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Journal articles on the topic 'Enzyme dynamics during catalysis'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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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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2

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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3

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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4

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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5

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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7

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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8

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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9

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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10

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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11

Perincherry, Lakshmipriya, Monika Urbaniak, Izabela Pawłowicz, Karolina Kotowska, Agnieszka Waśkiewicz, and Łukasz Stępień. "Dynamics of Fusarium Mycotoxins and Lytic Enzymes during Pea Plants’ Infection." International Journal of Molecular Sciences 22, no. 18 (2021): 9888. http://dx.doi.org/10.3390/ijms22189888.

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Fusarium species are common plant pathogens that cause several important diseases. They produce a wide range of secondary metabolites, among which mycotoxins and extracellular cell wall-degrading enzymes (CWDEs) contribute to weakening and invading the host plant successfully. Two species of Fusarium isolated from peas were monitored for their expression profile of three cell wall-degrading enzyme coding genes upon culturing with extracts from resistant (Sokolik) and susceptible (Santana) pea cultivars. The extracts from Santana induced a sudden increase in the gene expression, whereas Sokolik

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12

McGowan, Lauren C., and Donald Hamelberg. "Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover." Biophysical Journal 104, no. 1 (2013): 216–26. http://dx.doi.org/10.1016/j.bpj.2012.11.3815.

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13

Wang, Huan, Xiaozhe Dong, and De-Yi Zhang. "Transient Processes and Emerging Dynamics of Active Molecular Systems." ECS Meeting Abstracts MA2025-01, no. 13 (2025): 1047. https://doi.org/10.1149/ma2025-01131047mtgabs.

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We will discuss unexpected observations and new questions when we apply techniques that were conventionally not used for studying chemical processes. Inspecting biomacromolecular reactions at a single molecule level, with real-time observation by in situ liquid-phase electron microscopy (LP-EM), we found some pathways are as anticipated while others are surprising. Through direct imaging of molecular states at equilibrium, we tested the single molecule ergodicity.From time-lapsed images of a single enzyme catalysis event, during which mutual conformational adaption of enzyme and DNA, enzyme di

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14

Zheng, Zhong-liang, Mao-qing Ye, Zhen-yu Zuo, Zhi-gang Liu, Keng-chang Tai, and Guo-lin Zou. "Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation." Biochemical Journal 395, no. 3 (2006): 509–15. http://dx.doi.org/10.1042/bj20050772.

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Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33→Ala33, Asp60→Al

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15

Liu, Yu-Hong, and Lars Konermann. "Enzyme conformational dynamics during catalysis and in the ‘resting state’ monitored by hydrogen/deuterium exchange mass spectrometry." FEBS Letters 580, no. 22 (2006): 5137–42. http://dx.doi.org/10.1016/j.febslet.2006.08.042.

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16

Kanazhevskaya, Lyubov Yu, Denis A. Smyshliaev, Nadezhda A. Timofeyeva, et al. "Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy." Molecules 27, no. 15 (2022): 4960. http://dx.doi.org/10.3390/molecules27154960.

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Elucidation of physicochemical mechanisms of enzymatic processes is one of the main tasks of modern biology. High efficiency and selectivity of enzymatic catalysis are mostly ensured by conformational dynamics of enzymes and substrates. Here, we applied a stopped-flow kinetic analysis based on fluorescent spectroscopy to investigate mechanisms of conformational transformations during the removal of alkylated bases from DNA by ALKBH2, a human homolog of Escherichia coli AlkB dioxygenase. This enzyme protects genomic DNA against various alkyl lesions through a sophisticated catalytic mechanism s

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17

Pearce, F. Grant. "Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies." Biochemical Journal 399, no. 3 (2006): 525–34. http://dx.doi.org/10.1042/bj20060430.

