Imperial College London

ProfessorJaspervan Thor

Faculty of Natural SciencesDepartment of Life Sciences

Professor of Molecular Biophysics
 
 
 
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Contact

 

+44 (0)20 7594 5071j.vanthor Website

 
 
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Location

 

703Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

77 results found

Kaucikas M, Barber J, van Thor JJ, 2013, Polarization sensitive ultrafast mid-IR pump probe micro-spectrometer with diffraction limited spatial resolution, Optics Express, Vol: 21, Pages: 8357-8370

Journal article

Warren M, Kaucikas M, Fitzpatrick A, Champion P, Sage JT, van Thor JJet al., 2013, Ground state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa, Nature Communications

Journal article

Kaucikas M, Warren M, Michailovas A, Antanavicius R, van Thor JJet al., 2013, Beam patterns in OPO employing walk-off compensating BBO crystals, Laser Physics, Pages: 1-6

Journal article

Juozapavicius M, Kaucikas M, Dimitrov SD, Barnes PRF, van Thor JJ, O'Regan BCet al., 2013, Evidence for “Slow” Electron Injection in Commercially Relevant Dye-2 Sensitized Solar Cells by Vis−NIR and IR Pump−Probe Spectroscopy, J Phys Chem C

We present femtosecond to nanosecond transient absorption (TA)data on electron injection in dye-sensitized solar cells (DSSCs) fabricated with lowvolatility, commercially relevant electrolytes, with and without added lithium.Results are shown over an extended time range (300 fs−6.3 ns) and extendedwavelength range (800−1400 nm) for both N719 and C106 dyes. Kinetics weremeasured on both TiO2 and noninjecting ZrO2. Using the latter, we havedetermined the spectra and absorption coefficient of N719* across the wavelengthrange. We find an isosbestic point in the TA spectra on TiO2 near 900 nm for allcells, existing from <1 ps to >1 ns. We show how measurements near this isosbesticpoint can give a false impression of uniformly femtosecond injection dynamics inDSSCs. Comparison of dynamics measured at 1200 nm with mid-IR transient absorption measured at 5100 nm confirms amajority proportion of slow (>10 ps) electron injection in these commercially relevant cells. We also comment on a recentpublication which appears to directly contradict the results we present.

Journal article

van Thor JJ, Lincoln CN, Kellner B, Bourdakos KN, Thompson LM, Bearpark MJ, Champion PM, Sage JTet al., 2012, Ultrafast vibrational dynamics of parallel excited state proton transfer reactions in the Green Fluorescent Protein, VIBRATIONAL SPECTROSCOPY, Vol: 62, Pages: 1-6, ISSN: 0924-2031

Journal article

Kim TW, Lee JH, Choi J, Kim KH, van Wilderen LJ, Guerin L, Kim Y, Jung YO, Yang C, Kim J, Wulff M, van Thor JJ, Ihee Het al., 2012, Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump−Probe X-ray Solution Scattering., J. Am. Chem. Soc.

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump−probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 μs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.

Journal article

Lincoln CN, Fitzpatrick AE, van Thor JJ, 2012, Photoisomerisation Quantum Yield and Non-linear Cross-Sections with Femtosecond Excitation of the Photoactive Yellow Protein, Phys Chem Chem Phys, Pages: 15752-15764

Journal article

Juozapavicius M, Kaucikas M, van Thor JJ, O'Regan Bet al., 2012, Observation of Multi-Exponential Pico to Sub-Nanosecond Electron Injection in Optimized Dye-Sensitized Solar Cells With Visible-Pump Mid-Infrared-Probe Transient Absorption Spectroscopy, J. Phys. Chem. C

Journal article

Fitzpatrick AE, Lincoln CN, van Wilderen LJ, van Thor JJet al., 2011, Pump-Dump-Probe and Pump-Repump-Probe Ultrafast Spectroscopy Resolves Cross Section of an Early Ground State Intermediate and Stimulated Emission in the Photoreactions of the Pr Ground State of the Cyanobacterial Phytochrome Cph1., The Journal of Physical Chemistry B

