Insulin adsorption on functionalized silica surfaces: an accelerated molecular dynamics study
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Modeling"
DOI: 10.1007/s00894-018-3610-2
Abstract: We study the influence of surface functionalization of a silica surface on insulin adsorption using accelerated molecular dynamics simulation. Three different functional groups are studied, CH3, OH, and COOH. Due to the partial charges of… read more here.
Keywords: adsorption; surface polarity; molecular dynamics; accelerated molecular ... See more keywords
Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics.
Sign Up to like & getrecommendations! Published in 2020 at "Biochemistry"
DOI: 10.1021/acs.biochem.0c00633
Abstract: Substrate-induced conformational changes present in alkanesulfonate monooxygenase (SsuD) are crucial to catalysis and lead to distinct interactions between a dynamic loop region and the active site. Accelerated molecular dynamics (aMD) simulations have been carried out… read more here.
Keywords: alkanesulfonate monooxygenase; molecular dynamics; accelerated molecular; conformational changes ... See more keywords
Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation.
Sign Up to like & getrecommendations! Published in 2017 at "Biochemistry"
DOI: 10.1021/acs.biochem.6b00839
Abstract: Protease inhibition by metastable serine protease inhibitors (serpins) is mediated by one of the largest functional intradomain conformational changes known in biology. In this extensive structural rearrangement, protease-serpin complex formation triggers cleavage of the serpin… read more here.
Keywords: molecular dynamics; insertion; accelerated molecular; center loop ... See more keywords
Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.3c00138
Abstract: Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields… read more here.
Keywords: folding benchmarking; dynamics peptide; molecular dynamics; force fields ... See more keywords
Effects of Disulfide Bonds on Bindings of Inhibitors to BACE1 Decoded by Multiple Replica Accelerated Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2020 at "ACS chemical neuroscience"
DOI: 10.1021/acschemneuro.0c00234
Abstract: The β-amyloid cleaving enzyme 1 (BACE1) has been thought as an efficient target for treatment of Alzheimer's disease (AD). Deep insight into inhibitor-BACE1 binding mechanism is of significance for design of potent drugs toward BACE1.… read more here.
Keywords: molecular dynamics; replica accelerated; inhibitors bace1; accelerated molecular ... See more keywords
Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes
Sign Up to like & getrecommendations! Published in 2022 at "RSC Advances"
DOI: 10.1039/d1ra07936k
Abstract: Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode… read more here.
Keywords: gtp kras; switch; molecular dynamics; free energy ... See more keywords
Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of enzyme inhibition and medicinal chemistry"
DOI: 10.1080/14756366.2023.2195995
Abstract: Mutations highly affect the structural flexibility of two switch domains in M-RAS considered an important target of anticancer drug design. Gaussian accelerated molecular dynamics (GaMD) simulations were applied to probe the effect of mutations P40D,… read more here.
Keywords: molecular dynamics; gaussian accelerated; accelerated molecular; gtp ras ... See more keywords
Analysis of mutations of defensin protein using accelerated molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2020 at "PLoS ONE"
DOI: 10.1371/journal.pone.0241679
Abstract: Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein… read more here.
Keywords: protein; rsafp2; molecular dynamics; accelerated molecular ... See more keywords
Exploring the deactivation mechanism of human β 2 adrenergic receptor by accelerated molecular dynamic simulations
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.972463
Abstract: The β 2 adrenergic receptor (β2AR), one of important members of the G protein coupled receptors (GPCRs), has been suggested as an important target for cardiac and asthma drugs. Two replicas of Gaussian accelerated molecular… read more here.
Keywords: deactivation mechanism; accelerated molecular; adrenergic receptor; mechanism ... See more keywords
Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides
Sign Up to like & getrecommendations! Published in 2022 at "Foods"
DOI: 10.3390/foods11030327
Abstract: Angiotensin-converting enzyme (ACE)-inhibitory peptides extracted from food proteins can lower blood pressure by inhibiting ACE activity. A recent study showed that the inhibitory activity of IY (Ile-Tyr, a dipeptide derived from soybean protein) against ACE… read more here.
Keywords: converting enzyme; enzyme ace; gaussian accelerated; ace ... See more keywords
Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2023 at "Molecules"
DOI: 10.3390/molecules28072886
Abstract: G12 mutations heavily affect conformational transformation and activity of KRAS. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the GDP-bound wild-type (WT), G12A, G12D, and G12R KRAS to probe mutation-mediated impacts… read more here.
Keywords: g12 mutations; molecular dynamics; gaussian accelerated; conformational alterations ... See more keywords