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During catalysis, all Rubisco (D-ribulose-1,5-bisphosphate carboxylase/oxygenase) enzymes produce traces of several by-products. Some of these by-products are released slowly from the active site of Rubisco from higher plants, thus progressively inhibiting turnover. Prompted by observations that Form I Rubisco enzymes from cyanobacteria and red algae, and the Form II Rubisco enzyme from bacteria, do not show inhibition over time, the production and binding of catalytic by-products was measured to ascertain the underlying differences. In the present study we show that the Form IB Rubisco from t

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18

Kaufholz, Anna-Lena, Gregory A. Hunter, Gloria C. Ferreira, et al. "Aminolaevulinic acid synthase of Rhodobacter capsulatus: high-resolution kinetic investigation of the structural basis for substrate binding and catalysis." Biochemical Journal 451, no. 2 (2013): 205–16. http://dx.doi.org/10.1042/bj20121041.

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The first enzyme of haem biosynthesis, ALAS (5-aminolaevulinic acid synthase), catalyses the pyridoxal 5′-phosphate-dependent condensation of glycine and succinyl-CoA to 5-aminolaevulinic acid, CO2 and CoA. The crystal structure of Rhodobacter capsulatus ALAS provides the first snapshots of the structural basis for substrate binding and catalysis. To elucidate the functional role of single amino acid residues in the active site for substrate discrimination, substrate positioning, catalysis and structural protein rearrangements, multiple ALAS variants were generated. The quinonoid intermediates

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19

Kanazhevskaya, Lyubov Yu, Irina V. Alekseeva та Olga S. Fedorova. "A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB". Molecules 24, № 24 (2019): 4576. http://dx.doi.org/10.3390/molecules24244576.

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AlkB is a Fe(II)/α-ketoglutarate-dependent dioxygenase that repairs some alkylated bases of DNA and RNA in Escherichia coli. In the course of catalysis, oxidation of a co-substrate (α-ketoglutarate, αKG) leads to the formation of a highly reactive ‘oxyferryl’ enzyme-bound intermediate, Fe(IV) = O, ensuring hydroxylation of the alkyl nucleobase adducts. Previous studies have revealed that AlkB is a flexible protein and can adopt different conformations during interactions with cofactors and DNA. To assess the conformational dynamics of the enzyme in complex with single- or double-stranded DNA i

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20

Gnetko, L. V., L. P. Nerovnykh, M. M. Udychak, B. B. Siyukhova, and M. M. Kobleva. "Influence of enzymative catalysis on technological parameters of apple juice production." New Technologies 17, no. 4 (2021): 33–41. http://dx.doi.org/10.47370/2072-0920-2021-17-4-33-41.

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The article provides data on the investigation of the effect of enzymatic catalysis on the technological parameters of apple juice production. Apples are distinguished by the presence of a heterogeneous high-molecular complex of biopolymers, which complicates their processing: it prevents juice output, hinders its clarification, filterability of wine materials and negatively affects the colloidal stability of wines. Enzymatic catalysis based on the action of microbial preparations, contributes in many respects to the successful solution of the problems of intensifying technological processes o

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21

Bung, Navneet, Arijit Roy, Brenden Chen, et al. "Human hydroxymethylbilane synthase: Molecular dynamics of the pyrrole chain elongation identifies step-specific residues that cause AIP." Proceedings of the National Academy of Sciences 115, no. 17 (2018): E4071—E4080. http://dx.doi.org/10.1073/pnas.1719267115.

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Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway, catalyzes the head-to-tail condensation of four molecules of porphobilinogen (PBG) to form the linear tetrapyrrole 1-hydroxymethylbilane (HMB). Mutations in human HMBS (hHMBS) cause acute intermittent porphyria (AIP), an autosomal-dominant disorder characterized by life-threatening neurovisceral attacks. Although the 3D structure of hHMBS has been reported, the mechanism of the stepwise polymerization of four PBG molecules to form HMB remains unknown. Moreover, the specific roles of each of the critical act

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22

Ramírez-Sarmiento, César A., Felipe Engelberger, and Victoria Guixé. "An Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase." Catalysts 10, no. 5 (2020): 555. http://dx.doi.org/10.3390/catal10050555.

