scholarly journals Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

2010 ◽  
Vol 6 ◽  
Author(s):  
Ana Maria Castilla ◽  
M Morgan Conn ◽  
Pablo Ballester
Keyword(s):  
Hydrogen Bonding ◽  
Peptide Ligands ◽  
Binding Studies ◽  
Design Synthesis ◽  
Macrocyclic Receptors ◽  
H Nmr ◽  
Hydrogen Bonding Pattern ◽  
Conformational Equilibria ◽  
Β Sheets ◽  
Β Sheet

We present here the design, synthesis, and analysis of a series of receptors for peptide ligands inspired by the hydrogen-bonding pattern of protein β-sheets. The receptors themselves can be regarded as strands 1 and 3 of a three-stranded β-sheet, with cross-linking between the chains through the 4-position of adjacent phenylalanine residues. We also report on the conformational equilibria of these receptors in solution as well as on their tendency to dimerize. 1H NMR titration experiments are used to quantify the dimerization constants, as well as the association constant values of the 1:1 complexes formed between the receptors and a series of diamides and dipeptides. The receptors show moderate levels of selectivity in the molecular recognition of the hydrogen-bonding pattern present in the diamide series, selecting the α-amino acid-related hydrogen-bonding functionality. Only one of the two cyclic receptors shows modest signs of enantioselectivity and moderate diastereoselectivity in the recognition of the enantiomers and diastereoisomers of the Ala-Ala dipeptide (ΔΔG 0 1 (DD-DL) = −1.08 kcal/mol and ΔΔG 0 1 (DD-LD) = −0.89 kcal/mol). Surprisingly, the linear synthetic precursors show higher levels of stereoselectivity than their cyclic counterparts.

scholarly journals Parallel motif triplex formation via a new, bi-directional hydrogen bonding pattern incorporating a synthetic cyanuryl nucleoside into the sense chain

RSC Advances ◽  
2020 ◽  
Vol 10 (38) ◽  
pp. 22766-22774
Author(s):  
Akihiko Hatano ◽  
Kei Shimazaki ◽  
Maina Otsu ◽  
Gota Kawai
Keyword(s):  
Hydrogen Bonding ◽  
Tertiary Structure ◽  
H Nmr ◽  
Triplex Formation ◽  
Hydrogen Bonding Pattern ◽  
Base Moiety

The triplex formation ability of a sense chain containing a cyanuryl nucleoside was evaluated and the tertiary structure of the triplex was calculated using the NOE in 1H NMR by incorporating a 15N into the base moiety.

Amyloid structure

2014 ◽  
Vol 56 ◽  
pp. 1-10 ◽  
Author(s):  
Louise Serpell
Keyword(s):  
Hydrogen Bonding ◽  
Sequence Homology ◽  
Amyloid Fibrils ◽  
Side Chains ◽  
Primary Sequence ◽  
Sheet Structure ◽  
Β Sheets ◽  
The Stability ◽  
Β Sheet ◽  
Proteins And Peptides

Amyloid fibrils are formed by numerous proteins and peptides that share little sequence homology. The structures formed are highly ordered and extremely stable, being composed of β-sheet structure and stabilized along their length by hydrogen bonding. The fibrils are formed by several protofilaments that wind around one another in rope-like structures, lending further strength and stability to the resulting fibres. The fact that so many proteins and peptides form amyloid structures under suitable conditions, seems to suggest that the sequence of the precursor is unimportant. However, it is now clear that side chains play a central role in forming interactions between several β-sheets to further stabilize and regulate the structures. The primary sequence plays a central role in determining the rate of fibril formation, the stability of the resulting structure to degradation and the final morphology of the fibrils. The side chains regulate the elongation and growth, and also the lateral association of the protofilament and fibrils, having a significant impact on the final architecture.

scholarly journals Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial

2004 ◽  
Vol 13 (4) ◽  
pp. 1134-1147 ◽  
Author(s):  
Clara M. Santiveri ◽  
Jorge Santoro ◽  
Manuel Rico ◽  
M. Angeles Jiménez
Keyword(s):  
Hydrophobic Surface ◽  
Β Sheets ◽  
The Stability ◽  
Β Sheet

scholarly journals Probing the Role of Backbone Hydrogen Bonding in a Critical β Sheet of the Extracellular Domain of a Cys-Loop Receptor

ChemBioChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1385-1391 ◽  
Author(s):  
Kristin R. Gleitsman ◽  
Henry A. Lester ◽  
Dennis A. Dougherty
Keyword(s):  
Hydrogen Bonding ◽  
Extracellular Domain ◽  
Β Sheet

Substitutional and solvation effects on conformational equilibria. Effects on the interaction between opposing axial oxygen atoms

1969 ◽  
Vol 47 (23) ◽  
pp. 4441-4446 ◽  
Author(s):  
R. U. Lemieux ◽  
A. A. Pavia
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Hydrogen Bonding ◽  
Magnetic Resonance ◽  
Hydroxyl Groups ◽  
Evidence Based ◽  
Electrostatic Repulsion ◽  
Hydrogen Bridge ◽  
Conformational Equilibria ◽  
Free Hydroxyl ◽  
Oxygen Atoms

Evidence based both on nuclear magnetic resonance and rotation data primarily obtained from methyl 3-deoxy-β-L-erythro-pentopyranoside and a number of its derivatives is interpreted to show that the electrostatic repulsion between the oxygen atoms at the 2 and 4 positions is substantially less when these oxygens are linked to acyl groups than when in the form of either methyl ethers or as hydroxyl groups hydrogen bonded to solvent. Also, experimental evidence is presented which requires the hydrogen bridge between two axially disposed hydroxyl groups to be substantially strengthened by hydrogen bonding of the free hydroxyl by solvent.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

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