Dynamics enzyme catalysis. Medical search. Frequent questions

Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). (muni.cz)
To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. (fu-berlin.de)
Conformational entropy of FK506 binding to FKBP12 determined by NMR and molecular dynamics simulations. (lu.se)
This Account will focus principally on results from deuterium exchange mass spectrometric (DXMS) studies of PLA 2 interactions with membranes and extensive molecular dynamics (MD) simulations of their interactions with membranes and specific phospholipids bound in their catalytic and allosteric sites. (nih.gov)
Using theoretical modeling and atomistic molecular simulations at mic rosecond time scale, we are investigating the role of functionally important conformational sub-states in relation to optimal catalysis by the members of the pancreatic RNase enzyme family. (inrs.ca)
40,41 Attempts to understand those rate-limiting conformations have led to two studies in which we showed that the PATH algorithm 18 suggested previously unsuspected consistency with Molecular Dynamics (MD) simulations 23 and steady-state kinetics measurements of TrpRS catalysis 41 and TrpRS structural reaction path. (aip.org)
SORS:Exploring mechanistic details in enzyme catalysis through mutiscale hybrid QM/MM simulations. (bsc.es)
Our group uses computational modeling and simulations to understand molecular mechanisms and interactions between ligands and proteins that drive binding, inhibition, and catalysis. (yasminshamsudin.com)
We use molecular modelling and simulations to understand molecular mechanisms regulating inhibition and catalysis in enzymes. (yasminshamsudin.com)
We design and engineer functional proteins and enzymes based on predictions from quantum chemical and enhanced sampling molecular dynamics simulations. (yasminshamsudin.com)
Compared to traditional methods of in silico design, including molecular dynamics and biophysical simulations, the computational burden is reduced by 3-8 orders of magnitude. (catalysiscongress.com)
Structural analyses and computational modeling using molecular dynamics simulations provided an understanding of how product inhibition and multiple substrate binding modes influence key mechanistic steps of enzymatic PET hydrolysis. (inra.fr)
An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. (inra.fr)
In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes. (inra.fr)
However, the complexity of the system makes the direct measurements of the dynamics of the essential conformational changes very difficult, where molecular dynamics simulations provide a powerful tool to obtain a detailed understanding of these processes. (iupui.edu)
To achieve this, we develop new NMR methods and often interpret the results in combination with molecular dynamics simulations. (lu.se)
We have assessed and used computational tools for this aim, most of them based on molecular dynamics (MD) simulations. (lu.se)

When enzymes bind multiple substrates, such as dihydrofolate reductase (shown right), enzyme kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. (wikipedia.org)
The team, led by Professor Rudolf Allemann, used a combination of experimental and computational approaches to study the enzyme dihydrofolate reductase, an important target for anti-infective and anti-cancer drugs. (cardiff.ac.uk)
Combined experimental and theoretical investigations of the role of protein motions and hydride tunnelling in enzyme catalysis, using dihydrofolate reductase as a model system. (cardiff.ac.uk)

Research in biological chemistry at Cardiff covers a diverse range of themes including enzyme catalysis and synthetic biology, manipulating biomolecular interactions, biomolecular NMR spectroscopy and mass spectrometry, and organic synthesis and medicinal chemistry. (cardiff.ac.uk)
This includes the understanding of protein dynamics and enzyme catalysis, biomolecular interactions and assembly, and biophysical systems biology, as well as the development of quantum and classical mechanical methodologies. (msu.edu)

