Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

Zhou, Yu; Deng, Geng; Zheng, Yujun; Xu, Jing; Ashraf, Hamad; Yu, Zhi‐Wu

doi:10.1038/srep36932

Cited by 36 publications

(23 citation statements)

References 55 publications

(65 reference statements)

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“…When a hydrogen bonding C O group is π-conjugated, π-resonance decreases the electronegativity of the O atom, and this raises the energy of the in-plane lone pair of O, making it a stronger hydrogen bond acceptor. Gilli's work concluded by speculating on the many imaginable implications of RAHB in chemical and biological systems, including hydrogen-bonded dimers, the secondary structures of proteins, 88 and DNA base pairs (Figure 11b). In the 30 years following Gilli's proposal of the RAHB idea, opposing views either debating the importance of RAHB or the origin of the effect were put forth, based on a variety of theoretical approaches.…”

Section: Resonance-assisted Hydrogen Bondingmentioning

confidence: 99%

Hydrogen bond design principles

Karas

Das

et al. 2020

WIREs Comput Mol Sci

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Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electronegativity, steric effects, electrostatic effects, π-conjugation, and network cooperativity. Historical developments, along with experimental and computational efforts, leading up to the birth of the hydrogen bond concept, the discovery of nonclassical hydrogen bonds (C H…O, O H…π, dihydrogen bonding), and the proposal of hydrogen bond design principles (e.g., secondary electrostatic interactions, resonance-assisted hydrogen bonding, and aromaticity effects) are outlined. Applications of hydrogen bond design principles are presented.

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Section: Resonance-assisted Hydrogen Bondingmentioning

confidence: 99%

Hydrogen bond design principles

Karas

Das

et al. 2020

WIREs Comput Mol Sci

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“…1,2 The Resonance Assisted Hydrogen Bond (RAHB) is one of the strongest due to the enhancing produced by the presence of some degree of conjugation (for example hydrogen bonding networks in proteins) but there is still some debate on the nature of the interactions at play. [3][4][5] The RAHB forms between molecules (intermolecular) and also inside the single molecule as internal hydrogen bonds (IHB, intramolecular) and influences the molecular structure. Two similar families of molecules have been used as model systems in the studies of intramolecular RAHB systems: malonaldehyde and acetylacetone derivatives.…”

Section: Introductionmentioning

confidence: 99%

2-Chloromalonaldehyde, a model system of resonance-assisted hydrogen bonding: vibrational investigation

Gutiérrez-Quintanilla

Chevalier

Platakyté

et al. 2018

Phys. Chem. Chem. Phys.

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The chelated enol isomer of 2-chloromalonaldehyde (2-ClMA) is experimentally characterized for the first time by IR and Raman spectroscopies. The spectra are obtained by trapping the molecule in cryogenic matrices and analyzed with the assistance of theoretical calculations. Experiments were performed in argon, neon and para-hydrogen matrices. The results highlight puzzling matrix effects, beyond site effects, which are interpreted as due to a tunneling splitting of the vibrational levels related to the proton transfer along the internal hydrogen bond (IHB). 2-ClMA is thus one of the very few molecules in which the H tunneling has been observed in cryogenic matrices. The comparison with its parent molecule (malonaldehyde) shows experimentally and theoretically the weakening of the IHB upon chlorination, with a reduced cooperative effect in the resonance assisted hydrogen bond. In addition, the Cl substitution induces an important stabilization of two open enol conformers. These two open forms appear in the spectra of as-deposited samples, meaning that, in contrast with other well-studied molecules of the same family (β-dialdehydes and β-diketones), they are present in the gas phase at room temperature.

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“…This results in an increased nucleophilicity due to increased negative charge on the oxygen atom. 75 …”

Section: Resultsmentioning

confidence: 99%

QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase

Pereira

Silveira

Skaf

2021

J. Chem. Inf. Model.

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Glycoside hydrolases (GH) cleave carbohydrate glycosidic bonds and play pivotal roles in living organisms and in many industrial processes. Unlike acid-catalyzed hydrolysis of carbohydrates in solution, which can occur either via cyclic or acyclic oxocarbenium-like transition states, it is widely accepted that GH-catalyzed hydrolysis proceeds via a general acid mechanism involving a cyclic oxocarbenium-like transition state with protonation of the glycosidic oxygen. The GH45 subfamily C inverting endoglucanase from Phanerochaete chrysosporium (PcCel45A) defies the classical inverting mechanism as its crystal structure conspicuously lacks a general Asp or Glu base residue. Instead, PcCel45A has an Asn residue, a notoriously weak base in solution, as one of its catalytic residues at position 92. Moreover, unlike other inverting GHs, the relative position of the catalytic residues in PcCel45A impairs the proton abstraction from the nucleophilic water that attacks the anomeric carbon, a key step in the classical mechanism. Here, we investigate the viability of an endocyclic mechanism for PcCel45A using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, with the QM region treated with the self-consistent-charge density-functional tight-binding level of theory. In this mechanism, an acyclic oxocarbenium-like transition state is stabilized leading to the opening of the glucopyranose ring and formation of an unstable acyclic hemiacetal that can be readily decomposed into hydrolysis product. In silico characterization of the Michaelis complex shows that PcCel45A significantly restrains the sugar ring to the 4 C 1 chair conformation at the −1 subsite of the substrate binding cleft, in contrast to the classical exocyclic mechanism in which ring puckering is critical. We also show that PcCel45A provides an environment where the catalytic Asn92 residue in its standard amide form participates in a cooperative hydrogen bond network resulting in its increased nucleophilicity due to an increased negative charge on the oxygen atom. Our results for PcCel45A suggest that carbohydrate hydrolysis catalyzed by GHs may take an alternative route from the classical mechanism.

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Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

Cited by 36 publications

References 55 publications

Hydrogen bond design principles

Hydrogen bond design principles

2-Chloromalonaldehyde, a model system of resonance-assisted hydrogen bonding: vibrational investigation

QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase

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