Articles - 4hy8 mentioned but not cited (1)
- Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Jung YO, Lee JH, Kim J, Schmidt M, Moffat K, Srajer V, Ihee H. Nat Chem 5 212-220 (2013)
Reviews citing this publication (13)
- Learning from photobiology how to design molecular devices using a computer. Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M. Chem Soc Rev 43 4019-4036 (2014)
- Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics. Moffat K. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 369 20130568 (2014)
- A short history of structure based research on the photocycle of photoactive yellow protein. Schmidt M. Struct Dyn 4 032201 (2017)
- Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors. Lindner R, Heintz U, Winkler A. Front Mol Biosci 2 33 (2015)
- Dynamic structural science: recent developments in time-resolved spectroscopy and X-ray crystallography. Trincao J, Hamilton ML, Christensen J, Pearson AR. Biochem. Soc. Trans. 41 1260-1264 (2013)
- Deciphering Structural Photophysics of Fluorescent Proteins by Kinetic Crystallography. Bourgeois D. Int J Mol Sci 18 (2017)
- Relating Structure and Dynamics in RNA Biology. Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Cold Spring Harb Perspect Biol 11 (2019)
- Sample Delivery Media for Serial Crystallography. Nam KH. Int J Mol Sci 20 (2019)
- Towards the Idea of Molecular Brains. Timsit Y, Grégoire SP. Int J Mol Sci 22 11868 (2021)
- Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Timsit Y, Lescot M, Valiadi M, Not F. Int J Mol Sci 22 11311 (2021)
- Macromolecular movies, storybooks written by nature. Schmidt M. Biophys Rev 13 1191-1197 (2021)
- Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins. Domratcheva T, Schlichting I. Faraday Discuss. 207 9-26 (2018)
- Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Schmidt M. Int J Mol Sci 20 (2019)
Articles citing this publication (63)
- Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Tenboer J, Basu S, Zatsepin N, Pande K, Milathianaki D, Frank M, Hunter M, Boutet S, Williams GJ, Koglin JE, Oberthuer D, Heymann M, Kupitz C, Conrad C, Coe J, Roy-Chowdhury S, Weierstall U, James D, Wang D, Grant T, Barty A, Yefanov O, Scales J, Gati C, Seuring C, Srajer V, Henning R, Schwander P, Fromme R, Ourmazd A, Moffat K, Van Thor JJ, Spence JC, Fromme P, Chapman HN, Schmidt M. Science 346 1242-1246 (2014)
- Time-resolved serial femtosecond crystallography at the European XFEL. Pandey S, Bean R, Sato T, Poudyal I, Bielecki J, Cruz Villarreal J, Yefanov O, Mariani V, White TA, Kupitz C, Hunter M, Abdellatif MH, Bajt S, Bondar V, Echelmeier A, Doppler D, Emons M, Frank M, Fromme R, Gevorkov Y, Giovanetti G, Jiang M, Kim D, Kim Y, Kirkwood H, Klimovskaia A, Knoska J, Koua FHM, Letrun R, Lisova S, Maia L, Mazalova V, Meza D, Michelat T, Ourmazd A, Palmer G, Ramilli M, Schubert R, Schwander P, Silenzi A, Sztuk-Dambietz J, Tolstikova A, Chapman HN, Ros A, Barty A, Fromme P, Mancuso AP, Schmidt M. Nat Methods 17 73-78 (2020)
- Structural enzymology using X-ray free electron lasers. Kupitz C, Olmos JL, Holl M, Tremblay L, Pande K, Pandey S, Oberthür D, Hunter M, Liang M, Aquila A, Tenboer J, Calvey G, Katz A, Chen Y, Wiedorn MO, Knoska J, Meents A, Majriani V, Norwood T, Poudyal I, Grant T, Miller MD, Xu W, Tolstikova A, Morgan A, Metz M, Martin-Garcia JM, Zook JD, Roy-Chowdhury S, Coe J, Nagaratnam N, Meza D, Fromme R, Basu S, Frank M, White T, Barty A, Bajt S, Yefanov O, Chapman HN, Zatsepin N, Nelson G, Weierstall U, Spence J, Schwander P, Pollack L, Fromme P, Ourmazd A, Phillips GN, Schmidt M. Struct Dyn 4 044003 (2017)
