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Relevant bibliographies by topics / Enzyme dynamics during catalysis

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Academic literature on the topic 'Enzyme dynamics during catalysis'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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Journal articles on the topic "Enzyme dynamics during catalysis"

1

Eisenmesser, E. Z. "Enzyme Dynamics During Catalysis." Science 295, no. 5559 (2002): 1520–23. http://dx.doi.org/10.1126/science.1066176.

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Dasgupta, Medhanjali, Dominik Budday, Saulo H. P. de Oliveira, et al. "Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis." Proceedings of the National Academy of Sciences 116, no. 51 (2019): 25634–40. http://dx.doi.org/10.1073/pnas.1901864116.

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How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH mi

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Bauer, R., E. Danielsen, E. Friis, et al. "Dynamics and metal coordination geometry during active enzyme catalysis for the enzyme carboxypeptidase." Journal of Inorganic Biochemistry 59, no. 2-3 (1995): 390. http://dx.doi.org/10.1016/0162-0134(95)97488-c.

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Smith, Nathan, and Mark A. Wilson. "Understanding Cysteine Chemistry Using Conventional and Serial X-ray Protein Crystallography." Crystals 12, no. 11 (2022): 1671. http://dx.doi.org/10.3390/cryst12111671.

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Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging t

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Ferrall-Fairbanks, Meghan C., Chris A. Kieslich, and Manu O. Platt. "Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks." Proceedings of the National Academy of Sciences 117, no. 6 (2020): 3307–18. http://dx.doi.org/10.1073/pnas.1912207117.

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Enzymes are catalysts in biochemical reactions that, by definition, increase rates of reactions without being altered or destroyed. However, when that enzyme is a protease, a subclass of enzymes that hydrolyze other proteins, and that protease is in a multiprotease system, protease-as-substrate dynamics must be included, challenging assumptions of enzyme inertness, shifting kinetic predictions of that system. Protease-on-protease inactivating hydrolysis can alter predicted protease concentrations used to determine pharmaceutical dosing strategies. Cysteine cathepsins are proteases capable of c

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Rabe, Patrick, Jos J. A. G. Kamps, Kyle D. Sutherlin, et al. "X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis." Science Advances 7, no. 34 (2021): eabh0250. http://dx.doi.org/10.1126/sciadv.abh0250.

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Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of pro

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Kulik, Heather J. "Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer." Physical Chemistry Chemical Physics 20, no. 31 (2018): 20650–60. http://dx.doi.org/10.1039/c8cp03871f.

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Mori, Toshifumi, and Shinji Saito. "Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase." Journal of Chemical Theory and Computation 16, no. 5 (2020): 3396–407. http://dx.doi.org/10.1021/acs.jctc.9b01279.

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WILLIAMS, G. S. BLAIR, AFTAB M. HOSSAIN, SHIYING SHANG, DAVID E. KRANBUEHL, and CAREY K. BAGDASSARIAN. "EVOLUTION OF A CATALYTICALLY EFFECTIVE MODEL ENZYME: THE IMPORTANCE OF TUNED CONFORMATIONAL FLUCTUATIONS." Journal of Theoretical and Computational Chemistry 02, no. 03 (2003): 323–34. http://dx.doi.org/10.1142/s0219633603000586.

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Possible causal connections between the dynamics of a thermally fluctuating model enzyme molecule and catalysis are explored. The model is motivated by observations from experiment and simulation that amino acid residues residing in different enzymatic domains may show markedly different degrees of conformational freedom. Consequently, we are interested in the catalytic efficacy of an enzyme as a function of long-range many-atom cooperative effects resulting from strong, moderate, and weak interactions between enzymatic residues. Here we show and quantify through molecular dynamics simulations

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Park, Jae-Hyun, Ji-Hye Yun, Yingchen Shi, et al. "Non-Cryogenic Structure and Dynamics of HIV-1 Integrase Catalytic Core Domain by X-ray Free-Electron Lasers." International Journal of Molecular Sciences 20, no. 8 (2019): 1943. http://dx.doi.org/10.3390/ijms20081943.

