03325nas a2200145 4500008004100000245008500041210006900126260001200195520283400207100002103041700001903062700001303081700002003094856006503114 2021 eng d00aAnisotropic Terahertz Microscopy of Lysozyme in Different CrystalLattice Systems0 aAnisotropic Terahertz Microscopy of Lysozyme in Different Crysta c02/20213 a

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.

1 aMcKinney, J., A.1 aGeorge, D., K.1 aDeng, Y.1 aMarkelz, A., G. uhttps://www.cell.com/biophysj/fulltext/S0006-3495(20)31879-802497nas a2200193 4500008004100000245012000041210006900161260001200230300001200242490000600254520187500260100001302135700002102148700001902169700002002188700001502208700001802223856006202241 2021 eng d00aNear-Field Stationary Sample Terahertz Spectroscopic Polarimetry for Biomolecular Structural Dynamics Determination0 aNearField Stationary Sample Terahertz Spectroscopic Polarimetry  c02/2021 a658-6680 v83 a

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–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.

1 aDeng, Y.1 aMcKinney, J., A.1 aGeorge, D., K.1 aNiessen, K., A.1 aSharma, A.1 aMarkelz, A.G. uhttps://pubs.acs.org/doi/abs/10.1021/acsphotonics.0c0187601661nas a2200229 4500008004100000245005800041210005800099300001600157490000800173520102600181100001401207700001901221700001401240700001301254700001901267700002201286700001501308700001801323700002101341700002001362856004901382 2021 eng d00aPhonon Kinetics of Fructose at the Melting Transition0 aPhonon Kinetics of Fructose at the Melting Transition a12269-122760 v1253 a

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.

 

1 aDavie, A.1 aVandrevala, F.1 aDampf, S.1 aDeng, Y.1 aGeorge, D., K.1 aSylvester, E., D.1 aKorter, T.1 aEinarsson, E.1 aBenedict, J., B.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/52001859nas a2200241 4500008004500000020001400045245011000059210006900169260000800238300001400246490000800260520114300268653001501411100002101426700001501447700001601462700001301478700001901491700002201510700001601532700002001548856004901568 2020 Engldsh  a0006-349500aEvidence of Intramolecular Structural Stabilization in Light Activated State of Orange Carotenoid Protein0 aEvidence of Intramolecular Structural Stabilization in Light Act cFeb a208A-208A0 v1183 a

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 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.

10aBiophysics1 aMcKinney, J., A.1 aSharma, A.1 aCrossen, K.1 aDeng, Y.1 aGeorge, D., K.1 aLechno-Yossef, S.1 aKerfeld, C.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/25301739nas a2200205 4500008004500000020001400045245008900059210006900148260000800217300001400225490000800239520112900247653001501376100002101391700001701412700001901429700001601448700002001464856004901484 2020 Engldsh  a0006-349500aLong Range Correlated Motions of TIM and their Possible Influence on Enzyme Function0 aLong Range Correlated Motions of TIM and their Possible Influenc cFeb a207A-207A0 v1183 a

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 “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.

10aBiophysics1 aMcKinney, J., A.1 aDeng, Y., T.1 aGeorge, D., K.1 aRichard, J.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/25201881nas a2200181 4500008004100000245009900041210006900140260001600209520131100225100001701536700001501553700001301568700001501581700002201596700001601618700001601634856004901650 2020 eng d00aStabilization of Terahertz Vibrational Modes in Illuminated Orange Carotenoid Protein Crystals0 aStabilization of Terahertz Vibrational Modes in Illuminated Oran aBuffalo, NY3 a

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.

1 aMcKinney, J.1 aSharma, A.1 aDeng, Y.1 aGeorge, D.1 aLechno-Yossef, S.1 aKerfeld, C.1 aMarkelz, A. uhttps://markelz.physics.buffalo.edu/node/54401834nas a2200385 4500008004100000020001400041245007100055210006900126260002400195300001000219520062400229653001500853653003100868653002700899653003400926653003400960653004300994653001501037653002301052653003001075653001501105653001301120653004501133653002701178653001701205653002201222653002701244653002701271653004101298653001501339100001301354700001601367700001601383856004901399 2019 eng d a2162-203500aAngular Distortion Removal of THz Anisotropic Dichroism Microscope0 aAngular Distortion Removal of THz Anisotropic Dichroism Microsco aParis, Francec2019 a1 - 23 a

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.

