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2. Ultrafast structural changes direct the first molecular events of vision

Author

Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Published
2023
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3. Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays

Author

Pierrat, Olivier A., Liu, Manjuan, Collie, Gavin W., Shetty, Kartika, Rodrigues, Matthew J., Le Bihan, Yann-Vaï, Gunnell, Emma A., McAndrew, P. Craig, Stubbs, Mark, Rowlands, Martin G., Yahya, Norhakim, Shehu, Erald, Talbot, Rachel, Pickard, Lisa, Bellenie, Benjamin R., Cheung, Kwai-Ming J., Drouin, Ludovic, Innocenti, Paolo, Woodward, Hannah, Davis, Owen A., Lloyd, Matthew G., Varela, Ana, Huckvale, Rosemary, Broccatelli, Fabio, Carter, Michael, Galiwango, David, Hayes, Angela, Raynaud, Florence I., Bryant, Christopher, Whittaker, Steven, Rossanese, Olivia W., Hoelder, Swen, Burke, Rosemary, and van Montfort, Rob L. M.

Published
2022
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4. Active state structures of a bistable visual opsin bound to G proteins

Author

Tejero, Oliver, primary, Pamula, Filip, additional, Koyanagi, Mitsumasa, additional, Nagata, Takashi, additional, Afanasyev, Pavel, additional, Das, Ishita, additional, Deupi, Xavier, additional, Sheves, Mordechai, additional, Terakita, Akihisa, additional, Schertler, Gebhard F.X., additional, Rodrigues, Matthew J., additional, and Tsai, Ching-Ju, additional

Published
2024
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6. A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus

Author

Bolton, Rachel, primary, Machelett, Moritz M., additional, Stubbs, Jack, additional, Axford, Danny, additional, Caramello, Nicolas, additional, Catapano, Lucrezia, additional, Malý, Martin, additional, Rodrigues, Matthew J., additional, Cordery, Charlotte, additional, Tizzard, Graham J., additional, MacMillan, Fraser, additional, Engilberge, Sylvain, additional, von Stetten, David, additional, Tosha, Takehiko, additional, Sugimoto, Hiroshi, additional, Worrall, Jonathan A. R., additional, Webb, Jeremy S., additional, Zubkov, Mike, additional, Coles, Simon, additional, Mathieu, Eric, additional, Steiner, Roberto A., additional, Murshudov, Garib, additional, Schrader, Tobias E., additional, Orville, Allen M., additional, Royant, Antoine, additional, Evans, Gwyndaf, additional, Hough, Michael A., additional, Owen, Robin L., additional, and Tews, Ivo, additional

Published
2024
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7. A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus

Author

Bolton, Rachel, Machelett, Moritz M., Stubbs, Jack, Axford, Danny, Caramello, Nicolas, Catapano, Lucrezia, Malý, Martin, Rodrigues, Matthew J., Cordery, Charlotte, Tizzard, Graham J., MacMillan, Fraser, Engilberge, Sylvain, von Stetten, David, Tosha, Takehiko, Sugimoto, Hiroshi, Worrall, Jonathan A. R., Webb, Jeremy S., Zubkov, Mike, Coles, Simon, Mathieu, Eric, Steiner, Roberto A., Murshudov, Garib, Schrader, Tobias E., Orville, Allen M., Royant, Antoine, Evans, Gwyndaf, Hough, Michael A., Owen, Robin L., Tews, Ivo, Bolton, Rachel, Machelett, Moritz M., Stubbs, Jack, Axford, Danny, Caramello, Nicolas, Catapano, Lucrezia, Malý, Martin, Rodrigues, Matthew J., Cordery, Charlotte, Tizzard, Graham J., MacMillan, Fraser, Engilberge, Sylvain, von Stetten, David, Tosha, Takehiko, Sugimoto, Hiroshi, Worrall, Jonathan A. R., Webb, Jeremy S., Zubkov, Mike, Coles, Simon, Mathieu, Eric, Steiner, Roberto A., Murshudov, Garib, Schrader, Tobias E., Orville, Allen M., Royant, Antoine, Evans, Gwyndaf, Hough, Michael A., Owen, Robin L., and Tews, Ivo

