Yr Athro Rudolf Allemann

2024

• Srivastava, P. L. et al. 2024. Simulation-guided engineering enables a functional switch in selinadiene synthase toward hydroxylation. ACS Catalysis 14(14), pp. 11034–11043. (10.1021/acscatal.4c02032)
• González Requena, V., Srivastava, P. L., Miller, D. J. and Allemann, R. K. 2024. Single point mutation abolishes water capture in germacradien‐4‐ol synthase. ChemBioChem, article number: e202400290. (10.1002/cbic.202400290)
• Srivastava, P. L., Johnson, L. A., Miller, D. J. and Allemann, R. K. 2024. Production of non-natural terpenoids through chemoenzymatic synthesis using substrate analogs. In: Methods in Enzymology. Elsevier, (10.1016/bs.mie.2024.03.015)
• Johnson, L. A., Mart, R. J. and Allemann, R. K. 2024. A photoresponsive homing endonuclease for programmed DNA cleavage. ACS Synthetic Biology 13(1), pp. 195-205. (10.1021/acssynbio.3c00425)

2023

• Srivastava, P., Johns, S. T., Walters, R., Miller, D. J., Van der Kamp, M. W. and Allemann, R. K. 2023. Active site loop engineering abolishes water capture in hydroxylating sesquiterpene synthases. ACS Catalysis 13(21), pp. 14199-14204. (10.1021/acscatal.3c03920)

2022

• Allemann, R. K., Samperio, R., Mart, R., Luk, L., Tsai, Y., Jones, A. and Cruz Samperio, R. 2022. Spatio-temporal control of cell death by selective delivery of photo-activatable proteins. ChemBioChem 23(12), article number: e202200115. (10.1002/cbic.202200115)

2021

• Adesina, A. S., Luk, L. Y. P. and Allemann, R. K. 2021. Cryo‐kinetics reveal dynamic effects on the chemistry of human dihydrofolate reductase. ChemBioChem 22(14), pp. 2410-2414. (10.1002/cbic.202100017)
• Pospiech, M. et al. 2021. Bisphosphonate inhibitors of squalene synthase protect cells against cholesterol-dependent cytolysins. FASEB Journal 35(6), article number: e21640. (10.1096/fj.202100164R)
• Srivastava, P. L., Escorcia, A. M., Huynh, F., Miller, D. J., Allemann, R. K. and van der Kamp, M. W. 2021. Redesigning the molecular choreography to prevent hydroxylation in Germacradien-11-ol synthase catalysis. ACS Catalysis 11(3), pp. 1033–1041. (10.1021/acscatal.0c04647)

2020

• Huynh, F., Tailby, M., Finniear, A., Stephens, K., Allemann, R. K. and Wirth, T. 2020. Accelerating biphasic biocatalysis through new process windows. Angewandte Chemie International Edition 59(38), pp. 16490-16495. (10.1002/anie.202005183)
• Elsherbini, M., Huynh, F., Dunbabin, A., Allemann, R. and Wirth, T. 2020. Selective hydroboration - oxidation of terminal alkenes under flow conditions. Chemistry - A European Journal 26(50), pp. 11423-11425. (10.1002/chem.202001650)
• Adesina, A. S., Swiderek, K., Luk, L. Y. P., Moliner, V. and Allemann, R. K. 2020. Electric field measurements reveal the pivotal role of Cofactor-Substrate interaction in dihydrofolate reductase catalysis. ACS Catalysis 10(14), pp. 7907-7914. (10.1021/acscatal.0c01856)
• Johnson, L. A., Dunbabin, A., Benton, J. C. R., Mart, R. J. and Allemann, R. K. 2020. Modular chemoenzymatic synthesis of terpenes and their analogues. Angewandte Chemie International Edition 59(22), pp. 8486-8490. (10.1002/anie.202001744)
• Valikhani, D., Srivastava, P. L., Allemann, R. K. and Wirth, T. 2020. Immobilised enzymes for sesquiterpene synthesis in batch and flow systems. ChemCatChem 12(8), pp. 2194-22197. (10.1002/cctc.201902135)
• Day, A. H. et al. 2020. Targeted cell imaging properties of a deep red luminescent iridium(III) complex conjugated with a c-Myc signal peptide. Chemical Science 11(6), pp. 1599-1606. (10.1039/C9SC05568A)
• Cresser-Brown, J., Rizkallah, P., Jin, Y., Roth, C., Miller, D. J. and Allemann, R. K. 2020. An unexpected co-crystal structure of the calpain PEF(S) domain with Hfq reveals a potential chaperone function of Hfq. Acta Crystallographica Section F: Structural Biology Communications 76(2), pp. 81-85. (10.1107/S2053230X20001181)

2019

• Allemann, R. K., Scott, A. F., Luk, L. Y., Tuñón, I. and Moliner, V. 2019. Heavy enzymes and the rational redesign of protein catalysts. ChemBioChem 20(22), pp. 2807-2812. (10.1002/cbic.201900134)
• Angelastro, A., Ruiz-Pernía, J. J., Tuñón, I., Moliner, V., Luk, L. Y. P. and Allemann, R. K. 2019. Loss of hyperconjugative effects drives hydride transfer during dihydrofolate reductase catalysis. ACS Catalysis 9(11), pp. 10343-10349. (10.1021/acscatal.9b02839)
• Elsherbini, M., Allemann, R. K. and Wirth, T. 2019. 'Dark' singlet oxygen made easy. Chemistry - A European Journal 25(54), pp. 12486-12490. (10.1002/chem.201903505)
• Demiray, M., Miller, D. J. and Allemann, R. K. 2019. Harnessing enzyme plasticity for the synthesis of oxygenated sesquiterpenoids. Beilstein Journal of Organic Chemistry 15, pp. 2184-2190. (10.3762/bjoc.15.215)
• Kalvaitis, M. E., Johnson, L. A., Mart, R. J., Rizkallah, P. and Allemann, R. K. 2019. A noncanonical chromophore reveals structural rearrangements of the light-oxygen-voltage domain upon photoactivation. Biochemistry 58(22), pp. 2608-2616. (10.1021/acs.biochem.9b00255)
• Scott, A. F., Cresser-Brown, J., Williams, T. L., Rizkallah, P. J., Jin, Y., Luk, L. Y. and Allemann, R. K. 2019. Crystal structure and biophysical analysis of furfural detoxifying aldehyde reductase from clostridium beijerinkii. Applied and Environmental Microbiology (10.1128/AEM.00978-19)
• Ruiz-Pernía, J. J., Tuñón, I., Moliner, V. and Allemann, R. K. 2019. Why are some enzymes dimers? flexibility and catalysis in Thermotoga maritima dihydrofolate reductase. ACS Catalysis 9, pp. 5902-5911. (10.1021/acscatal.9b01250)
• Patel, S. G. et al. 2019. Cell-penetrating peptide sequence and modification dependent uptake and subcellular distribution of green florescent protein in different cell lines. Scientific Reports 9(1), pp. -., article number: 6298. (10.1038/s41598-019-42456-8)
• Loizzi, M., Miller, D. J. and Allemann, R. K. 2019. Silent catalytic promiscuity in the high-fidelity terpene cyclase δ-cadinene synthase. Organic & Biomolecular Chemistry 17(5), pp. 1206-1214. (10.1039/C8OB02821D)

