C Bellingham %V 10902 %@ 978-1-5106-2447-4 %G English %M WOS:000471820400020 %R https://doi.org/10.1117/12.2510522 %0 Conference Proceedings %B 2018 43rd International Conference on Infrared, Millimeter, and Terahertz Waves %D 2018 %T THz Anisotropy Identification using Tunable Compact Narrow Band THz Sources %A George, D. K. %A Markelz, A. G. %A McNee, I. %A Tekavec, P. %A Kozlov, V. %A Schunemann, P. %XWe demonstrate THz anisotropy signature determination of a protein crystal model using newly developed compact tunable narrow band THz sources for turn-key spectroscopic systems for the bio molecular community.
%B 2018 43rd International Conference on Infrared, Millimeter, and Terahertz Waves %S International Conference on Infrared Millimeter and Terahertz Waves %I Ieee %C New York %@ 978-1-5386-3809-5 %G English %M WOS:000449683700444 %R https://doi.org/10.1109/IRMMW-THz.2018.8510291 %0 Journal Article %J Photonics Research %D 2016 %T Modulated orientation-sensitive terahertz spectroscopy %A Singh, R. %A George, D. K. %A Bae, C. J. %A Niessen, K. A. %A Markelz, A. G. %K absorption-spectroscopy %K dynamics %K enzyme catalysis %K low-frequency modes %K lysozyme %K neutron-scattering %K Optics %K perspective %K polarization modulation %K proteins %K water %XIntramolecular vibrations of large macromolecules reside in the terahertz range. In particular, protein vibrations are closely spaced in frequency, resulting in a nearly continuous vibrational density of states. This density of vibrations interferes with the identification of specific absorption lines and their subsequent association with specific functional motions. This challenge is compounded with the absorption being dominated by the solvent and local relaxational motions. A strategy for removing the isotropic relaxational loss and isolating specific vibrations is to use aligned samples and polarization-sensitive measurements. Here, we demonstrate a technique to rapidly attain the anisotropic resonant absorbance using terahertz time domain spectroscopy and a spinning sample. The technique, modulated orientation-sensitive terahertz spectroscopy (MOSTS), has a nonzero signal only for anisotropic samples, as demonstrated by a comparison between a silicon wafer and a wire grid polarizer. For sucrose and oxalic acid molecular crystals, the MOSTS response is in agreement with modeled results for the intermolecular vibrations. Further, we demonstrate that, even in the presence of a large relaxational background, MOSTS isolates underlying vibrational resonances. (C) 2016 Chinese Laser Press
%B Photonics Research %V 4 %P A1-A8 %8 Jun %@ 2327-9125 %G English %9 Article %M WOS:000376658500001 %! Photonics Res.Photonics Res. %R https://doi.org/10.1364/PRJ.4.0000A1 %0 Conference Proceedings %B 2014 39th International Conference on Infrared, Millimeter, and Terahertz Waves %D 2014 %T Probing the Stability of Fluorescent Proteins by Terahertz Spectroscopy %A Xu, M. Y. %A George, D. K. %A Jimenez, R. %A Markelz, A. G. %K dynamics %XThe higher transmission through tissues of long wavelength light motivates the development of fluorescent proteins with excitation shifted to the red. However red fluorescent proteins (RFPs) are more susceptible to photobleaching than their shorter wavelength counterparts. In particular RFPs are more susceptible to photobleaching [1]. A possible reason for this is a decrease in the structural stability of the beta barrel. Measurements of structural stability include atomic root mean squared displacement <x(2)> measured by the X-ray B-factor and neutron quasi elastic scattering. To date, X-ray measurements of RFP's do not indicate a structural stability change and systematic scattering studies have not been performed. Using THz dielectric response we examine if the picosecond structural flexibility decreases with increasing FP stability.