In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. (wikipedia.org)
Such cases exist: for example, a mutase such as phosphoglucomutase catalyses the transfer of a phospho group from one position to another, and isomerase is a more general term for an enzyme that catalyses any one-substrate one-product reaction, such as triosephosphate isomerase . (wikipedia.org)
This rate-determining step may be a chemical reaction or a conformational change of the enzyme or substrates, such as those involved in the release of product(s) from the enzyme. (wikipedia.org)
in such cases, it is helpful to determine the enzyme structure with and without bound substrate analogues that do not undergo the enzymatic reaction. (wikipedia.org)
Beyond this limit the enzyme is saturated with substrate and the reaction rate ceases to increase. (wikipedia.org)
The reaction catalysed by an enzyme uses exactly the same reactants and produces exactly the same products as the uncatalysed reaction. (wikipedia.org)
Some theories propose that internal 'promoting motions' of the enzyme, specific motions that act to reduce the height or width of the energy barrier to the reaction, are used to drive the chemistry. (cardiff.ac.uk)
They found no significant role for 'promoting motions' in the reaction, but did demonstrate coupling of enzyme motions to the catalysed reaction on a femtosecond timescale (one millionth of a billionth of a second). (cardiff.ac.uk)
Enzyme dynamics therefore have a small, but measurable, effect on the chemical reaction rate. (cardiff.ac.uk)
Our research goals are to probe enzymatic reaction mechanisms, elucidating the role of protein dynamics and quantum mechanical effects in catalysis, and tailoring substrate selectivity for synthetic chemistry purposes. (cardiff.ac.uk)
This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. (fu-berlin.de)
Perhaps most remarkably, these chemical reactions are catalyzed by specific enzyme proteins that accelerate the reaction rates by a factor of 10 10 - 10 23 . (i-sis.org.uk)
We are interested in the design and engineering of enzymes with an expanded reaction scope, beyond what they have naturally evolved to catalyse. (nottingham.ac.uk)
These enzymes either are membrane-bound or are water-soluble and associate with membranes before extracting their phospholipid substrate molecule into their active site to carry out their enzymatic hydrolytic reaction. (nih.gov)
High resolution vibrational structural studies will be performed to determine the electronic nature of the reaction pathway and to dissect the role of specific active site molecular factors bringing about catalysis. (elsevierpure.com)
In a heterogeneous catalysis configuration, this reaction could generate long-lived Fe(IV) species with the correct additives. (lu.se)

The dynamics of loop motion and its relationship to ligand release and catalysis will be studied in PTP and HGPRT. (elsevierpure.com)
We address specific questions regarding the role of protein dynamics in various types of function and dysfunction, for example: ligand binding and allostery, enzyme catalysis, and protein misfolding and aggregation. (lu.se)
Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)

Enzyme kinetics is the study of the rates of enzyme-catalysed chemical reactions . (wikipedia.org)
Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism , how its activity is controlled, and how a drug or a modifier ( inhibitor or activator ) might affect the rate. (wikipedia.org)
8. Enzyme kinetics. (ujaen.es)
Characterization of the enzyme kinetics: determination of K m and V max (lab.1). (ujaen.es)

Along with her research team at Brandeis, Kern published a paper detailing their discoveries in which they utilized high-level biological computing and imaging to study the evolutionary shifts in protein structure of certain proteins and enzymes commonly involved in cancer over three million years of evolutionary history. (wikipedia.org)

How structural dynamics in an enzyme enhance catalytic efficiency and evolvability. (ibs.fr)
However, structural dynamics may also play a functional role in enzyme catalysis. (usf.edu)
Due to the instability of carbocation intermediates, the proteins' structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. (fu-berlin.de)

Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. (duke.edu)
We present evidence that when a PLA 2 associates with a membrane, the membrane association can result in a conformational change in the enzyme whereby the membrane association with an allosteric site on the enzyme stabilizes the enzyme in an active conformation on the membrane. (nih.gov)

Researchers from Cardiff University's School of Chemistry, along with colleagues from the University of Bristol, the University of València and Jaume I University in Castelló, have uncovered a mechanism by which enzyme motions couple to chemical reactions. (cardiff.ac.uk)
This remains a topic of considerable debate, particularly since the identification and analysis of dynamical effects in enzyme-catalyzed reactions has proven very challenging. (cardiff.ac.uk)
Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein Anc(HLD-RLuc) which catalyses both dehalogenase and luciferase reactions. (muni.cz)
the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. (liverpool.ac.uk)
Enzymes are involved in most reactions in nature. (lu.se)

Along with her father and husband, Kern published a paper on Vitamin B1 enzyme activation and was able to record the process unfolding utilizing a combination of NMR spectroscopy, X-ray crystallography, and biological computing. (wikipedia.org)
Vibrational spectroscopy yields a very high resolution of structure (better than 0.01 A), and such resolution is key to understanding enzymatic catalysis. (elsevierpure.com)
In my research group we primarily use nuclear magnetic resonance (NMR) spectroscopy to study protein dynamics over a wide range of time scales, from picoseconds to seconds. (lu.se)

