Tag: enzyme catalysis

Modeling catalysis in allosteric enzymes: Capturing conformational consequences.

Klem, H.; McCullagh, M.; Paton, R. S. Top. Catal. 2022, 65, 165–186

Cofactor-independent pinacolase directs non-Diels-Alderase biogenesis of the Brevianamides.

Ye, Y.; Du, L.; Zhang, X.; Newmister, S. A.; McCauley, M.; Alegre-Requena, J. V.; Zhang W.; Mu, S.; Minami, A.; Fraley, A. E.; Adrover-Castellano, M. L.; Carney, N.; Shende, V. K.; Oikawa, H.; Kato H.; Tsukamoto, S.; Paton, R. S.; Williams R. M.; , Sherman, D. H.; Li, S. Nat. Catal. 2020, 3, 497–506

Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins.

Hintzen, J. C. J.; Poater, J.; Kumar, K.; Al Temimi, A. H. K.; Pieters, B. J. G. E.; Paton, R. S.; Bickelhaupt, F. M.; Mecinović, J. Molecules 2020, 25, 1918

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger.

Pieters, B. J. G. E., Wuts, M. H. M., Poater, J.; Kumar, K.; White, P. B.; Kamps, J. J. A. G.; Sherman, W; Pruijn, G. J. M.; Paton, R. S.; Beuming, T.; Bickelhaupt, F. M.; Mecinović, J. Commun. Chem. 2020, 3, 69

Fungal Indole Alkaloid Biogenesis through Evolution of a Bifunctional Reductase/Diels-Alderase.

Dan, Q.; Newmister, S. A.; Klas, K. R.; Fraley, A. E.; McAfoos, T. J.; Somoza, A. D.; Sunderhaus, J. D.; Ye, Y.; Shende, V. V.; Yu, F.; Sanders, J. N.; Brown, W. C.; Zhao, L.; Paton, R. S.; Houk, K. N.; Smith, J. L.; Sherman, D. H.; Williams, R. M. Nat. Chem. 2019, 11, 972–980

Non‐Hydrolytic Beta‐Lactam Antibiotic Fragmentation by L,D‐Transpeptidases and Serine B‐Lactamase Cysteine Variants.

Lohans, C. T.; Chan, H. T. H.; Malla, T. R. Kumar, K.; Kamps, J. J. A. G.; McArdle, D. J. B.; van Groesen, E.; de Munnik, M.; Tooke, C. L.; Spencer, J.; Paton, R. S. Brem, J.; Schofield, C. J. Angew. Chem. Int. Ed. 2019, 131, 2012–2016

A New Mechanism for Beta-Lactamases: Class D Enzymes Degrade 1-Beta-Methyl Carbapenems via Lactone Formation.

Lohans, C. T.; van Groesen, E.; Brem, J.; Kumar, K.; Paton, R. S.; Schofield, C. J. Angew. Chem. Int. Ed. 2018, 57, 1282–1285

Post-Translational Site-Selective Protein Alpha-Deuteration.

Galan, S. R. G.; Wickens, J. R.; Dadova, J.; Ng, W.-L.; Zhang, X.; Simion, R. A.; Quinlan, R.; Pires, E.; Paton, R. S.; Caddick, S.; Chudasama, V.; Davis, B. G. Nat. Chem. Biol. 2018, 14, 955–963

Recognition of Shorter and Longer Trimethyllysine Analogues by Epigenetic Reader Proteins.

Al Temimi, A. H. K.; Belle, R.; Kumar, K.; Poater, J.; Betlem, P.; Pieters, B. J. G. E.; Paton, R. S.; Bickelhaupt, F. M.; Mecinović, J. Chem. Commun. 2018, 54, 2409–2412

Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella Denitrificans Kef Potassium Efflux System.