The primary photoreactions of the red absorbing ground state (Pr) of the cyanobacterial phytochrome Cph1 from Synechocystis PC 6803 involve C15=C16 Z-E photoisomerisation of its phycocyanobilin chromophore. The first observable ground state intermediate in pump-probe measurements of the photocycle, 'Lumi-R', is formed with picosecond kinetics, and involves excited state decay reactions that have 3 and 14 ps time constants. Here, we have studied the photochemical formation of the Lumi-R intermediate using multi pulse picosecond visible spectroscopy. Pump-dump-probe (PDP) and pump-repump-probe (PRP) experiments were carried out by employing two femtosecond visible pulses with 1, 14 and 160 ps delays, together with a broadband dispersive visible probe. The time delays between the two excitation pulses have been selected to allow interaction with the dominant (3 and 14 ps) kinetic phases of Lumi-R formation. The frequency dependence of the PDP and PRP amplitudes was investigated at 620 nm, 640 nm, 660 nm and 680 nm, covering excited state absorption (λmax = 620 nm), ground state absorption (λmax = 660 nm) and stimulated emission (λmax = 680 nm) cross sections. Experimental double difference transient absorbance signals (∆∆OD), from the PDP and PRP measurements required corrections to remove contributions from ground state repumping. The sensitivity of the resulting ∆∆OD signals was systematically investigated for possible connectivity schemes and photochemical parameters. When applying a homogeneous (sequentially decaying) connectivity scheme in both the 3 and 14 ps kinetic phases, evidence for repumping of an intermediate that has an electronic ground state configuration (GSI) is taken from the dump-induced S1 formation with 620, 640 and 660 nm wavelengths and 1 and 14 ps repump delays. Evidence for repumping a GSI is also seen, for the same excitation wavelengths, when imposing a target connectivity scheme proposed in refs1,2 for the 1 ps repump d

Journal article

Ramachandran PL, Lovett JE, Carl PJ, Cammarata M, Lee JH, Jung YO, Ihee H, Timmel CR, van Thor JJet al., 2011, The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 133, Pages: 9395-9404, ISSN: 0002-7863

Journal article

van Wilderen LJG, Lincoln CN, van Thor JJ, 2011, Modelling multi-pulse population dynamics from ultrafast spectroscopy, PLoS One, Vol: 6, Pages: 1-14, ISSN: 1932-6203

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is es

Journal article

Sage JT, Zhang Y, McGeehan J, Ravelli RBG, Weik M, Thor JJVet al., 2011, Infrared protein crystallography, Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol: 1841, Pages: 760-777

We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO2. Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Journal article

Ramachandran PL, Lovett JE, Carl PJ, Cammarata M, Lee JH, Jung YO, Ihee H, Timmel C, van Thor JJet al., 2011, Catching a short-lived photoreceptor intermediate with pulsed X-rays, ESRF Highlights 2011

Book chapter

Thor JJV, 2011, Photoconversion of the Green Fluorescent Protein and Related Proteins, Springer Series on Fluorescence, Editors: Wolfbeis, Hof

This review focuses on the mechanistic details of photochromic reactions of the green fluorescent protein (GFP) and also of its mutant derivatives and related fluorescent proteins. A number of distinct photochromic processes have so far been identified that have entirely different photochemical and chemical basis, which will be reviewed. In addition to bright fluorescence, the GFP from the jellyfish Aequorea victoria undergoes photochromic transformation with blue or UV illumination. The associated change in electronic absorption provides a spectroscopic contrast that can be used in fluorescence microscopy application to tag and track the movement of populations that are photoconverted. Key to the successful use of photoconversion for such microscopy experiments is in fact the relatively low quantum yield of the irreversible process. In the wild-type GFP, photoconversion is triggered by light-induced electron transfer from the buried anionic carboxylate of Glu222 to the optically excited protonated chromophore. An unstable carboxylate radical subsequently cleaves off a CO2 molecule in a “Kolbe” type reaction that has been trapped in a partially oriented site near the chromophore-binding site at 100K, as observed by low-temperature X-ray crystallography and cryo-infrared crystallography. Structural intermediates in the subsequent relaxation pathway involve motion of CO2, amino acids and H-bonded waters both in the chromophore vicinity and at longer range. This review provides an overview of the molecular characterisation using structural and spectroscopy methods of this photoconversion reaction of GFP. In addition, the mechanisms of photochromic reactions of mutants of GFP and related fluorescent proteins will be summarised and discussed. These include the cis–trans isomerisation and protonation changes in Dronpa, asFP595 and IrisFP and related proteins, light-induced maturation in aceGFPL, and photoinduced beta-elimination and backbone cleavage tha