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The ribokinase superfamily catalyzes the phosphorylation of a vast diversity of substrates, and its members are characterized by the conservation of a common structural fold along with highly conserved sequence motifs responsible for phosphoryl transfer (GXGD) and stabilization of the metal-nucleotide complex (NXXE). Recently, a third motif (HXE) exclusive from ADP-dependent enzymes was identified, with its glutamic acid participating in water-mediated interactions with the metal-nucleotide complex and in stabilization of the ternary complex during catalysis. In this work, we bioinformatically

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23

PARDO-AVILA, FÁTIMA, LIN-TAI DA, YING WANG, and XUHUI HUANG. "THEORETICAL INVESTIGATIONS ON ELUCIDATING FUNDAMENTAL MECHANISMS OF CATALYSIS AND DYNAMICS INVOLVED IN TRANSCRIPTION BY RNA POLYMERASE." Journal of Theoretical and Computational Chemistry 12, no. 08 (2013): 1341005. http://dx.doi.org/10.1142/s0219633613410058.

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RNA polymerase is the enzyme that synthesizes RNA during the transcription process. To understand its mechanism, structural studies have provided us pictures of the series of steps necessary to add a new nucleotide to the nascent RNA chain, the steps altogether known as the nucleotide addition cycle (NAC). However, these static snapshots do not provide dynamic information of these processes involved in NAC, such as the conformational changes of the protein and the atomistic details of the catalysis. Computational studies have made efforts to fill these knowledge gaps. In this review, we provid

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Chen, Tianpeng, Shimeng Wang, Huanqing Niu та ін. "Biofilm-Based Biocatalysis for Galactooligosaccharides Production by the Surface Display of β-Galactosidase in Pichia pastoris". International Journal of Molecular Sciences 24, № 7 (2023): 6507. http://dx.doi.org/10.3390/ijms24076507.

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Galactooligosaccharides (GOS) are one of the most important functional oligosaccharide prebiotics. The surface display of enzymes was considered one of the most excellent strategies to obtain these products. However, a rough industrial environment would affect the biocatalytic process. The catalytic process could be efficiently improved using biofilm-based fermentation with high resistance and activity. Therefore, the combination of the surface display of β-galactosidase and biofilm formation in Pichia pastoris was constructed. The results showed that the catalytic conversion rate of GOS was u

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Doshi, Urmi, Michael J. Holliday, Elan Z. Eisenmesser, and Donald Hamelberg. "Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation." Proceedings of the National Academy of Sciences 113, no. 17 (2016): 4735–40. http://dx.doi.org/10.1073/pnas.1523573113.

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Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dynamical features within individual macrostates by defining dynamics in terms of residue–residue contacts. The effects of substrate binding are observed to be largely sensed at a location over 15 Å from the

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26

Kostopoulos, Nikolaos, Zhao Ziwen, and Alina Sekretareva. "Nanoimpact Electrochemistry for Unraveling the Reactivity of Diffusion Limited Enzymes." ECS Meeting Abstracts MA2024-01, no. 42 (2024): 2377. http://dx.doi.org/10.1149/ma2024-01422377mtgabs.

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The ultimate challenge of modern electroanalytical chemistry is to reach a single-molecule level of detection. In this framework, nanoimpact electrochemistry (NIE) has been recently developed. It allows studying at high throughput the reactivity of small entities such as nanoparticles, cells, or proteins, that collide on a biased ultramicroelectrode (UME) inside a solution or suspension.1 The collisions cause disturbances in the recorded chronoamperogram such as current spikes or current steps.2 Single enzyme electrochemistry (SEE) can contribute to uncovering effects of dynamics and non-equil

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Liu, Ning, Hongli Xiao, Yongjian Zang, et al. "Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A." International Journal of Molecular Sciences 24, no. 23 (2023): 16795. http://dx.doi.org/10.3390/ijms242316795.

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Enzymes used in the synthesis of natural products are potent catalysts, capable of efficient and stereoselective chemical transformations. Lsd18 catalyzes two sequential epoxidations during the biosynthesis of lasalocid A, a polyether polyketide natural product. We performed protein engineering on Lsd18 to improve its thermostability and catalytic activity. Utilizing structure-guided methods of FoldX and Rosetta-ddG, we designed 15 mutants of Lsd18. Screening of these mutants using thermal shift assay identified stabilized variants Lsd18-T189M, Lsd18-S195M, and the double mutant Lsd18-T189M-S1

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28

Ying, Yining, Feifei Xu, Zhongwei Zhang, Piengtawan Tappiban, and Jinsong Bao. "Dynamic Change in Starch Biosynthetic Enzymes Complexes during Grain-Filling Stages in BEIIb Active and Deficient Rice." International Journal of Molecular Sciences 23, no. 18 (2022): 10714. http://dx.doi.org/10.3390/ijms231810714.