2018

• Kalash, L. et al. 2018. Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space. European Journal of Medicinal Chemistry 157, pp. 1264-1275. (10.1016/j.ejmech.2018.08.049)
• Huynh, F., Grundy, D. J., Jenkins, R. L., Miller, D. J. and Allemann, R. K. 2018. Sesquiterpene synthase-catalysed formation of a new medium-sized cyclic terpenoid ether from farnesyl diphosphate analogues. Chembiochem 19(17), pp. 1834-1838. (10.1002/cbic.201800218)
• Hallett, A. J. et al. 2018. Exploring the cellular uptake and localisation of phosphorescent rhenium fac-tricarbonyl metallosurfactants as a function of lipophilicity. Dalton Transactions 47(40), pp. 14241-14253. (10.1039/C8DT00669E)
• Behiry, E. M., Ruiz-Pernia, J. J., Luk, L., Tunon, I., Moliner, V. and Allemann, R. K. 2018. Isotope substitution of promiscuous alcohol dehydrogenase reveals the origin of substrate preference in the transition state. Angewandte Chemie International Edition 57(12), pp. 3128-3131. (10.1002/anie.201712826)
• Loizzi, M., Gonzalez Gonzalez, V., Miller, D. J. and Allemann, R. K. 2018. Nucleophilic water capture or proton loss: single amino acid switch converts δ-Cadinene synthase into germacradien-4-ol synthase. Chembiochem 19(1), pp. 100-105. (10.1002/cbic.201700531)

2017

• Angelastro, A., Dawson, W. M., Luk, L. Y. P., Loveridge, E. J. and Allemann, R. K. 2017. Chemoenzymatic assembly of isotopically labeled folates. Journal of the American Chemical Society 139(37), pp. 13047-13054. (10.1021/jacs.7b06358)
• Scott, A. F., Luk, L. Y. P. and Allemann, R. K. 2017. Chemical ligation and isotope labeling to locate dynamic effects. In: Imperiali, B. ed. Methods in Enzymology., Vol. 596. Elsevier, pp. 23-41., (10.1016/bs.mie.2017.06.040)
• Hughes, R. L., Johnson, L. A., Behiry, E. M., Loveridge, E. J. and Allemann, R. K. 2017. A rapid analysis of variations in conformational behavior during dihydrofolate reductase catalysis. Biochemistry 56(15), pp. 2126-2133. (10.1021/acs.biochem.7b00045)
• Loveridge, E. J. et al. 2017. Reduction of folate by dihydrofolate reductase from thermotoga maritima. Biochemistry 56(13), pp. 1879-1886. (10.1021/acs.biochem.6b01268)
• Tang, X., Demiray, M., Wirth, T. and Allemann, R. K. 2017. Concise synthesis of artemisinin from a farnesyl diphosphate analogue. Bioorganic & Medicinal Chemistry 26(7), pp. 1314-1319. (10.1016/j.bmc.2017.03.068)
• Demiray, M., Tang, X., Wirth, T., Faraldos, J. A. and Allemann, R. K. 2017. An efficient chemoenzymatic synthesis of dihydroartemisinic aldehyde. Angewandte Chemie International Edition 56(15), pp. 4347-4350. (10.1002/anie.201609557)
• Demiray, M., Tang, X., Wirth, T., Faraldos, J. A. and Allemann, R. K. 2017. Effiziente chemoenzymatische Synthese von dhydroartemisinaldehyd. Angewandte Chemie 129(15), pp. 4411-4415. (10.1002/ange.201609557)
• Angelastro, A., Dawson, W. M., Luk, L. Y. P. and Allemann, R. K. 2017. A versatile disulfide-driven recycling system for NADP+ with high cofactor turnover number. ACS Catalysis 7(2), pp. 1025-1029. (10.1021/acscatal.6b03061)
• Tang, X., Allemann, R. K. and Wirth, T. 2017. Optimising terpene synthesis with flow biocatalysis. European Journal of Organic Chemistry 2017(2), pp. 414-418. (10.1002/ejoc.201601388)