- Proteins in action: femtosecond to millisecond structural dynamics of a photoactive flavoprotein. Brust R, Lukacs A, Haigney A, Addison K, Gil A, Towrie M, Clark IP, Greetham GM, Tonge PJ, Meech SR. J. Am. Chem. Soc. 135 16168-16174 (2013)
- Protein structural dynamics revealed by time-resolved X-ray solution scattering. Kim JG, Kim TW, Kim J, Ihee H. Acc. Chem. Res. 48 2200-2208 (2015)
- Letter Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA. Nat Chem 6 258-259 (2014)
- Probing anisotropic structure changes in proteins with picosecond time-resolved small-angle X-ray scattering. Cho HS, Schotte F, Dashdorj N, Kyndt J, Anfinrud PA. J Phys Chem B 117 15825-15832 (2013)
- Letter Reply to 'contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein'. Jung YO, Lee JH, Kim J, Schmidt M, Moffat K, Šrajer V, Ihee H. Nat Chem 6 259-260 (2014)
- Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein. Kim TW, Yang C, Kim Y, Kim JG, Kim J, Jung YO, Jun S, Lee SJ, Park S, Kosheleva I, Henning R, van Thor JJ, Ihee H. Phys Chem Chem Phys 18 8911-8919 (2016)
- Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein. van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber T. Faraday Discuss. 171 439-455 (2014)
- Sub-100-ps structural dynamics of horse heart myoglobin probed by time-resolved X-ray solution scattering. Oang KY, Kim KH, Jo J, Kim Y, Kim JG, Kim TW, Jun S, Kim J, Ihee H. Chem Phys 422 137-142 (2014)
- Time-resolved crystallography using the Hadamard transform. Yorke BA, Beddard GS, Owen RL, Pearson AR. Nat. Methods 11 1131-1134 (2014)
- Graphene-based microfluidics for serial crystallography. Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Lab Chip 16 3082-3096 (2016)
- Probing the early stages of photoreception in photoactive yellow protein with ultrafast time-domain Raman spectroscopy. Kuramochi H, Takeuchi S, Yonezawa K, Kamikubo H, Kataoka M, Tahara T. Nat Chem 9 660-666 (2017)
- Towards time-resolved serial crystallography in a microfluidic device. Pawate AS, Šrajer V, Schieferstein J, Guha S, Henning R, Kosheleva I, Schmidt M, Ren Z, Kenis PJ, Perry SL. Acta Crystallogr F Struct Biol Commun 71 823-830 (2015)
- Tracking reaction dynamics in solution by pump-probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering). Kim J, Kim KH, Oang KY, Lee JH, Hong K, Cho H, Huse N, Schoenlein RW, Kim TK, Ihee H. Chem. Commun. (Camb.) 52 3734-3749 (2016)
- Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. Yun JH, Li X, Yue J, Park JH, Jin Z, Li C, Hu H, Shi Y, Pandey S, Carbajo S, Boutet S, Hunter MS, Liang M, Sierra RG, Lane TJ, Zhou L, Weierstall U, Zatsepin NA, Ohki M, Tame JRH, Park SY, Spence JCH, Zhang W, Schmidt M, Lee W, Liu H. Proc Natl Acad Sci U S A 118 e2020486118 (2021)
- High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Carrillo M, Pandey S, Sanchez J, Noda M, Poudyal I, Aldama L, Malla TN, Claesson E, Wahlgren WY, Feliz D, Šrajer V, Maj M, Castillon L, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Stojković EA, Schmidt M. Structure 29 743-754.e4 (2021)
- High-throughput instant quantification of protein expression and purity based on photoactive yellow protein turn off/on label. Kim Y, Ganesan P, Ihee H. Protein Sci. 22 1109-1117 (2013)
- Room temperature structures beyond 1.5 Å by serial femtosecond crystallography. Schmidt M, Pande K, Basu S, Tenboer J. Struct Dyn 2 041708 (2015)
- A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein. Wei L, Wang H, Chen X, Fang W, Wang H. Phys Chem Chem Phys 16 25263-25272 (2014)
- Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Pande K, Schwander P, Schmidt M, Saldin DK. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 369 20130332 (2014)
- Ultrafast X-Ray Crystallography and Liquidography. Ki H, Oang KY, Kim J, Ihee H. Annu Rev Phys Chem 68 473-497 (2017)
- Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-Resolved Small- and Wide-Angle X-ray Scattering. Cho HS, Schotte F, Dashdorj N, Kyndt J, Henning R, Anfinrud PA. J. Am. Chem. Soc. 138 8815-8823 (2016)
- An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway. Tachibana SR, Tang L, Zhu L, Takeda Y, Fushimi K, Ueda Y, Nakajima T, Kuwasaki Y, Sato M, Narikawa R, Fang C. Int J Mol Sci 22 5252 (2021)
- Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein. Gamiz-Hernandez AP, Kaila VR. Phys Chem Chem Phys 18 2802-2809 (2016)
- Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer. Schmidt M, Saldin DK. Struct Dyn 1 024701 (2014)
- The design and synthesis of alanine-rich α-helical peptides constrained by an S,S-tetrazine photochemical trigger: a fragment union approach. Courter JR, Abdo M, Brown SP, Tucker MJ, Hochstrasser RM, Smith AB. J. Org. Chem. 79 759-768 (2014)
- Unveiling the mechanism of photoinduced isomerization of the photoactive yellow protein (PYP) chromophore. Gromov EV. J Chem Phys 141 224308 (2014)
- Watching Proteins Function with Time-resolved X-ray Crystallography. Šrajer V, Schmidt M. J Phys D Appl Phys 50 (2017)
- An automated platform for in situ serial crystallography at room temperature. Ren Z, Wang C, Shin H, Bandara S, Kumarapperuma I, Ren MY, Kang W, Yang X. IUCrJ 7 1009-1018 (2020)
- Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics. Brinkmann LU, Hub JS. J Chem Phys 143 104108 (2015)
- Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging. Lee K, Kim Y, Jung J, Ihee H, Park Y. Sci Rep 8 3064 (2018)
- Spectroscopic studies of model photo-receptors: validation of a nanosecond time-resolved micro-spectrophotometer design using photoactive yellow protein and α-phycoerythrocyanin. Purwar N, Tenboer J, Tripathi S, Schmidt M. Int J Mol Sci 14 18881-18898 (2013)
- Thermal activation of 'allosteric-like' large-scale motions in a eukaryotic Lactate Dehydrogenase. Katava M, Maccarini M, Villain G, Paciaroni A, Sztucki M, Ivanova O, Madern D, Sterpone F. Sci Rep 7 41092 (2017)
- Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin. Pilmé J, Luppi E, Bergès J, Houée-Lévin C, de la Lande A. J Mol Model 20 2368 (2014)
- Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy. Kuramochi H, Tahara T. J Am Chem Soc 143 9699-9717 (2021)
- Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label. Blankenburg L, Schroeder L, Habenstein F, Błasiak B, Kottke T, Bredenbeck J. Phys Chem Chem Phys 21 6622-6634 (2019)
- Photoisomerization of Trans Ortho-, Meta-, Para-Nitro Diarylbutadienes: A Case of Regioselectivity. Agnihotri H, Paramasivam M, Palakollu V, Kanvah S. Photochem. Photobiol. 91 1324-1331 (2015)
- Absorption wavelength along chromophore low-barrier hydrogen bonds. Tsujimura M, Tamura H, Saito K, Ishikita H. iScience 25 104247 (2022)
- An Eight-State Molecular Sequential Switch Featuring a Dual Single-Bond Rotation Photoreaction. Gerwien A, Jehle B, Irmler M, Mayer P, Dube H. J Am Chem Soc 144 3029-3038 (2022)
- Biological function investigated by time-resolved structure determination. Schmidt M. Struct Dyn 10 010901 (2023)
- Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein. Konold PE, Arik E, Weißenborn J, Arents JC, Hellingwerf KJ, van Stokkum IHM, Kennis JTM, Groot ML. Nat Commun 11 4248 (2020)
