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Article

Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

1
Department of Chemistry and Biochemistry, California State University, Fresno, CA 93740, USA
2
Department of Medical Pathology and Laboratory Medicine, University of California School of Medicine, Davis, CA 95616, USA
*
Authors to whom correspondence should be addressed.
Academic Editor: Alberto Spisni
Int. J. Mol. Sci. 2021, 22(3), 1364; https://doi.org/10.3390/ijms22031364
Received: 1 January 2021 / Revised: 20 January 2021 / Accepted: 22 January 2021 / Published: 29 January 2021
Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state. View Full-Text
Keywords: NMR; MD; random coil; peptide; ensemble; conformation NMR; MD; random coil; peptide; ensemble; conformation
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MDPI and ACS Style

Krishnan, V.V.; Bentley, T.; Xiong, A.; Maitra, K. Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs. Int. J. Mol. Sci. 2021, 22, 1364. https://doi.org/10.3390/ijms22031364

AMA Style

Krishnan VV, Bentley T, Xiong A, Maitra K. Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs. International Journal of Molecular Sciences. 2021; 22(3):1364. https://doi.org/10.3390/ijms22031364

Chicago/Turabian Style

Krishnan, V. V., Timothy Bentley, Alina Xiong, and Kalyani Maitra. 2021. "Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs" International Journal of Molecular Sciences 22, no. 3: 1364. https://doi.org/10.3390/ijms22031364

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