2016

• Faraldos, J., Grundy, D., Cascon Salgado, O., Leoni, S., van der Kamp, M. W. and Allemann, R. 2016. Enzymatic synthesis of natural (+)-aristolochene from a non-natural substrate. Chemical Communications 52(97), pp. 14027-14030. (10.1039/C6CC08164A)
• Mart, R. and Allemann, R. 2016. Azobenzene photocontrol of peptides and proteins. Chemical Communications 52(83), pp. 12262-12277. (10.1039/C6CC04004G)
• Gonzalez, V., Grundy, D. J., Faraldos, J. A. and Allemann, R. K. 2016. The amino-terminal segment in the β-domain of δ-cadinene synthase is essential for catalysis. Organic & Biomolecular Chemistry 14(31), pp. 7451-7454. (10.1039/C6OB01398H)
• Ruiz-Pernía, J. J., Behiry, E., Luk, L. Y. P., Loveridge, E. J., Tuñón, I., Moliner, V. and Allemann, R. K. 2016. Minimization of dynamic effects in the evolution of dihydrofolate reductase. Chemical Science 7(5), pp. 3248-3255. (10.1039/C5SC04209G)
• Chen, M., Chou, W. K. W., Al-Lami, N., Faraldos, J., Allemann, R., Cane, D. E. and Christianson, D. W. 2016. Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase. Biochemistry 55(20), pp. 2864-2874. (10.1021/acs.biochem.6b00343)
• Mart, R., Meah, D. and Allemann, R. K. 2016. Photocontrolled exposure of pro-apoptotic peptide sequences in LOV proteins modulate Bcl-2 family interactions. Chembiochem 17(8), pp. 698-701. (10.1002/cbic.201500469)
• Grundy, D. J., Chen, M., Gonzalez, V., Leoni, S., Miller, D. J., Christianson, D. W. and Allemann, R. K. 2016. Mechanism of germacradien-4-ol synthase controlled water capture. Biochemistry 55(14), pp. 2112-2121. (10.1021/acs.biochem.6b00115)
• Loveridge, E. J. and Allemann, R. K. 2016. Pinpointing dynamic coupling in enzymes for efficient drug design. Future Science OA 2(1) (10.4155/fsoa.2015.0017)

2015

• Adams, S., Robinson, E., Miller, D. J., Rizkallah, P., Hallett, M. B. and Allemann, R. K. 2015. Conformationally restricted calpain inhibitors. Chemical Science 6(12), pp. 6865-6871. (10.1039/c5sc01158b)
• Luk, L. Y. P., Ruiz-Pernía, J. J., Adesina, A. S., Loveridge, E. J., Tuñón, I., Moliner, V. and Allemann, R. K. 2015. Chemical ligation and isotope labeling to locate dynamic effects during catalysis by dihydrofolate reductase. Angewandte Chemie International Edition 54(31), pp. 9016-9020. (10.1002/anie.201503968)
• Touchet, S., Chamberlain, K., Woodcock, C. M., Miller, D. J., Birkett, M. A., Pickett, J. A. and Allemann, R. K. 2015. Novel olfactory ligands via terpene synthases. Chemical Communications 51(35), pp. 7550-7553. (10.1039/C5CC01814E)
• Luk, L. Y. P., Loveridge, E. J. and Allemann, R. K. 2015. Protein motions and dynamic effects in enzyme catalysis. Physical Chemistry Chemical Physics 17, pp. 30817-30827. (10.1039/C5CP00794A)
• Allemann, R. K., Loveridge, E. and Luk, L. Y. P. 2015. Protein motions, dynamic effects and thermal stability in dihydrofolate reductase from the hyperthermophile thermotoga maritima. In: Olivares-Quiroz, L., Guzmán-López, O. and Jardón-Valadez, H. E. eds. Physical Biology of Proteins and Peptides: Theory, Experiment, and Simulation. Springer International Publishing, pp. 99-113., (10.1007/978-3-319-21687-4_6)

2014

• Luk, L. Y. P., Ruiz-Pernia, J. J., Dawson, W. M., Loveridge, E. J., Tuñón, I., Moliner, V. and Allemann, R. K. 2014. Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic com-pensatory effects on the rate constant. Journal of the American Chemical Society 136(49), pp. 17317-17323. (10.1021/ja5102536)
• Gonzalez, V., Touchet, S., Grundy, D. J., Faraldos, J. A. and Allemann, R. K. 2014. Evolutionary and mechanistic insights from the reconstruction of α-humulene synthases from a modern (+)-Germacrene A synthase. Journal of the American Chemical Society 136(41), pp. 14505-14512. (10.1021/ja5066366)
• Adams, S. E., Rizkallah, P., Miller, D. J., Robinson, E. J., Hallett, M. B. and Allemann, R. K. 2014. The structural basis of differential inhibition of human calpain by indole and phenyl α--mercaptoacrylic acids. Journal of Structural Biology 187(3), pp. 236-241. (10.1016/j.jsb.2014.07.004)
• Behiry, E. M., Luk, L. Y. P., Matthews, S. M., Loveridge, E. J. and Allemann, R. K. 2014. Role of the occluded conformation in bacterial dihydrofolate reductases. Biochemistry 53(29), pp. 4761-4768. (10.1021/bi500507v)
• Behiry, E. M., Evans, R. M., Guo, J. N., Loveridge, E. J. and Allemann, R. K. 2014. Loop Interactions during Catalysis by Dihydrofolate Reductase from Moritella profunda. Biochemistry 53(29), pp. 4769-4774. (10.1021/bi500508z)
• Luk, L. Y. P., Loveridge, E. J. and Allemann, R. K. 2014. Different dynamical effects in mesophilic and hyperthermophilic dihydrofolate reductases. Journal of the American Chemical Society 136(19), pp. 6862-6865. (10.1021/ja502673h)
• Guo, J. N., Luk, L. Y. P., Loveridge, E. J. and Allemann, R. K. 2014. Thermal adaptation of dihydrofolate reductase from the moderate thermophile geobacillus stearothermophilus. Biochemistry 53(17), pp. 2855-2863. (10.1021/bi500238q)