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Starch is the predominant reserve in rice (Oryza sativa L.) endosperm, which is synthesized by the coordinated efforts of a series of starch biosynthetic-related enzymes in the form of a multiple enzyme complex. Whether the enzyme complex changes during seed development is not fully understood. Here, we investigated the dynamic change in multi-protein complexes in an indica rice variety IR36 (wild type, WT) and its BEIIb-deficient mutant (be2b) at different developmental stages. Gel permeation chromatography (GPC) and Western blotting analysis of soluble protein fractions revealed most of the

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29

He, Shan, Yiran Wu, Daqi Yu, and Luhua Lai. "Microsomal prostaglandin E synthase-1 exhibits one-third-of-the-sites reactivity." Biochemical Journal 440, no. 1 (2011): 13–21. http://dx.doi.org/10.1042/bj20110977.

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mPGES-1 (microsomal prostaglandin E synthase-1) is a newly recognized target for the treatment of inflammatory diseases. As the terminal enzyme of the prostaglandin production pathway, mPGES-1 inhibition may have a low risk of side effects. Inhibitors of mPGES-1 have attracted considerable attention as next-generation anti-inflammatory drugs. However, as mPGES-1 is a membrane protein, its enzymatic mechanism remains to be disclosed fully. We used MD (molecular dynamics) simulations, mutation analysis, hybrid experiments and co-IP (co-immunoprecipitation) to investigate the conformation transit

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Hong, Xi-Zhi, Zheng-Gang Han, Jiang-Ke Yang, and Yi-Han Liu. "The Motion Paradigm of Pre-Dock Zearalenone Hydrolase Predictions with Molecular Dynamics and the Docking Phase with Umbrella Sampling." Molecules 28, no. 11 (2023): 4545. http://dx.doi.org/10.3390/molecules28114545.

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Zearalenone (ZEN) is one of the most prevalent estrogenic mycotoxins, is produced mainly by the Fusarium family of fungi, and poses a risk to the health of animals. Zearalenone hydrolase (ZHD) is an important enzyme capable of degrading ZEN into a non-toxic compound. Although previous research has investigated the catalytic mechanism of ZHD, information on its dynamic interaction with ZEN remains unknown. This study aimed to develop a pipeline for identifying the allosteric pathway of ZHD. Using an identity analysis, we identified hub genes whose sequences can generalize a set of sequences in

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31

Sadiq, S. Kashif. "Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis." Catalysts 10, no. 6 (2020): 684. http://dx.doi.org/10.3390/catal10060684.

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The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed re

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32

Kang, Wonchull, Chi Chung Lee, Andrew J. Jasniewski, Markus W. Ribbe, and Yilin Hu. "Structural evidence for a dynamic metallocofactor during N2 reduction by Mo-nitrogenase." Science 368, no. 6497 (2020): 1381–85. http://dx.doi.org/10.1126/science.aaz6748.

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The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N2) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as wel

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Madeddu, Francesco, Jessica Di Martino, Michele Pieroni, et al. "Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor." International Journal of Molecular Sciences 23, no. 23 (2022): 14652. http://dx.doi.org/10.3390/ijms232314652.

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Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors o

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34

Kim, Yu-Jin, Ho Young Jeong, Seung-Yeon Kang, et al. "Physiological Importance of Pectin Modifying Genes During Rice Pollen Development." International Journal of Molecular Sciences 21, no. 14 (2020): 4840. http://dx.doi.org/10.3390/ijms21144840.