%B 2014 39th International Conference on Infrared, Millimeter, and Terahertz Waves %S International Conference on Infrared Millimeter and Terahertz Waves %I Ieee %C New York %@ 978-1-4799-3877-3 %G English %M WOS:000378889200449 %R https://doi.org/10.1109/IRMMW-THz.2014.6956442 %0 Book Section %B Terahertz Biomedical Science and Technology %D 2014 %T Protein Dielectric Response at Terahertz Frequencies: Correlated and Diffusive Contributions %A George, D. K. %A Markelz, A. G. %B Terahertz Biomedical Science and Technology %I Taylor and Francis %V edited by Joo Huik Son %G eng %& 11 %R 10.1201/b17060 %0 Conference Proceedings %B Ultrafast Phenomena and Nanophotonics Xvii %D 2013 %T Measuring phonons in protein crystals %A Acbas, G. %A Niessen, K. A. %A George, D. K. %A Snell, E. %A Markelz, A. G. %E Betz, M. %E Elezzabi, A. Y. %E Song, J. J. %E Tsen, K. T. %K correlated motions %K dynamics %K mode %K molecular crystals %K molecular vibrations %K normal modes %K phonons %K protein dynamics %K spectroscopy %K Terahertz %XUsing Terahertz near field microscopy we find orientation dependent narrow band absorption features for lysozyme crystals. Here we discuss identification of protein collective modes associated with the observed features. Using normal mode calculations we find good agreement with several of the measured features, suggesting that the modes arise from internal molecular motions and not crystal phonons. Such internal modes have been associated with protein function.
%B Ultrafast Phenomena and Nanophotonics Xvii %S Proceedings of SPIE %I Spie-Int Soc Optical Engineering %C Bellingham %V 8623 %@ 978-0-8194-9392-7 %G English %M WOS:000322829300003 %R https://doi.org/10.1117/12.2006275 %0 Book Section %B Terahertz Spectroscopy and Imaging %D 2013 %T Terahertz Spectroscopy of Liquids and Biomolecules %A George, D. K. %A Markelz, A. G. %B Terahertz Spectroscopy and Imaging %I Springer-Verlag %C Berlin-Heidelberg %P 229-250 %G eng %& 9 %R 10.1007/978-3-642-29564-5_9 %0 Journal Article %J arXiv:1105.4425 %D 2012 %T Functional State Dependence of Picosecond Protein Dynamics %A Chen, J. Y. %A George, D. K. %A He, Y. %A Knab, J. R. %A Markelz, A.G. %B arXiv:1105.4425 %G eng %U http://arxiv.org/0054394 %0 Conference Proceedings %B 37th International Conference on Infrared, Millimeter, and Terahertz Waves %D 2012 %T Multi-component response in multilayer graphene revealed through terahertz and infrared magneto-spectroscopy %A Ellis, C. T. %A Stier, A. V. %A George, D. K. %A Tischler, J. G. %A Glaser, E. R. %A Myers-Ward, R. L. %A Tedesco, J. L. %A Eddy, C. R. %A Gaskill, D. K. %A Markelz, A. G. %A Cerne, J. %B 37th International Conference on Infrared, Millimeter, and Terahertz Waves %C Wollongong, Australia %8 9/2012 %G eng %R 10.1109/IRMMW-THz.2012.6380102 %0 Journal Article %J Physical Review Letters %D 2012 %T Terahertz Response and Colossal Kerr Rotation from the Surface States of the Topological Insulator Bi2Se3 %A Aguilar, R. V. %A Stier, A. V. %A Liu, W. %A Bilbro, L. S. %A George, D. K. %A Bansal, N. %A Wu, L. %A Cerne, J. %A Markelz, A. G. %A Oh, S. %A Armitage, N. P. %K bi2te3 %K Physics %XWe report the THz response of thin films of the topological insulator Bi2Se3. At low frequencies, transport is essentially thickness independent showing the dominant contribution of the surface electrons. Despite their extended exposure to ambient conditions, these surfaces exhibit robust properties including narrow, almost thickness-independent Drude peaks, and an unprecedentedly large polarization rotation of linearly polarized light reflected in an applied magnetic field. This Kerr rotation can be as large as 65 degrees and can be explained by a cyclotron resonance effect of the surface states.
%B Physical Review Letters %V 108 %P 5 %8 Feb %@ 0031-9007 %G English %9 Article %M WOS:000300576000025 %] 087403 %R https://doi.org/10.1103/physrevlett.108.087403