- Direct evidence for hula twist and single-bond rotation photoproducts. Gerwien A, Schildhauer M, Thumser S, Mayer P, Dube H. Nat Commun 9 2510 (2018)
- Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein. Umezaki U, Hatakenaka M, Onodera K, Mizutani H, Kim S, Nakasone Y, Terazima M, Kimura Y. Molecules 26 4554 (2021)
- Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state. Kuramochi H, Takeuchi S, Kamikubo H, Kataoka M, Tahara T. Sci Adv 5 eaau4490 (2019)
- Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Nat Commun 14 5507 (2023)
- High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures. Sanchez JC, Carrillo M, Pandey S, Noda M, Aldama L, Feliz D, Claesson E, Wahlgren WY, Tracy G, Duong P, Nugent AC, Field A, Šrajer V, Kupitz C, Iwata S, Nango E, Tanaka R, Tanaka T, Fangjia L, Tono K, Owada S, Westenhoff S, Schmidt M, Stojković EA. Struct Dyn 6 054701 (2019)
- Homogeneous batch micro-crystallization of proteins from ammonium sulfate. Stohrer C, Horrell S, Meier S, Sans M, von Stetten D, Hough M, Goldman A, Monteiro DCF, Pearson AR. Acta Crystallogr D Struct Biol 77 194-204 (2021)
- Mechanistic Elucidation of the Hula-Twist Photoreaction in Hemithioindigo. Fischer T, Leitner J, Gerwien A, Mayer P, Dreuw A, Dube H, Wachtveitl J. J Am Chem Soc 145 14811-14822 (2023)
- Molecular insights of exceptionally photostable electron acceptors for organic photovoltaics. Liu ZX, Yu ZP, Shen Z, He C, Lau TK, Chen Z, Zhu H, Lu X, Xie Z, Chen H, Li CZ. Nat Commun 12 3049 (2021)
- Practical considerations for the analysis of time-resolved x-ray data. Schmidt M. Struct Dyn 10 044303 (2023)
- Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data. Ki H, Gu J, Cha Y, Lee KW, Ihee H. Struct Dyn 10 034103 (2023)
- Protein and RNA dynamical fingerprinting. Niessen KA, Xu M, George DK, Chen MC, Ferré-D'Amaré AR, Snell EH, Cody V, Pace J, Schmidt M, Markelz AG. Nat Commun 10 1026 (2019)
- Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker. Kim Y, Yang C, Kim TW, Thamilselvan K, Kim Y, Ihee H. Int J Mol Sci 19 (2018)
- SVD-aided non-orthogonal decomposition (SANOD) method to exploit prior knowledge of spectral components in the analysis of time-resolved data. Ki H, Lee Y, Choi EH, Lee S, Ihee H. Struct Dyn 6 024303 (2019)
- Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism. Fadini A, Hutchison CDM, Morozov D, Chang J, Maghlaoui K, Perrett S, Luo F, Kho JCX, Romei MG, Morgan RML, Orr CM, Cordon-Preciado V, Fujiwara T, Nuemket N, Tosha T, Tanaka R, Owada S, Tono K, Iwata S, Boxer SG, Groenhof G, Nango E, van Thor JJ. J Am Chem Soc 145 15796-15808 (2023)
- Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy. Kong Q, Khakhulin D, Shkrob IA, Lee JH, Zhang X, Kim J, Kim KH, Jo J, Kim J, Kang J, Pham VT, Jennings G, Kurtz C, Spence R, Chen LX, Wulff M, Ihee H. Struct Dyn 6 064902 (2019)
- Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration. Haraguchi S, Shingae T, Fujisawa T, Kasai N, Kumauchi M, Hanamoto T, Hoff WD, Unno M. Proc. Natl. Acad. Sci. U.S.A. 115 8671-8675 (2018)
- Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms. Romei MG, Lin CY, Boxer SG. J Photochem Photobiol A Chem 401 112738 (2020)
- Structural basis of molecular logic OR in a dual-sensor histidine kinase. Shin H, Ren Z, Zeng X, Bandara S, Yang X. Proc. Natl. Acad. Sci. U.S.A. 116 19973-19982 (2019)
- Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate. Cao H, Skolnick J. Struct Dyn 6 024701 (2019)
- Ultrafast Structural Changes Decomposed from Serial Crystallographic Data. Ren Z. J Phys Chem Lett 10 7148-7163 (2019)