Book chapter

Ramachandran P, Lovett JE, Carl P, Cammarata M, Lee JH, Yung YO, Ihee H, Timmel C, van Thor JJet al., 2011, ESRF 2011 Highlight: Catching a short-lived photoreceptor intermediate with pulsed X-rays

Working paper

McClelland A, Demidov A, Benabbas A, Sun Y, Venugopal K, Sage T, van Thor J, Champion Pet al., 2010, Investigation of excited state proton transfer in green fluorescent protein, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol: 240, ISSN: 0065-7727

Journal article

McClelland A, Demidov A, Benabbas A, Sun YH, Venugopal K, Sage JT, van Thor JJ, Champion Pet al., 2010, Investigation of excited state proton transfer in green fluorescent protein, Abstracts of Papers of the American Chemical Society

Conference paper

McClelland A, Demidov A, Benabbas A, Sun YH, Venugopal K, Sage JT, van Thor JJ, Champion Pet al., 2010, Direct Observations of Low Frequency Vibrational Coherences in wt-GFP, XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY, Pages: 674-675

Conference paper

Wilderen LJGWV, Clark IP, Towrie M, Thor JJV, van Thor JJet al., 2009, Mid-infrared picosecond pump-dump-probe and pump-repump-probe experiments to resolve a ground-state intermediate in cyanobacterial phytochrome Cph1, J Phys Chem B, Vol: 113, Pages: 16354-16364

Multipulse picosecond mid-infrared spectroscopy has been used to study photochemical reactions of the cyanobacterial phytochrome photoreceptor Cph1. Different photophysical schemes have been discussed in the literature to describe the pathways after photoexcitation, particularly, to identify reaction phases that are linked to photoisomerisation and electronic decay in the 1566-1772 cm(-1) region that probes C=C and C=O stretching modes of the tetrapyrrole chromophore. Here, multipulse spectroscopy is employed, where, compared to conventional visible pump-mid-infrared probe spectroscopy, an additional visible pulse is incorporated that interacts with populations that are evolving on the excited- and ground-state potential energy surfaces. The time delays between the pump and the dump pulse are chosen such that the dump pulse interacts with different phases in the reaction process. The pump and dump pulses are at the same wavelength, 640 nm, and are resonant with the Pr ground state as well as with the excited state and intermediates. Because the dump pulse additionally pumps the remaining, partially recovered, and partially oriented ground-state population, theory is developed for estimating the fraction of excited-state molecules. The calculations take into account the model-dependent ground-state recovery fraction, the angular dependence of the population transfer resulting from the finite bleach that occurs with linearly polarized intense femtosecond optical excitation, and the partially oriented population for the dump field. Distinct differences between the results from the experiments that use a 1 or a 14 ps dump time favor a branching evolution from S1 to an excited state or reconfigured chromophore and to a newly identified ground-state intermediate (GSI). Optical dumping at 1 ps shows the instantaneous induced absorption of a delocalized C=C stretching mode at 1608 cm(-1), where the increased cross section is associated with the electronic ground-state struc

Journal article

van Thor JJ, Ronayne KL, Towrie M, Sage JTet al., 2009, Deriving molecular information from photoselection experiments of the green fluorescent protein using intense femtosecond pulses, CCLRC Central Laser Facility Annual Report 2007-2008, Publisher: CCLRC

Book chapter

van Thor JJ, 2009, Photoreactions and dynamics of the green fluorescent protein, Chem Soc Rev, Vol: 38, Pages: 2935-2950

The wild type green fluorescent protein (GFP) from Aequorea victoria has been extensively investigated with a strong focus on the photochemistry and structural dynamics that are linked with its diverse activities. GFP combines a number of remarkable, and some unique, features that are still intensely researched both experimentally and theoretically. The protein environment effectively inhibits deactivation pathways that are dominant in the isolated chromophore and is therefore responsible for the bright fluorescence. Its p-hydroxybenzylidene-imidazolidinone chromophore acts as a photoacid, and optical excitation triggers ultrafast proton transfer reactions in the active site. The microscopic details of the proton transfer mechanism through a hydrogen bonding network are discussed in this critical review. This property of the wild type GFP has provided the opportunity to characterise the role of the specific protein environment in the proton transfer reactions in comparison to photoacid reactions in the condensed phase. In addition, GFP displays a photochromic side reaction that is uniquely caused by electron transfer from a buried anionic glutamic acid to the optically excited chromophore. This phototransformation property has also been exploited in high resolution fluorescence microscopy techniques. The discussion in this review is extended to include vibrational spectroscopy and structural dynamics (106 references).