10aabsorption10aangular distortion removal10aBiomedical measurement10acontinuous iso-response curve10adetection light polarizations10adiscontinuous iso-response angle pairs10aDistortion10alight polarisation10amaterial characterization10aMicroscopy10aproteins10arapid anisotropic terahertz spectroscopy10arelative polarizations10aspectroscopy10astationary sample10aterahertz spectroscopy10aterahertz wave spectra10aTHz anisotropic dichroism microscope10avibrations1 aDeng, Y.1 aNiessen, K.1 aMarkelz, A. uhttps://ieeexplore.ieee.org/document/887379301100nas a2200169 4500008004500000020002200045245011300067210006900180260001900249520052500268100001700793700001700810700001500827700001900842700002000861856004900881 2019 Engldsh  a978-1-5386-8285-200aAnisotropic Terahertz Microscopy of Protein Collective Vibrations: Crystal Symmetry and Hydration Dependence0 aAnisotropic Terahertz Microscopy of Protein Collective Vibration aNew YorkbIeee3 a

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.

1 aMcKinney, J.1 aDeng, Y., T.1 aSharma, A.1 aGeorge, D., K.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/23500619nas a2200193 4500008004100000245008500041210006900126490000900195100001600204700002200220700001800242700001500260700002400275700001500299700001800314700002400332700002000356856004900376 2019 eng d00aBlue Shift of a Molecular Crystal Phonon at the Solid to Liquid Phase Transition0 aBlue Shift of a Molecular Crystal Phonon at the Solid to Liquid 0 v20191 aDavie, Alex1 aVandrevala, Farah1 aDeng, Yanting1 aGeorge, D.1 aSylvester, Eric, D.1 aKorter, T.1 aEinarsson, E.1 aBenedict, Jason, B.1 aMarkelz, Andrea uhttps://markelz.physics.buffalo.edu/node/27600524nas a2200169 4500008004500000020001400045245008200059210006900141260000800210300001400218490000800232653001500240100001700255700001700272700001600289856004900305 2019 Engldsh  a0006-349500aDeuteration and Inhibitor Binding Dependence of Protein Collective Vibrations0 aDeuteration and Inhibitor Binding Dependence of Protein Collecti cFeb a488A-488A0 v11610aBiophysics1 aDeng, Y., T.1 aMcKinney, J.1 aMarkelz, A. uhttps://markelz.physics.buffalo.edu/node/24800542nas a2200181 4500008004500000020001400045245007100059210006700130260000800197300001400205490000800219653001500227100002100242700001700263700001500280700001600295856004900311 2019 Engldsh  a0006-349500aThe Effect of Crystal Contact Forces on the Protein Global Motions0 aEffect of Crystal Contact Forces on the Protein Global Motions cFeb a489A-489A0 v11610aBiophysics1 aMcKinney, J., A.1 aDeng, Y., T.1 aGeorge, D.1 aMarkelz, A. uhttps://markelz.physics.buffalo.edu/node/25101391nas a2200277 4500008004500000020001400045245003600059210003500095260000800130300001600138490000700154520070700161653001200868653001700880653001300897653001000910653001100920653002800931653001400959653002900973653000901002100001601011700001701027700002001044856004901064 2019 Engldsh  a1094-408700aNear-field THz micropolarimetry0 aNearfield THz micropolarimetry cSep a28036-280470 v273 a