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HIV-1 integrase (HIV-1 IN) is an enzyme produced by the HIV-1 virus that integrates genetic material of the virus into the DNA of infected human cells. HIV-1 IN acts as a key component of the Retroviral Pre-Integration Complex (PIC). Protein dynamics could play an important role during the catalysis of HIV-1 IN; however, this process has not yet been fully elucidated. X-ray free electron laser (XFEL) together with nuclear magnetic resonance (NMR) could provide information regarding the dynamics during this catalysis reaction. Here, we report the non-cryogenic crystal structure of HIV-1 IN cata

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Dissertations / Theses on the topic "Enzyme dynamics during catalysis"

1

Nunez, Sara. "Importance of enzyme dynamics in catalysis." Thesis, University of Manchester, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.534144.

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Singh, Priyanka. "Enzyme catalysis and dynamics in dihydrofolate reductase." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/5635.

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Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate bindings, chemical conversions, and products release. The relationship between protein motions and catalytic activity is of considerable contemporary interest in enzymology. To understand the factors influencing the rates of enzyme catalyzed reactions, the dynamics of the protein-solvent-substrate complex must be considered. The enzyme dihydrofolate reductase from Escherichia coli (EcDHFR) is often used as a model system in various biophysical studies, incl

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Dannatt, Hugh. "The role of enzyme dynamics in catalysis by β-phosphoglucomutase". Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2781/.

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Bjelic, Sinisa. "Molecular Simulation of Enzyme Catalysis and Inhibition." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7468.

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Lopez, Murielle. "The Effect of Hydration on Enzyme Activity and Dynamics." The University of Waikato, 2008. http://hdl.handle.net/10289/2360.

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Water has long been assumed to be essential for biological function. To understand the molecular basis of the role of water in protein function, several studies have established a correlation between enzyme activity and hydration level. While a threshold of hydration of 0.2 h (grams of water per gram of dried protein) is usually accepted for the onset of enzyme activity, recent works show that enzyme activity is possible at water contents as low as 0.03 h (Lind et al., 2004). Diffusion limitation in these experiments was avoided by monitoring enzyme-catalyzed hydrolysis of gas-phase esters. Ho

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Hoeven, Robin. "Investigating the contribution of protein dynamics to catalysis in protochlorophyllide oxidoreductase." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/investigating-the-contribution-of-protein-dynamics-to-catalysis-in-protochlorophyllide-oxidoreductase(029dda21-023f-4fdb-a980-26db7eab4833).html.

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Enzyme dynamics has been established to play a crucial role in catalysis, and it has therefore become an important area of research to better understand enzymatic rate enhancements. The light-activated enzyme protochlorophyllide oxidoreductase (POR) is a well-studied model system where dynamics are known to be important for catalysis. The catalytic reaction involves a sequential hydride and proton transfer to reduce the C17-C18 double bond in the protochlorophyllide (Pchlide) substrate with NADPH as a cofactor to yield the chlorophyllide (Chlide) product. Both H-transfer steps are established

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Stojkovic, Vanja. "Contribution of active site dynamics to enzyme catalysis: study on a series of mutants of dihydrofolate reductase." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/5062.

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This thesis describes an effort to expand current knowledge of catalysis in biological systems. The focus is on understanding how enzymes activate covalent bonds and specifically to study C-H bond activation via enzymes. The work presented here examined the role of protein dynamics and hydrogen tunneling in enzyme catalysis. Dihydrofolate reductase from Escherichia coli (ecDHFR), which catalyzes a single hydride transfer reaction, was selected as the model system for these studies. Intrinsic kinetic isotope effects (KIEs) have been shown to be highly sensitive probes in examining the chemical

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Subramaniam, Srisunder. "Studies of conformational changes and dynamics accompanying substrate recognition, allostery and catalysis in bacteriophage lambda integrase." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111655332.