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Although cell wall dynamics, particularly modification of homogalacturonan (HGA, a major component of pectin) during pollen tube growth, have been extensively studied in dicot plants, little is known about how modification of the pollen tube cell wall regulates growth in monocot plants. In this study, we assessed the role of HGA modification during elongation of the rice pollen tube by adding a pectin methylesterase (PME) enzyme or a PME-inhibiting catechin extract (Polyphenon 60) to in vitro germination medium. Both treatments led to a severe decrease in the pollen germination rate and elonga

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35

Kuznetsova, Aleksandra A., Svetlana I. Senchurova, Anastasia A. Gavrilova, Timofey E. Tyugashev, Elena S. Mikushina, and Nikita A. Kuznetsov. "Substrate Specificity Diversity of Human Terminal Deoxynucleotidyltransferase May Be a Naturally Programmed Feature Facilitating Its Biological Function." International Journal of Molecular Sciences 25, no. 2 (2024): 879. http://dx.doi.org/10.3390/ijms25020879.

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Terminal 2′-deoxynucleotidyl transferase (TdT) is a unique enzyme capable of catalysing template-independent elongation of DNA 3′ ends during V(D)J recombination. The mechanism controlling the enzyme’s substrate specificity, which is necessary for its biological function, remains unknown. Accordingly, in this work, kinetic and mutational analyses of human TdT were performed and allowed to determine quantitative characteristics of individual stages of the enzyme–substrate interaction, which overall may ensure the enzyme’s operation either in the distributive or processive mode of primer extensi

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36

Horn, Michael, Karin Nienhaus, and Gerd Ulrich Nienhaus. "Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase." F1000Research 3 (November 28, 2014): 290. http://dx.doi.org/10.12688/f1000research.5836.1.

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Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-

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Horn, Michael, Karin Nienhaus, and Gerd Ulrich Nienhaus. "Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase." F1000Research 3 (December 12, 2014): 290. http://dx.doi.org/10.12688/f1000research.5836.2.

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Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-

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Kotsyuba, Elena, and Vyacheslav Dyachuk. "Effect of Air Exposure-Induced Hypoxia on Neurotransmitters and Neurotransmission Enzymes in Ganglia of the Scallop Azumapecten farreri." International Journal of Molecular Sciences 23, no. 4 (2022): 2027. http://dx.doi.org/10.3390/ijms23042027.

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The nervous system expresses neuromolecules that play a crucial role in regulating physiological processes. Neuromolecule synthesis can be regulated by oxygen-dependent enzymes. Bivalves are a convenient model for studying air exposure-induced hypoxia. Here, we studied the effects of hypoxia on the expression and dynamics of neurotransmitters, and on neurotransmitter enzyme distribution, in the central nervous system (CNS) of the scallop Azumapecten farreri. We analyzed the expression of the neurotransmitters FMRFamide and serotonin (5-HT) and the choline acetyltransferase (CHAT) and universal

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Nalian, Armen, and Alexei V. Iakhiaev. "Possible mechanisms contributing to oxidative inactivation of activated protein C: Molecular dynamics study." Thrombosis and Haemostasis 100, no. 07 (2008): 18–25. http://dx.doi.org/10.1160/th07-12-0750.

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SummaryActivated protein C (APC) is a serine protease, an effector enzyme of the natural anticoagulant pathway. APC is approved for treatment of severe sepsis characterized by the increased concentrations of H2O2 and hypochlorite. We found that treatment of APC with these oxidants markedly inhibits the cleavage of the APC-specific chromogenic substrate, suggesting that oxidants can induce changes in the structure of the active site of APC. Resistance of oxidant-treated APC to chemical digestion with cyanogen bromide (CNBr) implies that methionine oxidation can at least in part be responsible f

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REID, James D., Syeed HUSSAIN, Suneal K. SREEDHARAN, et al. "Variation in aspects of cysteine proteinase catalytic mechanism deduced by spectroscopic observation of dithioester intermediates, kinetic analysis and molecular dynamics simulations." Biochemical Journal 357, no. 2 (2001): 343–52. http://dx.doi.org/10.1042/bj3570343.

