Fluxional nature in cyclohexane and cyclopentane: spherical conformational landscape model revisited
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Chemical Sciences"
DOI: 10.1007/s12039-019-1701-y
Abstract: Spherical conformational landscape model was revisited to include yet another class of cyclic compounds; the derivatives of cyclohexane. The updated model is not only capable of explaining Raman spectral features in fluxional cyclopentane but is… read more here.
Keywords: spherical conformational; cyclopentane; conformational landscape; landscape model ... See more keywords
Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study.
Sign Up to like & getrecommendations! Published in 2020 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2020.08.030
Abstract: HIV infection is a global health epidemic with current FDA-approved HIV-1 Protease inhibitors (PIs) designed against subtype B protease, yet they are used in HIV treatment world-wide regardless of patient HIV classification. In this study,… read more here.
Keywords: conformational landscape; protease; study; hiv protease ... See more keywords
Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating
Sign Up to like & getrecommendations! Published in 2018 at "Cell reports"
DOI: 10.1016/j.celrep.2018.07.004
Abstract: SUMMARY The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into… read more here.
Keywords: conformational landscape; coverage 26s; landscape reveals; expanded coverage ... See more keywords
Matrix-isolation vibrational circular dichroism spectroscopy in structural studies of peptides: Conformational landscape of the Ac(-Ala)1–4-OMe depsipeptide series
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Spectroscopy"
DOI: 10.1016/j.jms.2018.06.005
Abstract: Abstract Depsipeptides are naturally occurring peptide analogues containing ester functionalities and are in the focus of numerous pharmaceutical researches and clinical studies owing to their enzyme inhibitor properties and cytotoxic activity against human tumor cell… read more here.
Keywords: depsipeptide series; conformational landscape; ala ome; ome depsipeptide ... See more keywords
Exploring the Conformational Landscape of a Lanthipeptide Synthetase Using Native Mass Spectrometry.
Sign Up to like & getrecommendations! Published in 2021 at "Biochemistry"
DOI: 10.1021/acs.biochem.1c00085
Abstract: Lanthipeptides are ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These genetically encoded peptides are biosynthesized by multifunctional enzymes (lanthipeptide synthetases) that possess relaxed substrate specificity and catalyze iterative rounds of post-translational modification. Recent… read more here.
Keywords: conformational landscape; native mass; mass spectrometry; lanthipeptide synthetase ... See more keywords
Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Medicinal Chemistry"
DOI: 10.1021/acs.jmedchem.2c00708
Abstract: Protein flexibility is important for ligand binding but often ignored in drug design. Considering proteins as ensembles rather than static snapshots creates opportunities to target dynamic proteins that lack FDA-approved drugs, such as the human… read more here.
Keywords: scale ligand; large scale; ligand; conformational landscape ... See more keywords
Cancer Conformational Landscape Shape Tumorigenesis.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.1c00906
Abstract: During tumorigenesis, DNA mutations in protein coding sequences can alter amino acid sequences which can change the structures of proteins. While the 3D structure of mutated proteins has been studied with atomic resolution, the precise… read more here.
Keywords: cell; tumorigenesis; conformational landscape; cancer conformational ... See more keywords
Direct protein-lipid interactions shape the conformational landscape of secondary transporters
Sign Up to like & getrecommendations! Published in 2018 at "Nature Communications"
DOI: 10.1038/s41467-018-06704-1
Abstract: Secondary transporters undergo structural rearrangements to catalyze substrate translocation across the cell membrane – yet how such conformational changes happen within a lipid environment remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS)… read more here.
Keywords: protein lipid; conformational landscape; direct protein; secondary transporters ... See more keywords
Hsp90 dependence of a kinase is determined by its conformational landscape
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/srep43996
Abstract: Heat shock protein 90 (Hsp90) is an abundant molecular chaperone, involved in the folding and activation of 60% of the human kinome. The oncogenic tyrosine kinase v-Src is one of the most stringent client proteins… read more here.
Keywords: hsp90 dependence; kinase; conformational landscape;
Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Chemistry"
DOI: 10.3389/fchem.2022.1087963
Abstract: Ubiquitin chains are flexible multidomain proteins that have important biological functions in cellular signalling. Computational studies with all-atom molecular dynamics simulations of the conformational spaces of polyubiquitins can be challenging due to the system size… read more here.
Keywords: ubiquitin chains; back mapping; conformational landscape; based sampling ... See more keywords