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Molina, Gustavo Avelar. "Caracterização biofísica da dinâmica catalítica de uma xilanase GH11." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/59/59138/tde-17042016-155242/.

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A dinâmica estrutural fundamentando a função das xilanases GH11 ainda não está clara. Novo conhecimento sobre a dinâmica catalítica dessas enzimas é crucial para a engenharia de novas enzimas melhoradas beneficiando, assim, diversas indústrias biotecnológicas e de química verde. Com base nesse fato, esse trabalho teve por objetivo obter novas informações acerca da dinâmica catalítica de uma xilanase GH11, através do uso de um conjunto de diversas técnicas avançadas de biofísica molecular em nível bulk e em nível de molécula única (inglês single molecule ou sm). Para isso, foram projetadas xil

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Mills, Landon C. "IMPACT OF CONFORMATIONAL CHANGE, SOLVATION ENVIRONMENT, AND POST-TRANSLATIONAL MODIFICATION ON DESULFURIZATION ENZYME 2'-HYDROXYBIPHENYL-2-SULFINATE DESULFINASE (DSZB) STABILITY AND ACTIVITY." UKnowledge, 2019. https://uknowledge.uky.edu/cme_etds/105.

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Naturally occurring enzymatic pathways enable highly specific, rapid thiophenic sulfur cleavage occurring at ambient temperature and pressure, which may be harnessed for the desulfurization of petroleum-based fuel. One pathway found in bacteria is a four-step catabolic pathway (the 4S pathway) converting dibenzothiophene (DBT), a common crude oil contaminant, into 2-hydroxybiphenyl (HBP) without disrupting the carbon-carbon bonds. 2’-Hydroxybiphenyl-2-sulfinate desulfinase (DszB), the rate-limiting enzyme in the enzyme cascade, is capable of selectively cleaving carbon-sulfur bonds. Accordingl

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Books on the topic "Enzyme dynamics during catalysis"

1

Klinman, Judith, and Sharon Hammes- Schiffer, eds. Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-38962-7.

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NATO Advanced Study Institute on the Enzyme Catalysis Process: Energetics, Mechanism, and Dynamics (1988 Barga, Italy). The enzyme catalysis process: Energetics, mechanism, and dynamics. Plenum Press, 1989.

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Klinman, Judith, and Sharon Hammes Schiffer. Dynamics in Enzyme Catalysis. Springer, 2015.

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Klinman, Judith, and Sharon Hammes Schiffer. Dynamics in Enzyme Catalysis. Springer, 2013.

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Klinman, Judith, and Sharon Hammes Schiffer. Dynamics in Enzyme Catalysis. Springer London, Limited, 2013.

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A, Cooper. Enzyme Catalysis Process: Energetics, Mechanism and Dynamics. Springer, 2013.

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A, Cooper. Enzyme Catalysis Process: Energetics, Mechanism and Dynamics. Springer London, Limited, 2013.

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Cooper, A. The Enzyme Catalysis Process:Energetics, Mechanism and Dynamics. Springer, 1989.

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A, Cooper. The Enzyme Catalysis Process: Energetics, Mechanism and Dynamics. Springer, 2014.

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Book chapters on the topic "Enzyme dynamics during catalysis"

1

Somorjai, R. L. "Proteins: Interactions and Dynamics." In The Enzyme Catalysis Process. Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-1607-8_3.

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Ma, Buyong, and Ruth Nussinov. "Structured Crowding and Its Effects on Enzyme Catalysis." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_316.

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Cheatum, Christopher M., and Amnon Kohen. "Relationship of Femtosecond–Picosecond Dynamics to Enzyme-Catalyzed H-Transfer." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_407.

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4

Arora, Karunesh, and Charles L. Brooks. "Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_408.