2013

• Ruiz-Pernia, J. J. et al. 2013. Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. Journal of the American Chemical Society 135(49), pp. 18689-18696. (10.1021/ja410519h)
• Cascón, O., Richter, G., Allemann, R. K. and Wirth, T. 2013. Efficient terpene synthase catalysis by extraction in flow. ChemPlusChem 78(11), pp. 1334-1337. (10.1002/cplu.201300303)
• Miller, D. J., Adams, S. E., Hallett, M. B. and Allemann, R. K. 2013. Calpain-1 inhibitors for selective treatment of rheumatoid arthritis: what is the future?. Future Medicinal Chemistry 5(17), pp. 2057-2074. (10.4155/fmc.13.172)
• Luk, L. Y. P. et al. 2013. Unraveling the role of protein dynamics in dihydrofolate reductase catalysis. Proceedings of the National Academy of Sciences of the United States of America 110(41), pp. 16344-16349. (10.1073/pnas.1312437110)
• Mart, R. J. et al. 2013. BH3 helix-derived biophotonic nanoswitches regulate cytochrome c release in permeabilised cells. Molecular BioSystems 9(11), pp. 2597-2603. (10.1039/c3mb70246d)
• Guo, J., Loveridge, E. J., Luk, L. Y. P. and Allemann, R. K. 2013. Effect of dimerization on dihydrofolate reductase catalysis. Biochemistry 52(22), pp. 3881-3887. (10.1021/bi4005073)
• Loveridge, E. J. et al. 2013. Aliphatic 1H, 13C and 15N chemical shift assignments of dihydrofolate reductase from the psychropiezophile Moritella profunda in complex with NADP+ and folate. Biomolecular NMR Assignments 7(1), pp. 61-64. (10.1007/s12104-012-9378-x)
• Wysoczanski, P., Mart, R. J., Loveridge, E. J., Williams, C., Whittaker, S. B., Crump, M. P. and Allemann, R. K. 2013. 1H, 13C and 15N chemical shift assignments of unliganded Bcl-xL and its complex with a photoresponsive Bak-derived peptide. Biomolecular NMR Assignments 7(2), pp. 187-191. (10.1007/s12104-012-9407-9)
• Li, J. et al. 2013. Rational engineering of plasticity residues of sesquiterpene synthases from 'Artemisia annua': Product specificity and catalytic efficiency. Biochemical Journal 451(3), pp. 417-426. (10.1042/BJ20130041)
• Li, J. et al. 2013. Rational engineering of plasticity residues of sesquiterpene synthases from Artemisia annua: product specificity and catalytic efficiency. Biochemical Journal -London- 451(3), pp. 417-426. (10.1042/BJ20130041)
• Chen, M. et al. 2013. Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase. Biochemistry 52(32), pp. 5441-5453. (10.1021/bi400691v)
• Pickett, J. A., Allemann, R. K. and Birkett, M. A. 2013. The semiochemistry of aphids. Natural Product Reports 30(10), pp. 1277-1283. (10.1039/c3np70036d)
• van der Kamp, M. W., Sirirak, J., Zurek, J., Allemann, R. K. and Mulholland, A. J. 2013. Conformational change and ligand binding in the aristolochene synthase catalytic cycle. Biochemistry 52(45), pp. 8094-8105. (10.1021/bi400898k)

2012

• Wysoczanski, P., Mart, R. J., Loveridge, E. J., Williams, C., Whittaker, S. B., Crump, M. P. and Allemann, R. K. 2012. NMR solution structure of a photoswitchable apoptosis activating Bak peptide bound to Bcl-xL. Journal of the American Chemical Society 134(18), pp. 7644-7647. (10.1021/ja302390a)
• Aros Orellana, D. F., Gonzalez, V., Allemann, R. K., Müller, C. T., Rosati, C. and Rogers, H. J. 2012. Volatile emissions of scented Alstroemeria genotypes are dominated by terpenes, and a myrcene synthase gene is highly expressed in scented Alstroemeria flowers. Journal of Experimental Botany 63(7), pp. 2739-2752. (10.1093/jxb/err456)
• Miller, D. J. and Allemann, R. K. 2012. Sesquiterpene synthases: Passive catalysts or active players?. Natural Product Reports 29(1), pp. 60-71. (10.1039/c1np00060h)
• Faraldos, J. A., Miller, D. J., Gonzalez, V., Yoosuf-Aly, F. Z., Cascón, O., Li, A. and Allemann, R. K. 2012. A 1,6-ring closure mechanism for (+)-δ-cadinene synthase?. Journal of the American Chemical Society 134(13), pp. 5900-5908. (10.1021/ja211820p)
• Mart, R. J., Wysoczanski, P., Kneissl, S., Ricci, A., Brancale, A. and Allemann, R. K. 2012. Design of photocontrolled RNA-binding peptidomimetics. ChemBioChem 13(4), pp. 515-519. (10.1002/cbic.201100800)
• Loveridge, E. J., Behiry, E. M., Guo, J. N. and Allemann, R. K. 2012. Evidence that a 'dynamic knockout' in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis. Nature Chemistry 4(4), pp. 292-297. (10.1038/nchem.1296)
• Faraldos, J. A., Gonzalez, V. and Allemann, R. K. 2012. The role of aristolochene synthase in diphosphate activation. Chemical Communications- Royal Society of Chemistry 48(26), pp. 3230-3232. (10.1039/c2cc17588f)
• Adams, S. E., Parr, C., Miller, D. J., Allemann, R. K. and Hallett, M. B. 2012. Potent inhibition of Ca2+-dependent activation of calpain-1 by novel mercaptoacrylates. MedChemComm 3(5), pp. 566-570. (10.1039/c2md00280a)
• Yoosuf-Aly, Z., Faraldos, J. A., Miller, D. J. and Allemann, R. K. 2012. Chemoenzymatic synthesis of the alarm pheromone (+)-verbenone from geranyl diphosphate. Chemical Communications 48, pp. 7040-7042. (10.1039/c2cc32883f)
• Cascón, O., Touchet, S., Miller, D. J., Gonzalez, V., Faraldos, J. A. and Allemann, R. K. 2012. Chemoenzymatic preparation of germacrene analogues. Chemical Communications 48(78), pp. 9702-9704. (10.1039/c2cc35542f)
• Faraldos, J. A., Gonzalez, V., Li, A., Yu, F., Köksal, M., Christianson, D. W. and Allemann, R. K. 2012. Probing the mechanism of 1,4-conjugate elimination reactions catalyzed by terpene synthases. Journal of the American Chemical Society 134(51), pp. 20844-20848. (10.1021/ja311022s)

