2017
DOI: 10.1002/jcc.24746
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Insulin mimetic peptide S371 folds into a helical structure

Abstract: Insulin plays a crucial physiological role in glucose control by initiating a number of signaling events on binding and activating its cell surface receptor. Insulin mimics have, therefore, become promising agents for treating diabetes and to probe the mechanism of interaction of insulin with its receptor. Specifically, many insulin-mimetic peptide sequences have been discovered and found to selectively function as agonists and antagonists, but their structures and the mechanistic details of their interactions… Show more

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Cited by 11 publications
(9 citation statements)
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“…The three main parameters in metadynamics that control the efficiency and accuracy of the free energy reconstruction from converged metadynamics potential ( V meta ) are W , δ , and τ G . The metadynamics method has been successfully applied to study many biophysical problems including computational drug design . In this work, we used an eigenvector as a CV that was computed based upon the atomic coordinates of the backbone C α atoms of all residues in α 4 through α 7 helices.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…The three main parameters in metadynamics that control the efficiency and accuracy of the free energy reconstruction from converged metadynamics potential ( V meta ) are W , δ , and τ G . The metadynamics method has been successfully applied to study many biophysical problems including computational drug design . In this work, we used an eigenvector as a CV that was computed based upon the atomic coordinates of the backbone C α atoms of all residues in α 4 through α 7 helices.…”
Section: Methodsmentioning
confidence: 99%
“…The metadynamics method has been successfully applied to study many biophysical problems including computational drug design. [60][61][62][63][64][65][66] In this work, we used an eigenvector as a CV 67…”
Section: Metadynamics Simulationsmentioning
confidence: 99%
“…Several other structural dissimilarity criteria are encountered in the literature, which are qualified as metrics [37] (see also [38][39][40]), such as hydrogen bonds, distance from surface, the number of residues, or the number of heavy or polar atoms, or the number of waters in the vicinity of a specific region, RMSF (Root Mean Square Fluctuation), SASA (Solvent Accessible Surface Area), and gyration radius.…”
Section: Comparison With Other Dissimilarity Measuresmentioning
confidence: 99%
“…[4] Mohammadiarani and Vashisth use, in their study, metadynamics to investigate the folding thermodynamics of an insulin peptide mimetic, which they discover has a strong helical propensity. [5] Okamoto and Ichiye present studies on proteins under high pressure, [6] [7] Dominy investigates the effect from metal ion in tumor Endothelial Marker 8 and Anthrax Protective Antigen, [8] and Pettitt explores phage-like packing structures with mean field sequence dependence. [9] Levy, Matubayasi and co-workers use an auxiliary (implicit solvent and vacuum) free energy surface to estimate, at a fraction of the computational cost, conformational free energy differences in explicit solvent for a couple of exemplar systems.…”
Section: Introductionmentioning
confidence: 99%
“…In the contribution from Nilsson and co‐workers, free energy methods are used to characterise the free energy change between locked nucleic acid and DNA nucleosides . Mohammadiarani and Vashisth use, in their study, metadynamics to investigate the folding thermodynamics of an insulin peptide mimetic, which they discover has a strong helical propensity . Okamoto and Ichiye present studies on proteins under high pressure, Dominy investigates the effect from metal ion in tumor Endothelial Marker 8 and Anthrax Protective Antigen, and Pettitt explores phage‐like packing structures with mean field sequence dependence .…”
mentioning
confidence: 99%