[NMR paper] Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Related ArticlesMolecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Authors: Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA, Campbell BA, Brown RF, Guo C, Schrodt M, Liu YT, Elcock AH
Abstract
Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. (3)JHNH? coupling constants and ?H? chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average (3)JHNH? and ?H? values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average ?-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.
PMID: 26579777 [PubMed - as supplied by publisher]
[NMR paper] pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study.
pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study.
J Phys Chem B. 2013 Apr 11;117(14):3689-706
Authors: Toal S, Meral D, Verbaro D, Urbanc B, Schweitzer-Stenner R
Abstract...
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[NMR paper] Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry.
Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry.
Related Articles Effects of cholesterol on membrane molecular dynamics studied by fast field cycling NMR relaxometry.
Phys Chem Chem Phys. 2013 Aug 22;
Authors: Hsieh CJ, Chen YW, Hwang DW
Abstract
Biological membranes are complex structures composed of various lipids and proteins. Different membrane compositions affect viscoelastic and hydrodynamic properties of membranes, which are critical to their functions. Lipid bilayer vesicles...
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[NMR paper] NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
J Phys Chem B. 2012 Dec 13;116(49):14207-15
Authors: Sonti R, Rai R, Ragothama S, Balaram P
Abstract
Cross strand aromatic interactions between a facing pair of...
[NMR paper] Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Related Articles Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Biophys J. 2005 Sep;89(3):2113-20
Authors: Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M
An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and...
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[NMR paper] Measurement of conformational constraints in an elastin-mimetic protein by residue-pa
Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR.
Related Articles Measurement of conformational constraints in an elastin-mimetic protein by residue-pair selected solid-state NMR.
J Biomol NMR. 2002 Feb;22(2):175-9
Authors: Hong M, McMillan RA, Conticello VP
We introduce a solid-state NMR technique for selective detection of a residue pair in multiply labeled proteins to obtain site-specific structural constraints. The method exploits the frequency-offset dependence of cross...
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[NMR paper] The solution conformations of amino acids from molecular dynamics simulations of Gly-
The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Related Articles The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Biochem Cell Biol. 1998;76(2-3):164-70
Authors: van der Spoel D
The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no...
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[NMR paper] Conformational preferences of synthetic peptides derived from the immunodominant site
Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR.
Related Articles Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR.
Biochemistry. 1990 Aug 28;29(34):7828-37
Authors: Dyson HJ, Satterthwait AC, Lerner RA, Wright PE
Proton nuclear magnetic resonance and ultraviolet circular dichroism spectroscopy have been used to probe the conformational...