Abstract

The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically possess a single futA gene. How the encoded FutA protein might bind different Fe oxidation states was previously unknown. Here, we use structural biology techniques at room temperature to probe the dynamic behavior of FutA. Neutron diffraction confirmed four negatively charged tyrosinates, that together with a neutral water molecule coordinate iron in trigonal bipyramidal geometry. Positioning of the positively charged Arg103 side chain in the second coordination shell yields an overall charge-neutral Fe(III) binding state in structures determined by neutron diffraction and serial femtosecond crystallography. Conventional rotation X-ray crystallography using a home source revealed X-ray-induced photoreduction of the iron center with observation of the Fe(II) binding state; here, an additional positioning of the Arg203 side chain in the second coordination shell maintained an overall charge neutral Fe(II) binding site. Dose series using serial synchrotron crystallography and an XFEL X-ray pump–probe approach capture the transition between Fe(III) and Fe(II) states, revealing how Arg203 operates as a switch to accommodate the different iron oxidation states. This switching ability of the Prochlorococcus FutA protein may reflect ecological adaptation by genome streamlining and loss of specialized FutA proteins.

Published
2024

8. Activating an invertebrate bistable opsin with the all-trans 6.11 retinal analog.

Author

Rodrigues, Matthew J., Tejero, Oliver, Mühle, Jonas, Pamula, Filip, Das, Ishita, Ching-Ju Tsai, Terakita, Akihisa, Sheves, Mordechai, and Schertler, Gebhard F. X.

Subjects
*G protein coupled receptors, *PERCEPTION in animals, *OPSINS, *JUMPING spiders, *LIGHT absorption
Abstract

Animal vision depends on opsins, a category of G protein-coupled receptor (GPCR) that achieves light sensitivity by covalent attachment to retinal. Typically binding as an inverse agonist, 11-cis retinal photoisomerizes to the all-trans isomer and activates the receptor, initiating downstream signaling cascades. Retinal bound to bistable opsins isomerizes back to the 11-cis state after absorption of a second photon, inactivating the receptor. Bistable opsins are essential for invertebrate vision and nonvisual light perception across the animal kingdom. While crystal structures are available for bistable opsins in the inactive state, it has proven difficult to form homogeneous populations of activated bistable opsins either via illumination or reconstitution with all-trans retinal. Here, we show that a nonnatural retinal analog, all-trans retinal 6.11 (ATR6.11), can be reconstituted with the invertebrate bistable opsin, Jumping Spider Rhodopsin-1 (JSR1). Biochemical activity assays demonstrate that ATR6.11 functions as a JSR1 agonist. ATR6.11 binding also enables complex formation between JSR1 and signaling partners. Our findings demonstrate the utility of retinal analogs for biophysical characterization of bistable opsins, which will deepen our understanding of light perception in animals. [ABSTRACT FROM AUTHOR]

Published
2024
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9. A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron binding protein FutA fromProchlorococcus

Author

Bolton, Rachel, primary, Machelett, Moritz M., additional, Stubbs, Jack, additional, Axford, Danny, additional, Caramello, Nicolas, additional, Catapano, Lucrezia, additional, Malý, Martin, additional, Rodrigues, Matthew J., additional, Cordery, Charlotte, additional, Tizzard, Graham J., additional, MacMillan, Fraser, additional, Engilberge, Sylvain, additional, von Stetten, David, additional, Tosha, Takehiko, additional, Sugimoto, Hiroshi, additional, Worrall, Jonathan A.R., additional, Webb, Jeremy S., additional, Zubkov, Mike, additional, Coles, Simon, additional, Mathieu, Eric, additional, Steiner, Roberto A., additional, Murshudov, Garib, additional, Schrader, Tobias E., additional, Orville, Allen M., additional, Royant, Antoine, additional, Evans, Gwyndaf, additional, Hough, Michael A., additional, Owen, Robin L., additional, and Tews, Ivo, additional

Published
2023
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11. Ultrafast structural changes direct the first molecular events of vision

Author

60452330, Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, Panneels, Valerie, 60452330, Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Abstract

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.

Published
2023

13. Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors

Author

Davis, Owen A., primary, Cheung, Kwai-Ming J., additional, Brennan, Alfie, additional, Lloyd, Matthew G., additional, Rodrigues, Matthew J., additional, Pierrat, Olivier A., additional, Collie, Gavin W., additional, Le Bihan, Yann-Vaï, additional, Huckvale, Rosemary, additional, Harnden, Alice C., additional, Varela, Ana, additional, Bright, Michael D., additional, Eve, Paul, additional, Hayes, Angela, additional, Henley, Alan T., additional, Carter, Michael D., additional, McAndrew, P. Craig, additional, Talbot, Rachel, additional, Burke, Rosemary, additional, van Montfort, Rob L. M., additional, Raynaud, Florence I., additional, Rossanese, Olivia W., additional, Meniconi, Mirco, additional, Bellenie, Benjamin R., additional, and Hoelder, Swen, additional

