Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis
Sign Up to like & getrecommendations! Published in 2021 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c01470
Abstract: Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard… read more here.
Keywords: sw1 sw2; gaussian accelerated; gtp; gdp gtp ... See more keywords
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00961
Abstract: S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation of bacterial gene expression at the level of transcription attenuation or translation inhibition. In this study, multiple independent Gaussian-accelerated molecular dynamics simulations were performed to… read more here.
Keywords: independent gaussian; sam; multiple independent; identification ... See more keywords
Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes
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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
Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides
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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
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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