These studies are both of fundamental interest and importance, such as studies of the coupling of enzyme motions to catalysis, and of more immediate societal relevance, such as the generation of new drugs (antimicrobial, anticancer, and anti-inflammatory agents), pest control agents and molecular tools, based on our growing knowledge of these systems and our key strengths in these fields. (cardiff.ac.uk)

Enzymology: determination of kinetic parameters and enzyme inhibition. (ujaen.es)

We study the role of conformational dynamics in protein function, conformational changes, enzyme catalysis, drug binding, and allostery. (tarheels.live)

Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. (embl.de)
In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. (dundee.ac.uk)

A thorough understanding of how enzymes achieve their phenomenal rate enhancements is of great importance to fields like biocatalysis, bioenergy, drug design, and the emerging field of synthetic biology. (cardiff.ac.uk)
I welcome enquiries from potential PhD candidates from Home, EU and international countries who are interested in the following research areas: catalysis, biocatalysis, enzyme engineering, artificial metalloenzymes, rational design. (nottingham.ac.uk)

EC 3.1.3.48 ) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. (embl.de)
l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. (dundee.ac.uk)

The main difference between ribozymes and enzymes is that RNA catalysts are composed of nucleotides, whereas enzymes are composed of amino acids. (wikipedia.org)
The audience will be able to use the described methods to rescue designed enzyme catalysts with lost function, folding, or stability. (catalysiscongress.com)

The catalytic activities of enzymes are typically associated with their unique structures. (usf.edu)
High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. (liverpool.ac.uk)
The carbohydrate binding site in Galectin-3 is preorganized to recognize a sugar-like framework of oxygens: ultra-high resolution structures and water dynamics. (lu.se)
We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. (dundee.ac.uk)
Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570. (dundee.ac.uk)
The growing demand for efficient PET hydrolases prompted us to solve high-resolution crystal structures of two metagenome-derived enzymes (PES-H1 and PES-H2) and notably also in complex with various PET substrate analogues. (inra.fr)

We found that the recombinantly expressed enzyme is monomeric, with 100-fold higher catalytic efficiency for thymidine compared to its second-best substrate, deoxyuridine, and is furthermore subject to feedback inhibition by dTTP. (bvsalud.org)

Development of inhibitors of the enzyme calpain-1, a potential target for anti-inflammatory therapy in diseases such as rheumatoid arthritis. (cardiff.ac.uk)

Key residues involved in substratebinding and those identified previously as mutational hotspots in homologous enzymes were subjected to mutagenesis. (inra.fr)

In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. (biomedcentral.com)
The role of structure in enzyme catalysis has been investigated for some time. (inrs.ca)
However, only recently insights int o the role of internal protein motions (protein dynamics) in enzyme catalysis have become available. (inrs.ca)
I t is now believed that dynamics and structure together play critical role in the function of bi omolecules including enzymes. (inrs.ca)
In this post, I will discuss the fundamental role energy plays in all living organisms and the role enzymes play in harnessing different forms of energy making life as we know it possible. (enzymit.com)

4pt] [1] Jianlan Wu and Jianshu Cao, ``Generalized Michaelis-Menten equation for conformation modulated monomeric enzymes,'' in Adv. Chem. (aps.org)

Atomic structure and dynamics link mechanism, phenotype and diseases to a mechanistic chemical explanation. (infn.it)

We apply genetic and chemical protein modification techniques, to modify the functionality of enzymes and further integrate them in metabolic pathways or use them as isolated entities outside the cells. (nottingham.ac.uk)

Examples are, probing enzyme motions crucial for catalysis, and of more immediate societal relevance, such as the generation of new antimicrobial, anticancer, anti-inflammatory and pest control agents, as well as developing molecular tools. (cardiff.ac.uk)
The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with water translational motions enabling protein flexibility. (researchgate.net)

She graduated with a B.S. in Chemistry from UC Berkeley in 2021, where she worked in Prof. Judith Klinman's group developing synthetic tools to study protein dynamics and energy transfer in enzyme catalysis. (ucla.edu)