Published
2022
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15. Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket

Author

Lloyd, Matthew G., primary, Huckvale, Rosemary, additional, Cheung, Kwai-Ming J., additional, Rodrigues, Matthew J., additional, Collie, Gavin W., additional, Pierrat, Olivier A., additional, Gatti Iou, Mahad, additional, Carter, Michael, additional, Davis, Owen A., additional, McAndrew, P. Craig, additional, Gunnell, Emma, additional, Le Bihan, Yann-Vaï, additional, Talbot, Rachel, additional, Henley, Alan T., additional, Johnson, Louise D., additional, Hayes, Angela, additional, Bright, Michael D., additional, Raynaud, Florence I., additional, Meniconi, Mirco, additional, Burke, Rosemary, additional, van Montfort, Rob L. M., additional, Rossanese, Olivia W., additional, Bellenie, Benjamin R., additional, and Hoelder, Swen, additional

Published
2021
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16. Achieving In Vivo Target Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders

Author

Bellenie, Benjamin R., primary, Cheung, Kwai-Ming J., additional, Varela, Ana, additional, Pierrat, Olivier A., additional, Collie, Gavin W., additional, Box, Gary M., additional, Bright, Michael D., additional, Gowan, Sharon, additional, Hayes, Angela, additional, Rodrigues, Matthew J., additional, Shetty, Kartika N., additional, Carter, Michael, additional, Davis, Owen A., additional, Henley, Alan T., additional, Innocenti, Paolo, additional, Johnson, Louise D., additional, Liu, Manjuan, additional, de Klerk, Selby, additional, Le Bihan, Yann-Vaï, additional, Lloyd, Matthew G., additional, McAndrew, P. Craig, additional, Shehu, Erald, additional, Talbot, Rachel, additional, Woodward, Hannah L., additional, Burke, Rosemary, additional, Kirkin, Vladimir, additional, van Montfort, Rob L. M., additional, Raynaud, Florence I., additional, Rossanese, Olivia W., additional, and Hoelder, Swen, additional

Published
2020
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17. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis

Author

Rodrigues, Matthew J, primary, Windeisen, Volker, additional, Zhang, Yang, additional, Guédez, Gabriela, additional, Weber, Stefan, additional, Strohmeier, Marco, additional, Hanes, Jeremiah W, additional, Royant, Antoine, additional, Evans, Gwyndaf, additional, Sinning, Irmgard, additional, Ealick, Steven E, additional, Begley, Tadhg P, additional, and Tews, Ivo, additional

Published
2017
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18. Achieving In VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders

Author

Bellenie, Benjamin R., Cheung, Kwai-Ming J., Varela, Ana, Pierrat, Olivier A., Collie, Gavin W., Box, Gary M., Bright, Michael D., Gowan, Sharon, Hayes, Angela, Rodrigues, Matthew J., Shetty, Kartika N., Carter, Michael, Davis, Owen A., Henley, Alan T., Innocenti, Paolo, Johnson, Louise D., Liu, Manjuan, de Klerk, Selby, Le Bihan, Yann-Vaï, Lloyd, Matthew G., McAndrew, P. Craig, Shehu, Erald, Talbot, Rachel, Woodward, Hannah L., Burke, Rosemary, Kirkin, Vladimir, van Montfort, Rob L. M., Raynaud, Florence I., Rossanese, Olivia W., and Hoelder, Swen

Abstract

Deregulation of the transcriptional repressor BCL6 enables tumorigenesis of germinal center B-cells, and hence BCL6 has been proposed as a therapeutic target for the treatment of diffuse large B-cell lymphoma (DLBCL). Herein we report the discovery of a series of benzimidazolone inhibitors of the protein–protein interaction between BCL6 and its co-repressors. A subset of these inhibitors were found to cause rapid degradation of BCL6, and optimization of pharmacokinetic properties led to the discovery of 5-((5-chloro-2-((3R,5S)-4,4-difluoro-3,5-dimethylpiperidin-1-yl)pyrimidin-4-yl)amino)-3-(3-hydroxy-3-methylbutyl)-1-methyl-1,3-dihydro-2H-benzo[d]imidazol-2-one (CCT369260), which reduces BCL6 levels in a lymphoma xenograft mouse model following oral dosing.

Published
2020
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19. Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase.

Author

Rodrigues MJ, Giri N, Royant A, Zhang Y, Bolton R, Evans G, Ealick SE, Begley T, and Tews I

Abstract

The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I 333 intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Published
2021
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