2011

• Loveridge, E. J. et al. 2011. The role of large-scale motions in catalysis by dihydrofolate reductase. Journal of the American Chemical Society 133(50), pp. 20561-20570. (10.1021/ja208844j)
• Faraldos, J. A., Antonczak, A. K., Gonzalez, V., Fullerton, R., Tippmann, E. M. and Allemann, R. K. 2011. Probing eudesmane cation−π interactions in catalysis by aristolochene synthase with non-canonical amino acids. Journal of the American Chemical Society 133(35), pp. 13906-13909. (10.1021/ja205927u)
• Fricke, T. et al. 2011. Chemical synthesis of cell-permeable apoptotic peptides from in vivo produced proteins. Bioconjugate Chemistry 22(9), pp. 1763-1767. (10.1021/bc200338u)
• Loveridge, E. J., Dawson, W. M., Evans, R. M., Sobolewska, A. and Allemann, R. K. 2011. Reduced Susceptibility of Moritella profunda Dihydrofolate Reductase to Trimethoprim is Not Due to Glutamate 28. The Protein Journal 30(8), pp. 546-548. (10.1007/s10930-011-9361-x)
• Faraldos, J. A. and Allemann, R. K. 2011. Inhibition of (+)-Aristolochene Synthase with Iminium Salts Resembling Eudesmane Cation. Organic Letters 13(5), pp. 1202-1205. (10.1021/ol2000843)
• Loveridge, E. J. and Allemann, R. K. 2011. Effect of pH on Hydride Transfer by Escherichia coli Dihydrofolate Reductase. ChemBioChem 12(8), pp. 1258-1262. (10.1002/cbic.201000794)
• Faraldos, J. A., Gonzalez, V., Senske, M. and Allemann, R. K. 2011. Templating effects in aristolochene synthase catalysis: elimination versus cyclisation. Organic & Biomolecular Chemistry 9(20), pp. 6920-6923. (10.1039/c1ob06184d)

2010

• Fricke, T., Mart, R. J., Watkins, C. L., Jones, A. T. and Allemann, R. K. 2010. Click chemistry for the generation of cell permeable apoptotic peptides. Drug Discovery Today 15(23-24), pp. 1088-1088. (10.1016/j.drudis.2010.09.375)
• Tey, L., Loveridge, E. J., Swanwick, R., Flitsch, S. L. and Allemann, R. K. 2010. Highly site-selective stability increases by glycosylation of dihydrofolate reductase. FEBS Journal 277(9), pp. 2171-2179. (10.1111/j.1742-4658.2010.07634.x)
• Edwards, W. R., Williams, A. J., Morris, J. L., Baldwin, A. J., Allemann, R. K. and Jones, D. D. 2010. Regulation of β-Lactamase activity by remote binding of Heme: functional coupling of unrelated proteins through domain insertion. Biochemistry 49(31), pp. 6541-6549. (10.1021/bi100793y)
• Loveridge, E. J., Tey, L. and Allemann, R. K. 2010. Solvent effects on catalysis by Escherichia coli dihydrofolate reductase. Journal of the American Chemical Society 132(3), pp. 1137-1143. (10.1021/ja909353c)
• Faraldos, J. A., Kariuki, B. and Allemann, R. K. 2010. Intermediacy of Eudesmane Cation during Catalysis by Aristolochene Synthase. Journal of Organic Chemistry 75(4), pp. 1119-1125. (10.1021/jo902397v)
• Loveridge, E. J. and Allemann, R. K. 2010. The Temperature Dependence of the Kinetic Isotope Effects of Dihydrofolate Reductase from Thermotoga maritima Is Influenced by Intersubunit Interactions. Biochemistry 49(25), pp. 5390-5396. (10.1021/bi100761x)
• Evans, R. M., Behiry, E. M., Tey, L., Guo, J., Loveridge, E. J. and Allemann, R. K. 2010. Catalysis by Dihydrofolate Reductase from the Psychropiezophile Moritella profunda. ChemBioChem 11(14), pp. 2010-2017. (10.1002/cbic.201000341)

2009

• Loveridge, E. J., Behiry, E. M., Swanwick, R. S. and Allemann, R. K. 2009. Different reaction mechanisms for mesophilic and thermophilic dihydrofolate reductases. Journal of the American Chemical Society 131(20), pp. 6926-6927. (10.1021/ja901441k)
• Allemann, R. K., Evans, R. M. and Loveridge, E. J. 2009. Probing coupled motions in enzymatic hydrogen tunnelling reactions. Biochemical Society Transactions 37, pp. 349-353. (10.1042/BST0370349)
• Gennadios, H. A. et al. 2009. Crystal structure of (+)-δ-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis. Biochemistry 48(26), pp. 6175-6183. (10.1021/bi900483b)
• Loveridge, E. J., Rodriguez, R. J., Swanwick, R. S. and Allemann, R. K. 2009. Effect of Dimerization on the Stability and Catalytic Activity of Dihydrofolate Reductase from the Hyperthermophile Thermotoga maritima. Biochemistry 48(25), pp. 5922-5933. (10.1021/bi900411a)
• Miller, D. J., Yu, F., Knight, D. W. and Allemann, R. K. 2009. 6- and 14-Fluoro farnesyl diphosphate: mechanistic probes for the reaction catalysed by aristolochene synthase. Organic & Biomolecular Chemistry 7(5), pp. 962-975. (10.1039/b817194g)
• Allemann, R. K. 2009. Cystine-based Scaffolds for Functional Miniature Proteins. In: Moroder, L. and Buchner, J. eds. Oxidative Folding of Peptides and Proteins. London: RSC Publishing, pp. 381-395., (10.1039/9781847559265-00381)
• Loveridge, E. J. and Allemann, R. K. 2009. Direct methods for the analysis of quantum-mechanical tunnelling: dihydrofolate reductase. In: Allemann, R. K. and Scrutton, N. S. eds. Quantum Tunnelling in Enzyme-Catalysed Reactions. London: RSC Publishing, pp. 179-198., (10.1039/9781847559975-00179)
• Allemann, R. K., Young, N. J., Ma, S., Truhlar, D. G. and Gao, J. 2009. Synthetic Efficiency in Enzyme Mechanisms Involving Carbocations: Aristolochene Synthase [Addition/Correction]. Journal of the American Chemical Society 131(27), pp. 9600. (10.1021/ja904281h)
• Hay, S. et al. 2009. Are the Catalytic Properties of Enzymes from Piezophilic Organisms Pressure Adapted?. ChemBioChem 10(14), pp. 2348-2353. (10.1002/cbic.200900367)
• Loveridge, E. J., Maglia, G. and Allemann, R. K. 2009. The Role of Arginine 28 in Catalysis by Dihydrofolate Reductase from the HyperthermophileThermotoga maritima. ChemBioChem 10(16), pp. 2624-2627. (10.1002/cbic.200900465)
• Carpenter, B. K. 2009. The transition-state theory description of enzyme catalysis for classically activated reactions. In: Allemann, R. K. and Scrutton, N. S. eds. Quantum tunnelling in enzyme-catalysed reactions. London: RSC Publishing, pp. 1-17., (10.1039/9781847559975-00001)
• Allemann, R. K. and Scrutton, N. S. eds. 2009. Quantum tunnelling in enzyme-catalysed reactions. RSC biomolecular sciences Vol. 18. Cambridge: RSC Publishing.