Journal article

van Thor JJ, Ronayne KL, Towrie M, Sage JTet al., 2008, Balance between parallel ultrafast excited state proton transfer reactions in GFP has a structural origin., Biophys J, Vol: 95, Pages: 1902-1912

The fluorescence photocycle of the green fluorescent protein is functionally dependent on the specific structural protein environment. A direct relationship between equilibrium protein side-chain conformation of glutamate 222 and reactivity is established, particularly the rate of ultrafast proton transfer reactions in the fluorescence photocycle. We show that parallel transformations in the photocycle have a structural origin, and we report on the vibrational properties of responsive amino acids on an ultrafast timescale. Blue excitation of GFP drives two parallel, excited-state deuteron transfer reactions with 10 ps and 75 ps time constants to the buried carboxylic acid side chain of glutamate 222 via a hydrogen-bonding network. Assignment of 1456 cm(-1) and 1441 cm(-1) modes to nu(sym) and assignment of 1564 cm(-1) and 1570 cm(-1) features to nu(asym) of E222 in the 10 ps and 75 ps components, respectively, was possible from the analysis of the transient absorption data of an E222D mutant and was consistent with photoselection measurements. In contrast to the wild-type, measurements of E222D can be described with only one difference spectrum, with the nu(sym) mode at 1435 cm(-1) and the nu(asym) mode at 1567 cm(-1), also correlating a large Deltanu(asym-sym) with slow excited-state proton transfer kinetics. Density Functional Theory calculations and published model compound and theoretical studies relate differences in Deltanu(asym-sym) to the strength and number of hydrogen-bonding interactions that are detected via equilibrium geometry and COO- stretching frequency differences of the carboxylate. The correlation of photocycle kinetics with side-chain conformation of the acceptor suggests that proton transfer from S205 to E222 controls the rate of the overall excited-state proton transfer process, which is consistent with recent theoretical predictions. Photoselection measurements show agreement for localized C=O vibrations of chromophore, Q69, and E222 with Den

Journal article

van Thor JJ, Ronayne KL, Towrie M, 2007, Formation of the early photoproduct Lumi-R of cyanobacterial phytochrome Cph1 observed by ultrafast mid-infrared spectroscopy, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 129, Pages: 126-132, ISSN: 0002-7863

Journal article

van Thor JJ, Mackeen M, Kuprov I, Dwek RA, Wormald MRet al., 2006, Chromophore structure in the photocycle of the cyanobacterial phytochrome Cph1, BIOPHYSICAL JOURNAL, Vol: 91, Pages: 1811-1822, ISSN: 0006-3495

Journal article

van Thor JJ, Sage JT, 2006, Charge transfer in green fluorescent protein, PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, Vol: 5, Pages: 597-602, ISSN: 1474-905X

Journal article

van Thor JJ, Towrie M, Ronayne K, Georgiev GY, Sage JTet al., 2006, Ultrafast and low barrier motions in the Photoreactions of the Green Fluorescent Protein, Conference on Genetically Engineered Probes for Biomedical Applications, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X

Conference paper

van Thor JJ, Zanetti G, Ronayne K, Towrie Met al., 2006, Picosecond time resolved infrared absorption measurements reporting on the structural events in the photocycle of Green Fluorescent Protein, CCLRC Central Laser Facility Annual Report 2004-2005, Publisher: CCLRC

Book chapter

van Thor JJ, Fisher N, Rich PR, 2005, Assignments of the Pfr-Pr FTIR difference spectrum of cyanobacterial phytochrome Cph1 using N-15 and C-13 isotopically labeled phycocyanobilin chromophore, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 109, Pages: 20597-20604, ISSN: 1520-6106

Journal article

van Thor JJ, Georgiev GY, Towrie M, Sage JTet al., 2005, Ultrafast and low barrier motions in the photoreactions of the green fluorescent protein, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 280, Pages: 33652-33659, ISSN: 0021-9258

Journal article

van Thor JJ, Zanetti G, Ronayne KL, Towrie Met al., 2005, Structural events in the photocycle of green fluorescent protein, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 109, Pages: 16099-16108, ISSN: 1520-6106

Journal article

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