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The possibility of a slow post-acylation conformational change during catalysis by cysteine proteinases was investigated by using a new chromogenic substrate, N-acetyl-Phe-Gly methyl thionoester, four natural variants (papain, caricain, actinidin and ficin), and stopped-flow spectral analysis to monitor the pre-steady state formation of the dithioacylenzyme intermediates and their steady state hydrolysis. The predicted reversibility of acylation was demonstrated kinetically for actinidin and ficin, but not for papain or caricain. This difference between actinidin and papain was investigated by

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Brock, Joseph S., Mats Hamberg, Navisraj Balagunaseelan, et al. "A dynamic Asp–Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase." Proceedings of the National Academy of Sciences 113, no. 4 (2016): 972–77. http://dx.doi.org/10.1073/pnas.1522891113.

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Microsomal prostaglandin E2 synthase type 1 (mPGES-1) is responsible for the formation of the potent lipid mediator prostaglandin E2 under proinflammatory conditions, and this enzyme has received considerable attention as a drug target. Recently, a high-resolution crystal structure of human mPGES-1 was presented, with Ser-127 being proposed as the hydrogen-bond donor stabilizing thiolate anion formation within the cofactor, glutathione (GSH). We have combined site-directed mutagenesis and activity assays with a structural dynamics analysis to probe the functional roles of such putative catalyt

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Hasan, Naimul, Alexander Keszei, Matthew Waas, Thomas Kislinger, Razq Hakem, and Mohammad Mazhab-Jafari. "Abstract 4494: Structure, dynamics and therapeutic potential of fatty acid synthase." Cancer Research 85, no. 8_Supplement_1 (2025): 4494. https://doi.org/10.1158/1538-7445.am2025-4494.

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Abstract De novo lipid synthesis is facilitated by the multifunctional enzyme fatty acid synthase (FASN), a hallmark of cancer associated with chemotherapeutic resistance and poor prognosis. Human FASN (hFASN) is a dynamic protein that undergoes significant conformational changes during catalysis, posing challenges for structural characterization. To date, no structural information is available for full-length hFASN, hindering our understanding of its catalytic mechanism and complicating rational drug design.Here, we report the structure of hFASN resolved using electron cryo-microscopy (cryoEM

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Zhdanova, Polina V., Alexander A. Chernonosov, Daria V. Prokhorova, Grigory A. Stepanov, Lyubov Yu Kanazhevskaya, and Vladimir V. Koval. "Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry." International Journal of Molecular Sciences 23, no. 3 (2022): 1129. http://dx.doi.org/10.3390/ijms23031129.

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The Cas9 endonuclease is an essential component of the CRISPR–Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR–Cas9 system. A deep understanding of the Cas9 mechanism and its structural-functional relationships is required to develop strategies for precise gene editing. Here, we present the first attempt to describe the solution structure of Cas9 from S. pyogenes using hydrogen-deuterium exchange mass spectrometry (HDX-MS) coupled to molecular dynamics s

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McGregor, Lindsay, Tamás Földes, Soi Bui, et al. "Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis." IUCrJ 8, no. 1 (2021): 46–59. http://dx.doi.org/10.1107/s2052252520013615.

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Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to dehydroisourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hydroxyisourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the `peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray

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Buckley, David, and John Tanner. "Visualization of transient states and molecular motions in the catalytic cycle of the proline catabolic bifunctional enzyme Proline Utilization A from kinetic crystallography and molecular dynamics simulations." Structural Dynamics 12, no. 2_Supplement (2025): A220. https://doi.org/10.1063/4.0000527.

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Proline utilization A (PutA) is a large, bifunctional enzyme composed of FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent L-glutamate γ-semialdehyde dehydrogenase (GSALDH) domains. The sequential actions of PRODH and GSALDH catalyze proline catabolism, i.e., the 4-electron oxidation of L-proline to L-glutamate via the intermediates Δ1-pyrroline-5-carboxylate (P5C) and L-glutamate γ-semialdehyde (GSAL). Crystal structures of PutAs have revealed a conserved, 42 Å long tunnel connecting the two active sites, implying a substrate channeling mechanism, which has been confirmed with ki

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Olla, Stefania, Chiara Siguri, Antonella Fais, Benedetta Era, Massimo Claudio Fantini, and Amalia Di Petrillo. "Inhibitory Effect of Quercetin on Oxidative Endogen Enzymes: A Focus on Putative Binding Modes." International Journal of Molecular Sciences 24, no. 20 (2023): 15391. http://dx.doi.org/10.3390/ijms242015391.

