ArticleBiophysical journal1999
Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. ligand-induced changes in the protein motions.
Article in Biophysical journal, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 47 citations in OpenAlex.
- Loop dynamics, allostery, and function in protein tyrosine phosphatases: insights from molecular simulations.Biochemical Society transactions · 2026Review
- Distal Mutations Rewire Allosteric Networks to Control Substrate Specificity in PTP1B.Biochemistry · 2025Article
- Effects of Glycerol and Phenolics onBiotech (Basel (Switzerland)) · 2025Article
- Does Fermentation Really Increase the Phenolic Content in Cereals? A Study on Millet.Foods (Basel, Switzerland) · 2020Article
- Phosphotyrosine isosteres: past, present and future.Organic & biomolecular chemistry · 2020Review
- In silico investigations on the binding efficacy and allosteric mechanism of six different natural product compounds towards PTP1B inhibition through docking and molecular dynamics simulations.Journal of molecular modeling · 2019Article
- Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches.PloS one · 2018Article
- Leveraging Reciprocity to Identify and Characterize Unknown Allosteric Sites in Protein Tyrosine Phosphatases.Journal of molecular biology · 2017Article
- Characterization of Protein Tyrosine Phosphatase 1B Inhibition by Chlorogenic Acid and Cichoric Acid.Biochemistry · 2017Article
- New insights in the activation of human cholesterol esterase to design potent anti-cholesterol drugs.Molecular diversity · 2014Article
- Article
- Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.Journal of biomolecular structure & dynamics · 2014Article
- Insights into the N-sulfation mechanism: molecular dynamics simulations of the N-sulfotransferase domain of NDST1 and mutants.PloS one · 2013Article
- Frequency response of a protein to local conformational perturbations.PLoS computational biology · 2013Article
- The effect of calciums on molecular motions of proteinase K.Journal of molecular modeling · 2011Article
- Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K.Journal of molecular modeling · 2010Article
- Molecular basis of phospholipase A2 activity toward phospholipids with sn-1 substitutions.Biophysical journal · 2008Article
- On the characterization of protein native state ensembles.Biophysical journal · 2007Article
- Mechanisms and free energies of enzymatic reactions.Chemical reviews · 2006Review
- Dynamics of the WPD loop of the Yersinia protein tyrosine phosphatase.Biophysical journal · 2006Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Activity of enzymes, such as protein tyrosine phosphatases (PTPs), is often associated with structural changes in the enzyme, resulting in selective and stereospecific reactions with the substrate. To investigate the effect of a substrate on the motions occurring in PTPs, we have performed molecular dynamics simulations of PTP1B and PTP1B complexed with a high-affinity peptide DADEpYL, where pY stands for phosphorylated tyrosine. The peptide sequence is derived from the epidermal growth factor receptor (EGFR988-993). Simulations were performed in water for 1 ns, and the concerted motions in the protein were analyzed using the essential dynamics technique. Our results indicate that the predominately internal motions in PTP1B occur in a subspace of only a few degrees of freedom. Upon substrate binding, the flexibility of the protein is reduced by approximately 10%. The largest effect is found in the protein region, where the N-terminal of the substrate is located, and in the loop region Val198-Gly209. Displacements in the latter loop are associated with the motions in the WPD loop, which contains a catalytically important aspartic acid. Estimation of the pKa of the active-site cysteine along the trajectory indicates that structural inhomogeneity causes the pKa to vary by approximately +/-1 pKa unit. In agreement with experimental observations, the active-site cysteine is negatively charged at physiological pH.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.