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

10abinding10aconductivity10adynamics10amodes10aOptics10apolarization modulation10aTerahertz10atime-domain spectroscopy10awse21 aNiessen, K.1 aDeng, Y., T.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/23900492nas a2200145 4500008004100000245008500041210006900126260001200195100001300207700001700220700001300237700001900250700002000269856005700289 2019 eng d00aProtein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence0 aProtein Intramolecular Motions with Deuteration and Inhibitor Bi c03/20191 aDeng, Y.1 aMcKinney, J.1 aRomo, T.1 aGrossfield, A.1 aMarkelz, A., G. uhttps://meetings.aps.org/Meeting/MAR19/Session/R63.302599nas a2200205 4500008004500000020001400045245005800059210005800117260000800175300001400183490000800197520204200205653001502247100001702262700001702279700001302296700001902309700001602328856004902344 2019 Engldsh  a0006-349500aSpectral Assignment of Lysozyme Collective Vibrations0 aSpectral Assignment of Lysozyme Collective Vibrations cFeb a564A-564A0 v1163 a
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°, b = 32.7A°, c = 35.1A°, α = 88.2°, β = 108.9°, γ = 111.9°, 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.
10aBiophysics1 aDeng, Y., T.1 aMcKinney, J.1 aRomo, T.1 aGrossfield, A.1 aMarkelz, A. uhttps://markelz.physics.buffalo.edu/node/24900708nas a2200229 4500008004500000020001400045245011700059210006900176260000800245300001400253490000800267653001500275100001700290700001700307700001700324700002300341700001600364700001200380700001700392700002000409856004900429 2018 Engldsh  a0006-349500aIncrease in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State0 aIncrease in Dynamical Collectivity and Directionality of Orange  cFeb a522A-522A0 v11410aBiophysics1 aDeng, Y., T.1 aLuck, C., H.1 aRomo, T., D.1 aGrossfield, A., M.1 aBandara, S.1 aRen, Z.1 aYang, X., J.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/24700501nas a2200145 4500008004100000245011200041210006900153490001200222100001100234700001300245700001300258700001500271700001600286856005300302 2018 eng d00aMeasuring Protein Intramolecular Dynamics with Terahertz Light: Functional Changes and Relevance to Biology0 aMeasuring Protein Intramolecular Dynamics with Terahertz Light F0 vH50.0011 aXu, M.1 aDeng, Y.1 aLuck, C.1 aSharma, A.1 aMarkelz, A. uhttp://meetings.aps.org/link/BAPS.2018.MAR.H50.100451nas a2200121 4500008004100000245010900041210006900150490001200219100001300231700001600244700001600260856005300276 2018 eng d00aRapid Terahertz Dichroism Near Field Microscopy for Biomolecular Intramolecular Vibrational Spectroscopy0 aRapid Terahertz Dichroism Near Field Microscopy for Biomolecular0 vA50.0081 aDeng, Y.1 aNiessen, K.1 aMarkelz, A. uhttp://meetings.aps.org/link/BAPS.2018.MAR.A50.800510nas a2200157 4500008004100000245005500041210005500096260003100151300001200182100001800194700001700212700002600229700002500255700002300280856004900303 2018 eng d00aTerahertz Light Fingerprints Biomolecular Dynamics0 aTerahertz Light Fingerprints Biomolecular Dynamics bOptical Society of America aSW3D. 51 aDeng, Yanting1 aXu, Mengyang1 aNiessen, Katherine, A1 aGeorge, Deepu, Koshy1 aMarkelz, Andrea, G uhttps://markelz.physics.buffalo.edu/node/18204125nas a2200841 4500008004500000020001400045245005400059210005000113260000800163300000700171490000700178520199900185653001202184653001502196653002202211653001502233653001602248653002902264653001202293653002702305653001402332653001902346653001402365653000802379653002902387100002002416700002102436700002102457700001902478700002102497700001502518700001602533700001502549700001802564700002102582700002102603700002302624700001602647700002602663700001402689700001702703700002402720700001602744700001302760700002602773700001902799700001402818700002002832700001902852700002002871700002002891700001402911700001902925700001602944700001202960700001802972700001902990700001603009700001403025700002003039700001503059700001403074700001303088700001503101700001403116700001403130700001603144700001503160700001503175700002303190700002103213856004903234 2017 Engldsh  a0022-372700aThe 2017 terahertz science and technology roadmap0 a2017 terahertz science and technology roadmap cFeb a490 v503 a

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 'real world' 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.

