scholarly journals Conformational properties of N-acetyl-N-methyl-alpha,beta-dehydroalanine N'-methylamide.

2006 ◽  
Vol 53 (1) ◽  
pp. 227-232 ◽  
Author(s):  
Agnieszka Macedowska ◽  
Dawid Siodłak ◽  
Barbara Rzeszotarska
Keyword(s):  
Cyclic Peptides ◽  
Conformational Flexibility ◽  
Biological Action ◽  
Torsion Angles ◽  
Dehydroamino Acids ◽  
Theoretical Methods ◽  
Conformational Properties ◽  
Alpha Beta

The conformational properties of Ac-Delta(Me)Ala-NHMe (N-acetyl-N-methyl-alpha,beta-dehydroalanine N'-methylamide), as the simplest model of N-methyl-alpha,beta-dehydroamino acids, was examined with theoretical methods and in comparison with Ac-DeltaAla-NHMe and Ac-DeltaAla-NMe(2). The N-terminal amide of the Delta(Me)Ala residue easily adopts the configuration cis and the torsion angles phi, psi are highly flexible. The Delta(Me)Ala residue is a conformational flexibilizer as compared to the parent DeltaAla, which is a conformational stiffener. This seems to be the reason why Delta(Me)Ala is found in small natural cyclic peptides, where it ensures the conformational flexibility necessary for biological action.

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

Propargyloxyproline Regio- and Stereoisomers for Click-Conjugation of Peptides: Synthesis and Application in Linear and Cyclic Peptides

2015 ◽  
Vol 68 (9) ◽  
pp. 1365 ◽  
Author(s):  
Susan E. Northfield ◽  
Simon J. Mountford ◽  
Jerome Wielens ◽  
Mengjie Liu ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Peptide Synthesis ◽  
Cyclic Peptides ◽  
Click Reaction ◽  
Fluorescent Labels ◽  
Peptide Conjugates ◽  
Conformational Properties ◽  
Peptides Synthesis

The use of the click reaction for the introduction of conjugate groups, such as affinity or fluorescent labels, to a peptide for the study of peptide biochemistry and pharmacology is widespread. However, the nature and location of substituted 1,2,3-triazoles in peptide sequences may markedly affect conformation or binding as compared with native sequences. We have examined the preparation and application of propargyloxyproline (Pop) residues as a precursor to such peptide conjugates. Pop residues are available in a range of regio- and stereoisomers from hydroxyproline precursors and are readily prepared in Fmoc-protected form. They can be incorporated routinely in peptide synthesis and broadly retain the conformational properties of the parent proline containing peptides. This is exemplified by the preparation of biotin- and fluorophore-labelled peptides derived from linear and cyclic peptides.

Conformational analysis of the disaccharide methyl α-D-mannopyranosyl-(1→3)-2-O-acetyl-β-D-mannopyranoside monohydrate

2019 ◽  
Vol 75 (6) ◽  
pp. 610-615 ◽  
Author(s):  
Wenhui Zhang ◽  
Qingquan Wu ◽  
Allen G. Oliver ◽  
Anthony S. Serianni
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Nmr Spectroscopy ◽  
Structural Parameters ◽  
Side Chain ◽  
Glycosidic Linkage ◽  
Torsion Angles ◽  
Conformational Properties ◽  
Statistical Program ◽  
Acetyl Group

The crystal structure of methyl α-D-mannopyranosyl-(1→3)-2-O-acetyl-β-D-mannopyranoside monohydrate, C15H26O12·H2O, (II), has been determined and the structural parameters for its constituent α-D-mannopyranosyl residue compared with those for methyl α-D-mannopyranoside. Mono-O-acetylation appears to promote the crystallization of (II), inferred from the difficulty in crystallizing methyl α-D-mannopyranosyl-(1→3)-β-D-mannopyranoside despite repeated attempts. The conformational properties of the O-acetyl side chain in (II) are similar to those observed in recent studies of peracetylated mannose-containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in (II) elongates by ∼0.02 Å upon O-acetylation. The phi (φ) and psi (ψ) torsion angles that dictate the conformation of the internal O-glycosidic linkage in (II) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated (II) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ∼16°) than for φ (Δ = ∼6°).

scholarly journals Conformational investigation of alpha,beta-dehydropeptides. XIII. Conformational properties of N-acetyl-alpha,beta-dehydrovaline N',N'-dimethylamide.

2004 ◽  
Vol 51 (1) ◽  
pp. 145-152 ◽  
Author(s):  
Dawid Siodłak ◽  
Barbara Rzeszotarska ◽  
Małgorzata A Broda ◽  
Anna E Kozioł ◽  
Edyta Kołodziejczyk
Keyword(s):  
Type Ii ◽  
Beta Turn ◽  
X Ray ◽  
X Ray Crystallography ◽  
Tertiary Amide ◽  
Conformational Investigation ◽  
Conformational Properties ◽  
Alpha Beta ◽  
Solid State Conformation ◽  
Ab Initio Dft

The crystal structure of Ac-DeltaVal-NMe(2) (DeltaVal = alpha,beta-dehydrovaline) was determined by X-ray crystallography. The found angles phi = -60 degrees and psi = 125 degrees correspond exactly to the respective values of the (i + 1)th residue in idealised beta-turn II/VIa. Ab initio/DFT studies revealed that the molecule adopts the angle psi restricted only to about |130 degrees | and very readily attains the angle phi = about -50 degrees. This is in line with its solid-state conformation. Taken together, these data suggest that the DeltaVal residue combined with a C-terminal tertiary amide is a good candidate at the (i + 1)th position in a type II/VIa beta-turn.

The conformational properties of α ,β -dehydroamino acids with a C -terminal ester group

2011 ◽  
Vol 17 (10) ◽  
pp. 690-699 ◽  
Author(s):  
Dawid Siodłak ◽  
Justyna Grondys ◽  
Małgorzata A. Broda
Keyword(s):  
Ester Group ◽  
Dehydroamino Acids ◽  
Conformational Properties
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