Establishing the catalytic mechanism of human pancreatic α-amylase with QM/MM methods.

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Journal of Chemical Theory and Computation

• Publication date

  2015-05-22

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1021/acs.jctc.5b00222PMID 26575550
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Amylase inhibitors and their biomedical applications

  2013cited by this paper
• α-Amylase inhibitors: a review of raw material and isolated compounds from plant source.

  2012cited by this paper
• A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

  2012cited by this paper
• QM/MM study of the catalytic mechanism of GalNAc removal from GM2 ganglioside catalyzed by human β-hexosaminidaseA.

  2011cited by this paper
• QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions.

  2010cited by this paper
• DFT studies on the β-glycosidase catalytic mechanism: The deglycosylation step

  2010cited by this paper
• Directed "in situ" inhibitor elongation as a strategy to structurally characterize the covalent glycosyl-enzyme intermediate of human pancreatic alpha-amylase.

  2009cited by this paper
• The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

  2008cited by this paper
• GLYCAM06: A generalizable biomolecular force field. Carbohydrates

  2008cited by this paper
• Traditionally used plants in diabetes therapy: phytotherapeutics as inhibitors of alpha-amylase activity

  2006cited by this paper
• Comparison of multiple Amber force fields and development of improved protein backbone parameters

  2006cited by this paper
• Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics

  2004cited by this paper
• HIV-1 protease: mechanism and drug discovery.

  2003cited by this paper
• Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.

  2002cited by this paper
• Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques.

  2000cited by this paper
• A NEW ONIOM IMPLEMENTATION IN GAUSSIAN98. PART I. THE CALCULATION OF ENERGIES, GRADIENTS, VIBRATIONAL FREQUENCIES AND ELECTRIC FIELD DERIVATIVES

  1999cited by this paper
• Optimized density functionals from the extended G2 test set

  1998cited by this paper
• Density‐functional thermochemistry. IV. A new dynamical correlation functional and implications for exact‐exchange mixing

  1996cited by this paper
• Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields

  1994cited by this paper
• Density-functional thermochemistry. III. The role of exact exchange

  1993cited by this paper
• On the convergence of the SHAKE algorithm

  1991cited by this paper
• Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure

  1988cited by this paper
• Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

  1988cited by this paper
• Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint

  1988cited by this paper
• Natural localized molecular orbitals

  1985cited by this paper
• Natural population analysis

  1985cited by this paper
• Natural bond orbital analysis of near‐Hartree–Fock water dimer

  1983cited by this paper
• Electronic structure theory

  1981cited by this paper
• Natural hybrid orbitals

  1980cited by this paper
• Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis

  1980cited by this paper
• The Protein Data Bank: a computer-based archival file for macromolecular structures.

  1977cited by this paper

• Structural Stabilization and Activity Enhancement of Glucoamylase via the Machine-Learning Technique and Immobilization.

  2025cites this paper
• 6-O-acetyldaidzen and frangulin B from Halodule uninervis as novel α-amylase inhibitors: A molecular dynamics perspective

  2025cites this paper
• A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis

  2025cites this paper
• Recent advances in the synthesis and medicinal perspective of pyrazole-based α-amylase inhibitors as antidiabetic agents.

  2024cites this paper
• Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables

  2024cites this paper
• Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations

  2024cites this paper
• Unveiling α-Amylase Inhibition: A Bioinformatics Perspective on Peptide Properties and Amino Acid Contributions

  2024cites this paper
• How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques

  2023cites this paper
• QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update

  2023cites this paper
• Determination of Antioxidant and α–Amylase Inhibition Properties of Alligator Pepper (Aframomum Melegueta): A Potential Therapeutic Against Diabetes Mellitus

  2022cites this paper
• Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics

  2022cites this paper
• Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms.

  2022cites this paper
• Modulating the digestibility of cassava starch by esterification with phenolic acids

  2021cites this paper
• The role of first principles simulations in studying (bio)catalytic processes

  2021cites this paper
• Natural and pharmacological chaperones against accelerated protein degradation: uroporphyrinogen III synthase and congenital erythropoietic porphyria

  2020cites this paper
• Insights in the Evaluation of Gluten Dietary Avoidance in Healthy Subjects

  2020cites this paper
• Evolutionary coupling saturation mutagenesis: Coevolution‐guided identification of distant sites influencing Bacillus naganoensis pullulanase activity

  2020cites this paper
• Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

  2020cites this paper
• Anthocyanins as Antidiabetic Agents—In Vitro and In Silico Approaches of Preventive and Therapeutic Effects

  2020cites this paper
• Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis

  2020cites this paper
• In vivo challenges of anti-diabetic peptide therapeutics: Gastrointestinal stability, toxicity and allergenicity

  2020cites this paper
• Hereditary tyrosinemia type I–associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate

  2019cites this paper
• The role of conserved arginine in the GH70 family: a computational study of the structural features and their implications on the catalytic mechanism of GTF-SI from Streptoccocus mutans.

  2019cites this paper
• Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase

  2019cites this paper
• The odd loop regions of XenA and XenB enzymes modulate their interaction with nitro-explosives and provide structural support for their regioselectivity.

  2019cites this paper
• Correction to: Inhibitor discovery from pomegranate rind for targeting human salivary α-amylase

  2018cites this paper
• Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation.

  2018cites this paper
• Mechanistic Pathway on Human α-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations.

  2018cites this paper
• Biochemical characterization and molecular mechanism of acid denaturation of a novel α-amylase from Aspergillus niger

  2018cites this paper
• A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans.

  2018cites this paper
• Computational insight into the broad substrate specificity of enzymes that process nucleic acids

  2018cites this paper
• ONIOM and FMO-EDA study of metabotropic glutamate receptor 1: Quantum insights into the allosteric binding site

  2018cites this paper
• Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

  2017cites this paper
• Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

  2017cites this paper
• Trimethylphosphate and Dimethylphosphate Hydrolysis by Binuclear CdII , MnII , and ZnII -FeII Promiscuous Organophosphate-Degrading Enzyme: Reaction Mechanisms.

  2017cites this paper
• The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac.

  2016cites this paper
• Amylolysis of eight different starches with four different species of alpha-amylase

  2016cites this paper
• Evaluating the Substrate Selectivity of Alkyladenine DNA Glycosylase: The Synergistic Interplay of Active Site Flexibility and Water Reorganization.

  2016cites this paper