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Oxidative stress is defined as an imbalance between the production of free radicals and reactive oxygen species (ROS) and the ability of the body to neutralize them by anti-oxidant defense systems. Cells can produce ROS during physiological processes, but excessive ROS can lead to non-specific and irreversible damage to biological molecules, such as DNA, lipids, and proteins. Mitochondria mainly produce endogenous ROS during both physiological and pathological conditions. Enzymes like nicotinamide adenine dinucleotide phosphate oxidase (NOX), xanthine oxidase (XO), lipoxygenase (LOX), myeloper

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Si, Yunlong, Xing Wang, Guosong Yang, et al. "Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate." International Journal of Molecular Sciences 20, no. 18 (2019): 4394. http://dx.doi.org/10.3390/ijms20184394.

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All living things have pyrophosphatases that hydrolyze pyrophosphate and release energy. This energetically favorable reaction drives many energetically unfavorable reactions. An accepted catalytic model of pyrophosphatase shows that a water molecule activated by two divalent cations (M1 and M2) within the catalytic center can attack pyrophosphate in an SN2 mechanism and thus hydrolyze the molecule. However, our co-crystal structure of Acinetobacter baumannii pyrophosphatase with pyrophosphate shows that a water molecule from the solvent may, in fact, be the actual catalytic water. In the co-c

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Stolyarchuk, Maxim, Marina Botnari, and Luba Tchertanov. "Vitamin K Epoxide Reductase Complex–Protein Disulphide Isomerase Assemblies in the Thiol–Disulphide Exchange Reactions: Portrayal of Precursor-to-Successor Complexes." International Journal of Molecular Sciences 25, no. 8 (2024): 4135. http://dx.doi.org/10.3390/ijms25084135.

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The human Vitamin K Epoxide Reductase Complex (hVKORC1), a key enzyme that converts vitamin K into the form necessary for blood clotting, requires for its activation the reducing equivalents supplied by its redox partner through thiol–disulphide exchange reactions. The functionally related molecular complexes assembled during this process have never been described, except for a proposed de novo model of a ‘precursor’ complex of hVKORC1 associated with protein disulphide isomerase (PDI). Using numerical approaches (in silico modelling and molecular dynamics simulation), we generated alternative

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Aguilar-Toalá, José E., Abraham Vidal-Limon, Andrea M. Liceaga, Maria L. Zambrano-Zaragoza, and David Quintanar-Guerrero. "Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (Phalaris canariensis L.) Bioactive Peptides and Skin-Aging Enzymes." International Journal of Molecular Sciences 24, no. 17 (2023): 13420. http://dx.doi.org/10.3390/ijms241713420.

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Food bioactive peptides are well recognized for their health benefits such as antimicrobial, antioxidant, and antihypertensive benefits, among others. Their drug-like behavior has led to their potential use in targeting skin-related aging factors like the inhibition of enzymes related with the skin-aging process. In this study, canary seed peptides (CSP) after simulated gastrointestinal digestion (<3 kDa) were fractioned by RP-HPLC and their enzyme-inhibition activity towards elastase and tyrosinase was evaluated in vitro. CSP inhibited elastase (IC50 = 6.2 mg/mL) and tyrosinase (IC50 = 6.1

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Agnew, Aidan, Ciara Nulty, and Emma M. Creagh. "Regulation, Activation and Function of Caspase-11 during Health and Disease." International Journal of Molecular Sciences 22, no. 4 (2021): 1506. http://dx.doi.org/10.3390/ijms22041506.

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Caspase-11 is a pro-inflammatory enzyme that is stringently regulated during its expression and activation. As caspase-11 is not constitutively expressed in cells, it requires a priming step for its upregulation, which occurs following the stimulation of pathogen and cytokine receptors. Once expressed, caspase-11 activation is triggered by its interaction with lipopolysaccharide (LPS) from Gram-negative bacteria. Being an initiator caspase, activated caspase-11 functions primarily through its cleavage of key substrates. Gasdermin D (GSDMD) is the primary substrate of caspase-11, and the GSDMD

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