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Daily, Michael D., Haibo Yu, George N. Phillips, and Qiang Cui. "Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_409.

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Schrank, Travis P., James O. Wrabl, and Vincent J. Hilser. "Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_410.

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Schulenburg, Cindy, and Donald Hilvert. "Protein Conformational Disorder and Enzyme Catalysis." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_411.

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Schwartz, Steven D. "Protein Dynamics and the Enzymatic Reaction Coordinate." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_412.

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Wand, A. Joshua, Veronica R. Moorman, and Kyle W. Harpole. "A Surprising Role for Conformational Entropy in Protein Function." In Dynamics in Enzyme Catalysis. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/128_2012_418.

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Fillaux, Francois. "Nonlinear Coupling and Vibrational Dynamics." In The Enzyme Catalysis Process. Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-1607-8_8.

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Conference papers on the topic "Enzyme dynamics during catalysis"

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Carey, P. C. "Studies of enzymes by resonance Raman spectroscopy." In International Laser Science Conference. Optica Publishing Group, 1986. http://dx.doi.org/10.1364/ils.1986.thg3.

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By creating a resonance Raman probe in the active site of an enzyme, it is possible to obtain the vibrational spectrum associated with those bonds undergoing catalytic transformation. The approach involves reacting thionoesters RC(= S)OCH3 with a class of enzymes known as cysteine proteases which have an essential SH group in their active sights HS-enzyme. The reaction produces an intermediate RC(= S) S-enzyme which is a dithioester with a λmax near 315 nm. The 324-nm excited RR spectra of the dithioester provide a wealth of detail on the substrate during catalysis; the confirmation of the sub

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Zapata-Romero, Gilberto A., Markus Doerr, and Martha C. Daza. "Enantioselective lipase-catalyzed O-acylation of (RS)-propranolol: analysis of the hydrogen bonds essential for catalysis." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020131.

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We investigated the effect of the acyl group size in the enantioselectivity of the acylation of propranolol, an amino alcohol used as β-adrenergic blocking agent. We applied a methodology frequently used to model enantioselectivity that is based on the hydrogen bonds present in the tetrahedral intermediate, which occurs in lipase-catalyzed reactions. We sampled the conformations of the tetrahedral intermediate corresponding to the esterification of both enantiomers of propranolol with ethanoyl and butanoyl, employing molecular dynamics simulation together with a quantum mechanics/molecular mec

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Chirkova, V. Yu, D. N. Shcherbakov, and I. Yu Evdokimov. "DAILY DYNAMICS OF THE ACTIVITY OF RECOMBINANT PHOSPHOLIPASE C OBTAINED IN THE BACILLUS MOJAVENSIS SYSTEM DURING SUBMERGED CULTIVATION IN A SEMI-INDUSTRIAL FERMENTER." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-146.

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As a result of experimental deep cultivation of a new strain-producer of recombinant phospholipase C in the Bacillus mojavensis system in a semi-industrial 250-liter bioreactor, an enzyme preparation was obtained with a maximum phospholipase activity of 307.35 units/ml after 8 h of operation at 37 ºС.

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Abuelzm, Ehab, D. Ghosh, B. Ghosh, and A. R. Mohammed. "Novel Application of Modified Enzymatic Fluid System for Freeing Stuck Pipe in Gas Wells." In ADIPEC. SPE, 2024. http://dx.doi.org/10.2118/222951-ms.

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Abstract While Enzymatic treatment is considered safe for downhole tools and an effective technique for the removal of biopolymer-based drilling mud cake formed during drilling, a novel application of enzymatic system has been developed and successfully utilized to release stuck pipe while drilling. An enzyme's function is intrinsically linked to its three-dimensional structure, defining how it achieves substrate binding, catalysis, and regulation. Stuck pipe contingency especially in horizontal/multilateral wells demands large volumes of harsh chemicals like acid, solvents, and other chemical

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