2008

• Miller, D. J., Yu, F. and Allemann, R. K. 2008. FLUO 14-Study of sesquiterpene cyclization reactions using fluorinated farnesyl diphosphate analogs. Abstracts of Papers of the American Chemical Society 236
• Shishova, E. Y. et al. 2008. X-ray crystallographic studies of substrate binding to aristolochene synthase suggest a metal ion binding sequence for catalysis. Journal of Biological Chemistry 283(22), pp. 15431-15439. (10.1074/jbc.M800659200)
• Allemann, R. K. 2008. Chemical wizardry? The generation of diversity in terpenoid biosynthesis. Pure and Applied Chemistry 80(8), pp. 1791-1798. (10.1351/pac200880081791)
• Edwards, W. R., Busse, K., Allemann, R. K. and Jones, D. D. 2008. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Research 36(13) (10.1093/nar/gkn363)
• Fütterer, K., Ravelli, R. B. G., White, S. A., Nicoll, A. J. and Allemann, R. K. 2008. Differential specific radiation damage in the CuII-bound and PdII-bound forms of an α-helical foldamer: A case study of crystallographic phasing by RIP and SAD. Acta Crystallographica Section D: Biological Crystallography 64(3), pp. 264-272. (10.1107/S0907444907065948)
• Hay, S. et al. 2008. Secondary kinetic isotope effects as probes of environmentally-coupled enzymatic hydrogen tunneling reactions. ChemPhysChem 9(11), pp. 1536-1539. (10.1002/cphc.200800291)
• Loveridge, E. J., Evans, R. M. and Allemann, R. K. 2008. Solvent Effects on Environmentally Coupled Hydrogen Tunnelling During Catalysis by Dihydrofolate Reductase from Thermotoga maritima. Chemistry-a European Journal 14(34), pp. 10782-10788. (10.1002/chem.200801804)
• Miller, D. J., Gao, J., Truhlar, D. G., Young, N. J., Gonzalez, V. and Allemann, R. K. 2008. Stereochemistry of eudesmane cation formation during catalysis by aristolochene synthase from Penicillium roqueforti. Organic & Biomolecular Chemistry 6(13), pp. 2346-2354. (10.1039/b804198a)
• Kneissl, S., Loveridge, E. J., Williams, C., Crump, M. P. and Allemann, R. K. 2008. Photocontrollable peptide-based switches target the anti-apoptotic protein Bcl-xL. ChemBioChem 9(18), pp. 3046-3054. (10.1002/cbic.200800502)

2007

• Yu, F., Miller, D. J. and Allemann, R. K. 2007. Probing the reaction mechanism of aristolochene synthase with 12,13-difluorofarnesyl diphosphate. Chemical Communications- Royal Society of Chemistry(40), pp. 4155-4157. (10.1039/b709562g)
• Miller, D. J., Yu, F. and Allemann, R. K. 2007. Aristolochene synthase-catalyzed cyclization of 2-fluorofarnesyl-diphosphate to 2-fluorogermacrene A. Chembiochem 8(15), pp. 1819-1825. (10.1002/cbic.200700219)
• Miller, D. J., Yu, F., Young, N. J. and Allemann, R. K. 2007. Competitive inhibition of aristolochene synthase by phenyl-substituted farnesyl diphosphates: evidence of active site plasticity. Organic & Biomolecular Chemistry 5(20), pp. 3287-3298. (10.1039/b713301b)
• Miller, D. J. and Allemann, R. K. 2007. myo-Inositol Monophosphatase: A Challenging Target for Mood Stabilising Drugs. Mini-Reviews in Chemistry 7(2), pp. 107-113. (10.2174/138955707779802624)
• Pang, J. and Allemann, R. K. 2007. Molecular dynamics simulation of thermal unfolding of Thermatoga maritima DHFR. Physical Chemistry Chemical Physics 9(6), pp. 711-718. (10.1039/b611210b)
• Allemann, R. K., Young, N. J., Ma, S., Truhlar, D. G. and Gao, J. 2007. Synthetic Efficiency in Enzyme Mechanisms Involving Carbocations:  Aristolochene Synthase. Journal of the American Chemical Society 129(43), pp. 13008-13013. (10.1021/ja0722067)

2006

• Nicoll, A. J., Miller, D. J., Fütterer, K., Ravelli, R. and Allemann, R. K. 2006. Designed high affinity Cu2+ -Binding α-Helical foldamer. Journal of the American Chemical Society 128(28), pp. 9187-9193. (10.1021/ja061513u)
• Allemann, R. K. et al. 2006. Protein motions during catalysis by dihydrofolate reductases. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 361(1472), pp. 1317-1321. (10.1098/rstb.2006.1865)
• Maglia, G., Swanwick, R. S., Tey, L. and Allemann, R. K. 2006. Coupling of protein motions and hydrogen transfer during catalysis by Escherichia coli dihydrofolate reductase. Biochemical Journal 394(1), pp. 259-265. (10.1042/BJ20051464)
• Pang, J., Pu, J., Gao, J., Truhlar, D. G. and Allemann, R. K. 2006. Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase Is Dominated by Quantum Mechanical Tunneling and Is Promoted by Both Inter- and Intramonomeric Correlated Motions. Journal of the American Chemical Society 128(24), pp. 8015-8023. (10.1021/ja061585l)
• Forcat, S. and Allemann, R. K. 2006. Stabilisation of transition states prior to and following eudesmane cation in aristolochene synthase. Organic & Biomolecular Chemistry 4(13), pp. 2563-2567. (10.1039/b604147g)