10aex-vivo10ageneration10ametal wave-guides10anear-field10aperformance10aphotoconductive emitters10aPhysics10aquantum-cascade lasers10aradiation10asemiconductors10aTerahertz10athz10atime-domain spectroscopy1 aDhillon, S., S.1 aVitiello, M., S.1 aLinfield, E., H.1 aDavies, A., G.1 aHoffmann, M., C.1 aBooske, J.1 aPaoloni, C.1 aGensch, M.1 aWeightman, P.1 aWilliams, G., P.1 aCastro-Camus, E.1 aCumming, D., R. S.1 aSimoens, F.1 aEscorcia-Carranza, I.1 aGrant, J.1 aLucyszyn, S.1 aKuwata-Gonokami, M.1 aKonishi, K.1 aKoch, M.1 aSchmuttenmaer, C., A.1 aCocker, T., L.1 aHuber, R.1 aMarkelz, A., G.1 aTaylor, Z., D.1 aWallace, V., P.1 aZeitler, J., A.1 aSibik, J.1 aKorter, T., M.1 aEllison, B.1 aRea, S.1 aGoldsmith, P.1 aCooper, K., B.1 aAppleby, R.1 aPardo, D.1 aHuggard, P., G.1 aKrozer, V.1 aShams, H.1 aFice, M.1 aRenaud, C.1 aSeeds, A.1 aStohr, A.1 aNaftaly, M.1 aRidler, N.1 aClarke, R.1 aCunningham, J., E.1 aJohnston, M., B. uhttps://markelz.physics.buffalo.edu/node/22400599nas a2200193 4500008004500000020001400045245009200059210006900151260000800220300001400228490000800242653001500250100001500265700002000280700001700300700001900317700002000336856004900356 2017 Engldsh  a0006-349500aEscaping the Water Cage: Protein Intramolecular Vibrations and the Dynamical Transition0 aEscaping the Water Cage Protein Intramolecular Vibrations and th cFeb a318A-318A0 v11210aBiophysics1 aXu, M., Y.1 aNiessen, K., A.1 aDeng, Y., T.1 aMichki, N., S.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/25600508nas a2200145 4500008004100000245011600041210006900157260001200226100001300238700001100251700001200262700002000274700001600294856005200310 2017 eng d00aGlobal Picosecond Structural Dynamics of Orange Carotenoid Protein in Photo/Chemical Activated Signaling States0 aGlobal Picosecond Structural Dynamics of Orange Carotenoid Prote c03/20171 aDeng, Y.1 aXu, M.1 aLiu, H.1 aBlankenship, R.1 aMarkelz, A. uhttp://meetings.aps.org/link/BAPS.2017.MAR.S4.200552nas a2200181 4500008004100000020001400041245006300055210006300118260001000181300001400191490000800205100002700213700001700240700001800257700002200275700002400297856004900321 2017 eng d a0006-349500aImportance of Protein Vibration Directionality on Function0 aImportance of Protein Vibration Directionality on Function cFeb 3 a353A-353A0 v1121 aNiessen, Katherine, A.1 aXu, Mengyang1 aDeng, Yanting1 aSnell, Edward, H.1 aMarkelz, Andrea, G. uhttps://markelz.physics.buffalo.edu/node/25400601nas a2200193 4500008004500000020001400045245009300059210006900152260000800221300001400229490000800243653001500251100001700266700001500283700001600298700002400314700002000338856004900358 2017 Engldsh  a0006-349500aOrange Carotenoid Protein Picosecond Dynamics Changes with Photo and Chemical Activation0 aOrange Carotenoid Protein Picosecond Dynamics Changes with Photo cFeb a441A-441A0 v11210aBiophysics1 aDeng, Y., T.1 aXu, M., Y.1 aLiu, H., J.1 aBlankenship, R., E.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/25001585nas a2200181 4500008004500000020002200045245010500067210006900172260001900241520099700260100001501257700001601272700001501288700001701303700001401320700002001334856004901354 2016 Engldsh  a978-1-4673-8485-800aAnisotropic Absorption Measurements Reveal Protein Dynamical Transition in Intramolecular Vibrations0 aAnisotropic Absorption Measurements Reveal Protein Dynamical Tra aNew YorkbIeee3 a

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.

1 aXu, M., Y.1 aNiessen, K.1 aMichki, N.1 aDeng, Y., T.1 aSnell, E.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/24602250nas a2200157 4500008004100000245009400041210006900135260001700204520170800221100001801929700001701947700002701964700002001991700002402011856005702035 2016 eng d00aDirect Measurements of the Long-Range Collective Vibrations of Photoactive Yellow Protein0 aDirect Measurements of the LongRange Collective Vibrations of Ph aBaltimore MD3 a

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

1 aDeng, Yanting1 aXu, Mengyang1 aNiessen, Katherine, A.1 aSchmidt, Marius1 aMarkelz, Andrea, G. uhttps://onlinelibrary.wiley.com/doi/10.1002/pro.302602427nas a2200169 4500008004100000245012000041210006900161260001800230520183800248100001702086700002302103700001802126700001802144700001802162700002002180856005702200 2016 eng d00a The Role of Dynamical Transition in Protein Function: Coupling of Protein Collective Vibrations and Water Dynamics0 aRole of Dynamical Transition in Protein Function Coupling of Pro aBaltimore, MD3 a

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.

1 aXu, Mengyang1 aNiessen, Katherine1 aDeng, Yanting1 aMichki, Nigel1 aSnell, Edward1 aMarkelz, Andrea uhttps://onlinelibrary.wiley.com/doi/10.1002/pro.3026