Nevertheless, even the conformational heterogeneity of globular proteins due to their internal dynamics requires the use of such representations. (biomedcentral.com)
Arvind Ramanathan successfully defended his thesis entitled "Internal Dynamics and Energetics During Enzyme Catalysis. (cmu.edu)

We find that nafamostat has a higher MC population than camostat and GBPA, suggesting that nafamostat is more readily available to form the stable covalent enzyme-substrate intermediate, effectively explaining its high potency. (rsc.org)

Enzymes are fundamental to life. (cardiff.ac.uk)
This work significantly advances our fundamental understanding of enzyme catalysis. (cardiff.ac.uk)
Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis. (fu-berlin.de)

Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. (muni.cz)

We have expertise in the synthesis and catalytic applications of ligands and metal complexes compatible with proteins, bioconjugation of small molecules to proteins, expression and purification of recombinant enzymes, enzyme engineering and enzyme immobilisation. (nottingham.ac.uk)

In order to increase the adsorption towards their unnatural substrate, the enzymes are fused to carbohydrate-binding modules (CBMs) leading to enhanced activity. (inra.fr)

Many scientists are indeed coming around to the view that proteins act quantum mechanically, or, as some of us have proposed years ago, enzyme proteins are quantum molecular machines that transform energy coherently (see [2] The Rainbow and the Worm, The Physics of Organisms , I-SIS publication). (i-sis.org.uk)

Finally, understanding these muscle disorders enables a better understanding of the dynamics of muscle and body metabolism. (medscape.com)

In most Gram-negative pathogens, the hydrolysis of UDP-2,3-diacylglucosamine to generate lipid X in lipid A biosynthesis is catalysed by the membrane-associated enzyme LpxH. (duke.edu)
Some of the enzymes which generate aromatic radicals that break down most prominent bacterial strains found were isolated and tax- the complex linkages present in lignin to compounds of lower onomically identified using 16S ribosomal RNA (rRNA) se- molecular weight. (lu.se)

One research project in our lab is aimed at obtaining a deeper understanding of conformational dynamics, enzyme catalysis, as well as the chemomechanical coupling mechanisms under which the chemical free energy is converted into mechanical work in ABC-transporters. (iupui.edu)

The stability of the lead compound complexes was evaluated via molecular dynamics (MD) simulation for 100 nanoseconds. (bvsalud.org)

The enzymes of the ribonuclease (RNase) family possess identica l or similar active site residues and conserved fold architecture. (inrs.ca)

Here the authors report a protein-engineering framework based on InDel mutagenesis and fragment transplantation resulting in greater catalysis and longer glow-type bioluminescence of the ancestral luciferase. (muni.cz)
Insertion-deletion (InDel) backbone mutagenesis of Anc(HLD-RLuc) challenged the scaffold dynamics. (muni.cz)

Before graduate school, Flora interned at different biotech companies to explore sustainable methods in catalysis and product development. (ucla.edu)

In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)

NMR investigations of protein structure and dynamics in response to environmental changes. (cardiff.ac.uk)

The PLA 2 s constitute a paradigm for how membranes interact allosterically with proteins, causing conformational changes and activation of the proteins to enable them to extract and bind a specific phospholipid from a membrane for catalysis, which is probably generalizable to intracellular and extracellular transport and phospholipid exchange processes as well as other specific biological functions. (nih.gov)

Anatomy6

Organisms6

Chemicals and Drugs80

Analytical, Diagnostic and Therapeutic Techniques and Equipment35

Phenomena and Processes75

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science8

Health Care7

Simulations17

Dihydrofolate reductase3

Biomolecular interactions2

Reaction16

Ligand3

Kinetics4

Proteins and enzymes1

Structural dynamics3

Allosteric2

Reactions5

Spectroscopy3

Coupling of enzyme motions1

Kinetic Parameters1

Allostery1

Interactions2

Biocatalysis2

Catalyse2

Catalysts2

Structures6

Inhibition1

Inhibitors1

Homologous1

Role5

Monomeric1

Mechanism1

Pathways1

Motions2

Synthetic1

Internal dynamics2

Intermediate1

Fundamental3

Elusive1

Purification1

Unnatural1

Quantum1

Metabolism1

Generate2

Mechanisms1

Stability1

Residues1

Mutagenesis2

Methods1

Ligands1

Protein structure and dyna1

Activation1