2005

• Guerrero, L., Smart, O. S., Weston, C. J., Allemann, R. K. and Woolley, G. A. 2005. Photochemical Regulation of DNA-Binding Specificity of MyoD. Angewandte Chemie International Edition 44(47), pp. 7778-7782. (10.1002/anie.200502666)
• Swanwick, R. S., Daines, A. M., Flitsch, S. L. and Allemann, R. K. 2005. Synthesis of homogenous site-selectively glycosylated proteins. Organic & Biomolecular Chemistry 3(4), pp. 572-574. (10.1039/b417133k)
• Swanwick, R. S., Daines, A. M., Tey, L., Flitsch, S. L. and Allemann, R. K. 2005. Increased Thermal Stability of Site-Selectively Glycosylated Dihydrofolate Reductase. ChemBioChem 6(8), pp. 1338-1340. (10.1002/cbic.200500103)
• Guerrero, L., Smart, O. S., Woolley, G. A. and Allemann, R. K. 2005. Photocontrol of DNA Binding Specificity of a Miniature Engrailed Homeodomain. Journal of the American Chemical Society 127(44), pp. 15624-15629. (10.1021/ja0550428)

2004

• Swanwick, R. S., Shrimpton, P. J. and Allemann, R. K. 2004. Pivotal role of Gly 121 in dihydrofolate reductase from Escherichia coli: the altered structure of a mutant enzyme may form the basis of its diminished datalytic performance. Biochemistry 43(14), pp. 4119-4127. (10.1021/bi036164k)
• Miller, D. J., Bashir-Uddin Surfraz, M., Akhtar, M., Gani, D. and Allemann, R. K. 2004. Removal of the phosphate group in mechanism-based inhibitors of inositol monophosphatase leads to unusual inhibitory activity. Organic & Biomolecular Chemistry 2(5), pp. 671-688. (10.1039/b312808c)
• Turner, E. C., Cureton, C. H., Weston, C. J., Smart, O. S. and Allemann, R. K. 2004. Controlling the DNA Binding Specificity of bHLH Proteins through Intramolecular Interactions. Chemistry & Biology 11(1), pp. 69-77. (10.1016/j.chembiol.2003.12.015)
• Bashir-Uddin Surfraz, M., Akhtar, M. and Allemann, R. K. 2004. Bis-benzyl protected 6-amino cyclitols are poisonous to Pd/C catalysed hydrogenolysis of benzyl ethers. Tetrahedron Letters 45(6), pp. 1223-1226. (10.1016/j.tetlet.2003.11.130)
• Weston, C. J., Cureton, C. H., Calvert, M. J., Smart, O. S. and Allemann, R. K. 2004. A Stable Miniature Protein with Oxaloacetate Decarboxylase Activity. ChemBioChem 5(8), pp. 1075-1080. (10.1002/cbic.200300805)
• Forcat, S. and Allemann, R. K. 2004. Dual role for phenylalanine 178 during catalysis by aristolochene synthase. Chemical Communications(18), pp. 2094-2095. (10.1039/b407932a)
• Nicoll, A. J. and Allemann, R. K. 2004. Nucleophilic and general acid catalysis at physiological pH by a designed miniature esterase. Organic & Biomolecular Chemistry 2(15), pp. 2175-2180. (10.1039/b404730c)
• Nicoll, A. J. and Allemann, R. K. 2004. Miniature proteomics: designing alpha-helical miniature proteins. Recent Research Developments in Chemistry 2, pp. 227-243.

2003

• Allemann, R. K. and Maglia, G. 2003. Evidence for Environmentally Coupled Hydrogen Tunneling during Dihydrofolate Reductase Catalysis. Journal of the American Chemical Society 125(44), pp. 13372-13373. (10.1021/ja035692g)
• Bashir-Uddin Surfraz, M., Miller, D. J., Gani, D. and Allemann, R. K. 2003. Product-like inhibitors of inositol monophosphatase. Tetrahedron Letters 44(41), pp. 7677-7679. (10.1016/S0040-4039(03)01878-1)
• Shrimpton, P., Mullaney, A. and Allemann, R. K. 2003. Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase. Proteins: Structure, Function and Bioinformatics 51(2), pp. 216-223. (10.1002/prot.10370)
• Maglia, G., Javed, M. and Allemann, R. K. 2003. Hydride transfer during catalysis by dihydrofolate reductase from Thermotoga maritima. Biochemical Journal 374(2), pp. 529-535. (10.1042/BJ20030412)
• Deligeorgopoulou, A., Taylor, S. E., Forcat, S. and Allemann, R. K. 2003. Stabilisation of eudesmane cation by tryptophan 334 during aristolochene synthase catalysis. Chemical Communications(17), pp. 2162-2163. (10.1039/b306867f)

2002

• Kohler, U. and Allemann, R. K. 2002. Transcription factors. In: Creighton, T. E. ed. Encyclopedia of Molecular Biology. Oxford: Wiley, (10.1002/047120918X.emb1569)
• Shrimpton, P. and Allemann, R. K. 2002. Role of water in the catalytic cycle of E. coli dihydrofolate reductase. Protein Science 11(6), pp. 1442-1451. (10.1110/ps.5060102)
• Calvert, M. J., Ashton, P. R. and Allemann, R. K. 2002. Germacrene A Is a Product of the Aristolochene Synthase-Mediated Conversion of Farnesylpyrophosphate to Aristolochene. Journal of the American Chemical Society 124(39), pp. 11636-11641. (10.1021/ja020762p)
• Calvert, M. J., Taylor, S. E. and Allemann, R. K. 2002. Tyrosine 92 of aristolochene synthase directs cyclisation of farnesyl pyrophosphate. Chemical Communications(20), pp. 2384-2385. (10.1039/b206517g)
• Taylor, S. E., Rutherford, T. J. and Allemann, R. K. 2002. Design of a folded, conformationally stable oxaloacetate decarboxylase. Journal of the Chemical Society, Perkin Transactions 2 2(4), pp. 751-755. (10.1039/b200057c)

