The emerging role of hydrogen bond interactions in polyglutamine structure, stability and association

Soft Matter ◽  
2013 ◽  
Vol 9 (8) ◽  
pp. 2359-2364 ◽  
Author(s):  
Natasha H. Rhys ◽  
Lorna Dougan
Keyword(s):  
Hydrogen Bond ◽  
Structure Stability ◽  
Hydrogen Bond Interactions

Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

2021 ◽  
Vol 11 (1) ◽  
pp. 127-134
Author(s):  
Nhung Ngo Thi Hong ◽  
Huong Dau Thi Thu ◽  
Trung Nguyen Tien
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Energy Surface ◽  
Covalent Bond ◽  
Electrostatic Energy ◽  
Substantial Contribution ◽  
Structure Stability ◽  
Dispersion Terms ◽  
Insight Into

Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

scholarly journals The synthesis of a pyridine-N-oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions

2016 ◽  
Vol 14 (33) ◽  
pp. 7972-7981 ◽  
Author(s):  
Nicholas H. Evans ◽  
Charles E. Gell ◽  
Michael J. G. Peach
Keyword(s):  
Hydrogen Bond ◽  
Nmr Spectroscopy ◽  
Computational Modelling ◽  
Amide Hydrogen ◽  
X Ray ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions

A pyridine-N-oxide containing rotaxane has been prepared in 32% yield. The role of macrocycle structure in successful pseudo-rotaxane formation has been rationalised by a combination of NMR spectroscopy, X-ray crystallography and computational modelling.

scholarly journals Supramolecular polymerisation in water; elucidating the role of hydrophobic and hydrogen-bond interactions

Soft Matter ◽  
2016 ◽  
Vol 12 (11) ◽  
pp. 2887-2893 ◽  
Author(s):  
Christianus M. A. Leenders ◽  
Matthew B. Baker ◽  
Imke A. B. Pijpers ◽  
René P. M. Lafleur ◽  
Lorenzo Albertazzi ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Self Assembly ◽  
The Self ◽  
Hydrogen Bond Interactions

The self-assembly of a family of benzene-1,3,5-tricarboxamides (BTAs) in water is studied systematically to elucidate the role of hydrophobic and hydrogen-bond interactions.

scholarly journals X-Ray Crystallographic Structure of the Norwalk Virus Protease at 1.5-Å Resolution

2006 ◽  
Vol 80 (10) ◽  
pp. 5050-5058 ◽  
Author(s):  
Corinne E. Zeitler ◽  
Mary K. Estes ◽  
B. V. Venkataram Prasad
Keyword(s):  
Hydrogen Bond ◽  
Conformational Changes ◽  
Cysteine Proteases ◽  
Catalytic Triad ◽  
Strong Hydrogen Bond ◽  
Crystallographic Structure ◽  
Viral Gastroenteritis ◽  
Norwalk Virus ◽  
Hydrogen Bond Interactions

ABSTRACT Norwalk virus (NV), a member of the Caliciviridae family, is the major cause of acute, epidemic, viral gastroenteritis. The NV genome is a positive sense, single-stranded RNA that encodes three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral cysteine protease into six nonstructural proteins. We have determined the structure of the NV protease to 1.5 and 2.2 Å from crystals grown in the absence or presence, respectively, of the protease inhibitor AEBSF [4-(2-aminoethyl)-benzenesulfonyl fluoride]. The protease, which crystallizes as a stable dimer, exhibits a two-domain structure similar to those of other viral cysteine proteases with a catalytic triad composed of His 30, Glu 54, and Cys 139. The native structure of the protease reveals strong hydrogen bond interactions between His 30 and Glu 54, in the favorable syn configuration, indicating a role of Glu 54 during proteolysis. Mutation of this residue to Ala abolished the protease activity, in a fluorogenic peptide substrate assay, further substantiating the role of Glu 54 during proteolysis. These observations contrast with the suggestion, from a previous study of another norovirus protease, that this residue may not have a prominent role in proteolysis (K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, and N. Tanaka, J. Virol. 79:13685-13693, 2005). In the structure from crystals grown in the presence of AEBSF, Glu 54 undergoes a conformational change leading to disruption of the hydrogen bond interactions with His 30. Since AEBSF was not apparent in the electron density map, it is possible that these conformational changes are due to subtle changes in pH caused by its addition during crystallization.

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