Pliotas, C.; Grayer, S. C.; Ekkerman, S.; Chan, A. K. N.; Healy, J.; Marius, P.; Bartlett, W.; Khan, A.; Cortopassi, W. A.; Chandler, S. A.; Rasmussen, T.; Benesch, J. L. P.; Paton, R. S.; Claridge, T. D. W.; Miller, S.; Booth, I. R.; Naismith, J. H.; Conway, S. J. Biochemistry 2017, 56, 4219–4234

Investigating D-Lysine Stereochemistry for Epigenetic Methylation, Demethylation and Recognition.

Belle, R.; Al Temimi, A. H. K.; Kumar, K.; Pieters, B. J. G. E.; Dunford, J.; Tumber, A.; Johansson, C.; Brown, T.; Schofield, C. J.; Hopkinson, R. J.; Paton, R. S.; Kawamura, A.; Mecinović, J. Chem. Commun. 2017, 53, 13264–13267

Structural and Stereoelectronic Insights into Oxygenase Catalyzed Formation of Ethylene from 2-Oxoglutarate.

Zhang, Z.; Smart, T. J.; Choi, H.; Hardy, F.; Lohans, C. T.; Abboud, M. I.; Richardson, M. S. W.; Paton, R. S.; McDonough, M. A.; Schofield, C. J. Proc. Nat. Acad. Sci. 2017, 4667–4672

Cation–Pi Interactions in CREBBP Bromodomain Inhibition: An Electrostatic Model for Small-Molecule Binding Affinity and Selectivity.

Cortopassi, W. A.; Kumar, K.; Paton, R. S. Org. Biomol. Chem. 2016, 14, 10926–10938

Investigations on Recyclization and Hydrolysis in Avibactam Mediated Serine B-Lactamase Inhibition.

Choi, H.; Paton, R. S.; Park, H.; Schofield, C. J. Org. Biomol. Chem. 2016, 14, 4116–4128

Mechanisms of Histone-Modifying and Reading Enzymes: the Role of the Protein Environment from a Computational Perspective.

Cortopassi, W. A.; Kumar, K.; Duarte, F.; Pimentel, A. S.; Paton, R. S. J. Mol. Graph. Model. 2016, 67, 69–84

Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of Protein Environment.

Cortopassi, W. E.; Simion, R. A.; Hornsby, C. E.; Costa Franca, T. C.; Paton, R. S. Chem. Eur. J. 2015, 21, 18983–18992

Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions.

Brand, M.; Measures, A.; Wilson, B.; Cortopassi, W. A.; Alexander, R.; Hoss, M.; Hewings, D. S.; Paton, R. S.; Conway, S. J. ACS Chem. Bio. 2015, 10, 22–39

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced Fit Pocket Stabilized by a Cation-Pi Interaction.

Rooney, T. P. C.; Filippakopoulos, P.; Fedorov, O.; Picaud, S.; Cortopassi, W. A.; Hay, D. A.; Martin, S.; Tumber, A.; Rogers, C. M.; Philpott, M.; Wang, M.; Thompson, A. L.; Heightman, T. D.; Pryde, D. C.; Cook, A.; Paton, R. S.; Müller-Knapp, S.; Knapp, S.; Brennan, P. E.; Conway, S. J. Angew. Chem. Int. Ed. 2014, 126, 6240–6244

Natural Product Biosynthesis: It’s All Downhill from Here.

Hornsby, C. E.; Paton, R. S. Nat. Chem. 2014, 6, 88–89

Quantum Mechanical Calculations Suggest That Lytic Polysaccharide Monooxygenases Employ a Copper-Oxyl, Oxygen-Rebound Mechanism.

Kim, S.; Sandgren, M.; Paton, R. S.; Beckham, G. T. Proc. Nat. Acad. Sci. 2014, 111, 149–154

Enzymatic Catalysis of Anti-Baldwin Ring-Closure in Polyether Biosynthesis.

Hotta, K.; Chen, X.; Paton, R. S.; Minami, A.; Li, H. Swaminathan, K. T.; Mathews, I. I.; Watanabe, K.; Oikawa, H.; Houk, K. N.; Kim, C. Y. Nature 2012, 483, 355–358