2001

• Taylor, S. E., Rutherford, T. J. and Allemann, R. K. 2001. Design, synthesis and characterisation of a peptide with oxaloacetate decarboxylase activity. Biorganic and Medicinal Chemistry Letters 11(19), pp. 2631-2635. (10.1016/S0960-894X(01)00519-4)

1999

• Dezan, C., Meierhans, D., Künne, A. G. E. and Allemann, R. K. 1999. Acquisition of myogenic specificity through replacement of one amino acid of MASH-1 and introduction of an additional α-helical turn. Biological Chemistry 380(6), pp. 705-710. (10.1515/BC.1999.088)
• Allemann, R. K. 1999. DNA-protein binding specificity. In: Creighton, T. E. ed. Encyclopedia of Molecular Biology., Vol. 2. New York: Wiley, pp. 743-745.
• Allemann, R. K. 1999. DNA-protein interaction thermodynamics. In: Creighton, T. E. ed. Encyclopedia of Molecular Biology., Vol. 2. New York: Wiley, pp. 745-755.
• Allemann, R. K. 1999. MADS-Box proteins. In: Creighton, T. E. ed. Encyclopedia of Molecular Biology., Vol. 3. New York: Wiley, pp. 1430-1431.
• Allemann, R. K. 1999. Transcription factors. In: Creighton, T. E. ed. Encyclopedia of Molecular Biology., Vol. 4. New York: Wiley, pp. 2586-2593.

1998

• Sieber, M. and Allemann, R. K. 1998. Single chain dimers of MASH-1 bind DNA with enhanced affinity. Nucleic Acids Research 26(6), pp. 1408-1413. (10.1093/nar/26.6.1408)
• Künne, A. G. E., Sieber, M., Meierhans, D. and Allemann, R. K. 1998. Thermodynamics of the DNA binding reaction of transcription factor MASH-1. Biochemistry 37(12), pp. 4217-4223. (10.1021/bi9725374)
• Meierhans, D. and Allemann, R. K. 1998. The N-terminal methionine is a major determinant of the DNA binding specificity of MEF-2C. Journal of Biological Chemistry 273(40), pp. 26052-26060. (10.1074/jbc.273.40.26052)
• Sieber, M. and Allemann, R. K. 1998. Arginine (348) is a major determinant of the DNA binding specificity of transcription factor E12. Biological Chemistry 379(6), pp. 731-735.

1997

• Meierhans, D. and Allemann, R. K. 1997. High level expression in soluble form, one step purification, and characterization of the DNA binding domain of MEF-2C. Protein Expression and Purification 11(3), pp. 297-303. (10.1006/prep.1997.0795)
• Künne, A. G. E. and Allemann, R. K. 1997. Covalently linking BHLH subunits of MASH-1 increases specificity of DNA Binding. Biochemistry 36(5), pp. 1085-1091. (10.1021/bi962185l)
• Meierhans, D., Sieber, M. and Allemann, R. K. 1997. High affinity binding of MEF-2C correlates with DNA bending. Nucleic Acids Research 25(22), pp. 4537-4544. (10.1093/nar/25.22.4537)
• Allemann, R. K. and Egli, M. 1997. DNA recognition and bending. Chemistry & Biology 4(9), pp. 643-650. (10.1016/S1074-5521(97)90218-0)

1996

• Künne, A., Meierhans, D. and Allemann, R. K. 1996. Basic helix-loop-helix protein MyoD displays modest DNA binding specificity. FEBS Letters 391(1-2), pp. 79-83. (10.1016/0014-5793(96)00707-7)

1995

• Meierhans, D., el-Ariss, C., Neuenschwander, M., Sieber, M., Stackhouse, J. F. and Allemann, R. K. 1995. DNA Binding Specificity of the Basic-Helix-Loop-Helix Protein MASH-1. Biochemistry 34(35), pp. 11026-11036. (10.1021/bi00035a008)

1993

• Johnsson, K., Allemann, R. K., Widmer, H. and Benner, S. A. 1993. Synthesis, structure and activity of artificial, rationally designed catalytic polypeptides. Nature 365(6446), pp. 530-532. (10.1038/365530a0)

1991

• Whiting, J., Marshall, H., Cook, M., Krumlauf, R., Rigby, P. W., Stott, D. and Allemann, R. K. 1991. Multiple spatially specific enhancers are required to reconstruct the pattern of Hox-2.6 gene expression. Genes & Development 5(11), pp. 2048-2059. (10.1101/gad.5.11.2048)
• Hunt, P. et al. 1991. The branchial Hox code and its implications for gene regulation, patterning of the nervous system and head evolution. Development 113(S2), pp. 63-77.

1990

• Johnson, K., Allemann, R. K. and Benner, S. A. 1990. Designed enzymes. In: Bleasdale, C. and Golding, R. eds. Molecular mechanisms in bioorganic processes. London: Royal Society of Chemistry, pp. 166-187.

1989

• Benner, S. A. and Allemann, R. K. 1989. The return of pancreatic ribonucleases. Trends in Biochemical Sciences 14(10), pp. 396-397. (10.1016/0968-0004(89)90282-X)

1988

• Allemann, R. K., Hung, R. and Benner, S. A. 1988. Stereochemical profile of the dehydrogenases of Drosophila melanogaster. Journal of the American Chemical Society 110(16), pp. 5555-5560. (10.1021/ja00224a046)

1987

• Benner, S. A. and Allemann, R. K. 1987. Natural Selection, Protein Engineering, and the last Riboorganism: Rational Model Building in Biochemistry. In: Evolution of Catalytic Function. CSH Symposia on Quantitative Biology Vol. 52. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, pp. 53-63.