Related ArticlesConformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies.
J Biomol Struct Dyn. 2015 Sep;33(9):1850-65
Authors: Kulkarni AK, Ojha RP
Abstract
Solution conformation of the cyclic hexapeptide sequence, [cyclo-S-Cys-Tyr-Ile-Gln-Asn-Cys-S] (CYIQNC) - a disulfide-linked fragment of a neurohypophyseal peptide hormone oxytocin (OT) - has been investigated by high-field one-dimensional (1D) and two-dimensional (2D) NMR spectroscopic methods and compared with the results obtained from computer simulation studies. (1)H-NMR results based on temperature dependence of amide proton chemical shifts and nuclear Overhauser effect indicate that peptide in solution populates different conformations, characterized by two fused ?-turns. The segment Ile(3)-Gln(4)-Asn(5)-Cys(6) yields a preferred type-III ?-turn at residues 4, 5 (HB, 3HN*->*6CO), while the segment Cys(6), Cys(1)-Tyr(2)-Ile(3) exhibits inherently weaker, flexible ?-turn either of type I/II'/III/half-turn at residues 1, 2 (HB, 6HN*->*3CO). The computer simulation studies using a mixed protocol of distance geometry-simulated annealing followed by constrained minimization, restrained molecular dynamics, and energy minimization showed the possibility of existence of additional conformations with the hydrogen bonds, (a) 5HN*->*3CO and (b) 2HN*->*6CO. These results, therefore, indicate that the additional conformations obtained from both NMR and simulation studies can also be possible to the peptide. These additional conformations might have very small population in the solution and did not show their signatures in these conditions. These findings will be helpful in designing more analogs with modifications in the cyclic moiety of OT.
Insights into furanose solution conformations: beyond the two-state model
Insights into furanose solution conformations: beyond the two-state model
Abstract
A two-state model is commonly used for interpreting ring conformations of furanoses based on NMR scalar 3 J-coupling constants, with the ring populating relatively narrow distributions in the North and the South of the pseudorotation itinerary. The validity of this simple approach has been questioned, and is examined here in detail employing molecular dynamics (MD) simulations with a new GLYCAM force field parameter set for furanoses....
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[NMR paper] Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
Bioorg Med Chem Lett. 2015 Mar 15;25(6):1284-7
Authors: Shi Y, Ardá A, Pinto BM
Abstract
UDP-galactopyranose mutase (UGM) is...
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[NMR paper] Three-dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model.
Three-dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model.
Three-dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model.
Magn Reson Chem. 2015 Jul 1;
Authors: Gonnella NC, Grinberg N, Mcloughlin M, Choudhary O, Fandrick K, Ma S
Abstract
The three-dimensional solution conformation of teicoplanin aglycone was determined using NMR spectroscopy. A combination of...
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[NMR paper] Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Related Articles Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Chem Biol Drug Des. 2014 Apr 25;
Authors: Kulkarni AK, Ojha RP
Abstract
Among various strategies, the de novo design and in silico approaches are being used to develop the short peptides, models of modified peptides and mimetics as clinically useful drugs with improved stability and...
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04-29-2014 12:04 PM
[NMR paper] Micelle-bound conformations of neurohypophyseal hormone analogues modified with a C?-disubstituted residue: NMR and molecular modelling studies.
Micelle-bound conformations of neurohypophyseal hormone analogues modified with a C?-disubstituted residue: NMR and molecular modelling studies.
Related Articles Micelle-bound conformations of neurohypophyseal hormone analogues modified with a C?-disubstituted residue: NMR and molecular modelling studies.
J Biomol Struct Dyn. 2013;31(7):748-64
Authors: Sikorska E, Kwiatkowska A
Abstract
In this study, by applying a combined approach of NMR measurements and molecular modelling, the conformations and the interactions with membrane-like...
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[NMR paper] NMR and molecular dynamics studies of the interaction of melatonin with calmodulin.
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Protein Sci. 2004 Nov;13(11):2925-38
Authors: Turjanski AG, Estrin DA, Rosenstein RE, McCormick JE, Martin SR, Pastore A, Biekofsky RR, Martorana V
Pineal hormone melatonin (N-acetyl-5-methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca(2+) concentration via activation of its G-protein-coupled...
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[NMR paper] Backbone NMR assignments of a high molecular weight protein (47 kDa), cyclic AMP rece
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J Biomol NMR. 2000 Jan;16(1):79-80
Authors: Won HS, Yamazaki T, Lee TW, Jee JG, Yoon MK, Park SH, Otomo T, Aiba H, Kyogoku Y, Lee BJ
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[NMR paper] The solution conformations of amino acids from molecular dynamics simulations of Gly-
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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...
Conformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies.
Linear Mode
