Related ArticlesConformational flexibility and loss of structural rigidity for a model hexapeptide, GRGDTP: 1H-NMR and molecular dynamics studies.
Biopolymers. 2013 Jul;99(7):460-71
Authors: Kulkarni AK, Ojha RP
Abstract
The NMR and molecular dynamics methods are used to study the conformations of a hexapeptide, GRGDTP, which has been shown to be accessible to various types of cell-adhesion based cellular behaviors such as cell-to-matrix interactions, cell differentiation, immunogenicity development, gene expression, angiogenesis, metastasis, sex determination and gamete fusion. (1)H-NMR results indicate the existence of weak 5->2 hydrogen bonded ?-turn type-III. Molecular simulation studies using a mixed protocol of distance geometry, constrained minimization, restrained molecular dynamics followed by energy minimization resulted additional conformations that include about 64% of population of inverse ?-turn (HB, 3->1) and about 35% population of ?-turn (HB, 4->2). The inter-proton distances observed in ?-and inverse ?-turns are also consistent with the NMR constraints. The variable internal hydrogen bonding due to ?-turns initiated at Gly and Arg, and its tendency to inter-convert between ?-and inverse ?-turn conformations imply that the peptide is flexible in nature.
[NMR paper] Conformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies.
Conformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies.
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J Biomol Struct Dyn. 2015 Sep;33(9):1850-65
Authors: Kulkarni AK, Ojha RP
Abstract
Solution conformation of the cyclic hexapeptide sequence, (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...
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[NMR paper] Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
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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
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Abstract
UDP-galactopyranose mutase (UGM) is...
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[NMR paper] Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
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Adv Exp Med Biol. 2015;842:217-30
Authors: Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y,...
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Peptides. 2014 Mar;53:270-7
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[NMR paper] Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
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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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[NMR paper] Structural Elucidation of Transmembrane Transporter Protein Bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy.
Structural Elucidation of Transmembrane Transporter Protein Bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy.
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Biochim Biophys Acta. 2013 Jun 14;
Authors: Choudhury AR, Perdih A, Zuperl S, Sikorska E, Solmajer T, Jurga S, Zhukov I, Novi? M
Abstract
Membrane proteins...
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Structural Elucidation of Transmembrane Transporter Protein Bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
Structural Elucidation of Transmembrane Transporter Protein Bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy
Publication date: Available online 14 June 2013
Source:Biochimica et Biophysica Acta (BBA) - Biomembranes</br>
Author(s): Amrita Roy Choudhury , Andrej Perdih , Špela Župerl , Emilia Sikorska , Tom Solmajer , Stefan Jurga , Igor Zhukov , Marjana Novi?</br>
Membrane proteins represent about a third of the gene products in most organisms, as revealed by the genome sequencing...
Conformational flexibility and loss of structural rigidity for a model hexapeptide, GRGDTP: 1H-NMR and molecular dynamics studies.
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