Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation.

The journal of physical chemistry. B - 27 Jul 2017

Dutta Debodyuti, Mishra Sabyashachi

Abstract excerpt

The mechanism of the catalytic hydrolysis of N-succinyl diaminopimelic acid (SDAP) by the microbial enzyme DapE in its wild-type (wt) form as well as three of its mutants (E134D, H67A, and H349A) is investigated employing a hybrid quantum mechanics/molecular mechanics (QM/MM) method coupled with molecular dynamics (MD) simulations, wherein the time evolution of the atoms of the QM and MM regions are obtained from...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Binding Sites
Share to Catalysis
Share to Catalytic Domain

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Hydrolysis

Share to Microbiota

Share to Molecular Dynamics Simulation

Share to Mutation

Source

Identifiers

PMID: 28664734
DOI: 10.1021/acs.jpcb.7b04431

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 5 Sept 2026. Manifest publication-graph-cohort-2026-09-05.1.

Source receipt: pubmed, retrieved 5 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation.PMID 28664734Read ↗

Loss of Catalytic Activity in the E134D, H67A, and H349A Mutants of DapE: Mechanistic Analysis with QM/MM Investigation.Semantic proximity Read ↗

Modulating Enzyme's Conformational Space: Impact of Substrate Binding, Mode Alteration, and Active Site Mutation in DapC, an Aminotransferase Enzyme of Lysine Biosynthetic Pathway.Semantic proximity Read ↗

Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations.Semantic proximity Read ↗

Unraveling the Origins of Changing Product Specificity Properties of Arginine Methyltransferase PRMT7 by the E181D and E181D/Q329A Mutations through QM/MM MD and Free-Energy Simulations.Semantic proximity Read ↗

Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from SimulationsSemantic proximity Read ↗

QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily.Semantic proximity Read ↗

Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates.Semantic proximity Read ↗

Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase.Semantic proximity Read ↗

Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.Semantic proximity Read ↗

Molecular modeling of conformational dynamics and its role in enzyme evolution.Semantic proximity Read ↗

A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations.Semantic proximity Read ↗

Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.