ArticleNature communications2024
Activation and friction in enzymatic loop opening and closing dynamics.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Site-directed mutagenesis and semi-rational design to enhance chitinolytic activity of bacterial exochitinase.Microbial cell factories · 2026Article
- Loop dynamics govern MALT1 activation revealed by integrative AlphaFold, MD, and NMR analysis.Scientific reports · 2026Article
- SegDesign: A modular framework for controllable protein segment engineering.Protein science : a publication of the Protein Society · 2026Article
- TPTE, a testis-specific PTEN family member, drives spermatogenesis via PI(4,5)PCell death & disease · 2026Article
- Single-engineered-residue solvation perturbations regulate global protein architecture and function.Nature communications · 2026Article
- Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase.JACS Au · 2026Article
- Loop dynamics, allostery, and function in protein tyrosine phosphatases: insights from molecular simulations.Biochemical Society transactions · 2026Review
- Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses.bioRxiv : the preprint server for biology · 2025Article
- Loop engineering of AtCas9 for effective and broad genome editing.Cell insight · 2025Article
- Dynamic claw of dengue protease unveils druggability potential with high affinity allosteric inhibitors.PNAS nexus · 2025Article
- PRL-3: unveiling a new horizon in cancer therapy.Acta pharmacologica Sinica · 2025Review
- Orchestrating function: Concerted dynamics, allostery, and catalysis in protein tyrosine phosphatases.Current opinion in structural biology · 2025Review
- Article
- Structural insights into the substrate binding mechanism of the class I dehydratase MadB.Communications biology · 2025Article
- Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l‑Asparaginase Type 1 for Leukemia Drug Design.ACS catalysis · 2025Article
- Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.Communications biology · 2024Article
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Authors and funding
6 authors.
Funding
Abstract
Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.
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