Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA

Analysis of the structures of two complexes of 5 S rRNA with homologous ribosomal proteins,Escherichia coliL25 andThermus thermophilusTL5, revealed that amino acid residues interacting with RNA can be divided into two different groups. The first group consists of non-conserved residues, which form intermolecular hydrogen bonds accessible to solvent. The second group, comprised of strongly conserved residues, form intermolecular hydrogen bonds that are shielded from solvent. Site-directed mutagenesis was used to introduce mutations into the RNA-binding site of protein TL5. We found that replacement of residues of the first group does not influence the stability of the TL5·5 S rRNA complex, whereas replacement of residues of the second group leads to destabilization or disruption of the complex. Stereochemical analysis shows that the replacements of residues of the second group always create complexes with uncompensated losses of intermolecular hydrogen bonds. We suggest that these shielded intermolecular hydrogen bonds are responsible for the recognition between the protein and RNA.

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Understanding the role of cations and hydrogen bonds on the stability of aerobic granules from the perspective of the aggregation and adhesion behavior of extracellular polymeric substances

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.148659 ◽

2021 ◽

pp. 148659

Author(s):

Zhengwen Li ◽

Huiqi Li ◽

Lianfa Zhao ◽

Xiang Liu ◽

Chunli Wan

Keyword(s):

Hydrogen Bonds ◽

Extracellular Polymeric Substances ◽

Aerobic Granules ◽

Adhesion Behavior ◽

The Stability

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Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study

RSC Advances ◽

10.1039/d0ra07526d ◽

2020 ◽

Vol 10 (67) ◽

pp. 40969-40982

Author(s):

Surjit Bhai ◽

Bishwajit Ganguly

Keyword(s):

Nucleic Acids ◽

Dft Study ◽

Base Pairs ◽

Canonical Base ◽

The Stability

Hg2+-mediated PNA–PNA mispair duplex (PTTTTP) is more energetically favoured compared to DNA–DNA mispair duplex (DTTTTD).

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Cover Picture: The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics (ChemistryOpen 3/2015)

ChemistryOpen ◽

10.1002/open.201580301 ◽

2015 ◽

Vol 4 (3) ◽

pp. 197-197

Author(s):

L. Guillaumes ◽

S. Simon ◽

C. Fonseca Guerra

Keyword(s):

Hydrogen Bonds ◽

Base Pairs ◽

Adenine Thymine

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The role of aromatic rings as hydrogen-bond acceptors in molecular recognition

Philosophical Transactions of the Royal Society of London Series A Physical and Engineering Sciences ◽

10.1098/rsta.1993.0122 ◽

1993 ◽

Vol 345 (1674) ◽

pp. 105-112 ◽

Cited By ~ 96

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Gas Phase ◽

Signal Transmission ◽

Aromatic Rings ◽

Aromatic Interactions ◽

Proton Donors ◽

The Stability ◽

Intramolecular Hydrogen

Observations of phenol-benzene and ammonia—benzene complexes in the gas phase show that hydrogen bonds link their proton donors to the π electrons of the benzene with a bond energy of between 2 and 4 kcal mol -1 , large enough to be biologically significant. Intramolecular hydrogen bonds between OH and NH donors and aromatic acceptors have also been found in crystal structures of organic compounds. NH-aromatic interactions stabilize x-helices if donors and acceptors occur at successive turns of the helix. These interactions also contribute to the stability of several proteins and play an important part in cellular and synaptic signal transmission.

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Thermodynamic basis of the α-helix and DNA duplex

European Biophysics Journal ◽

10.1007/s00249-021-01520-w ◽

2021 ◽

Author(s):

A. I. Dragan ◽

C. Crane-Robinson ◽

P. L. Privalov

Keyword(s):

Hydrogen Bonds ◽

Double Helix ◽

Van Der Waals ◽

Van Der Waals Interactions ◽

Base Pairs ◽

The Stability ◽

Α Helix ◽

Dna Double Helix ◽

Conjugate Base ◽

Thermodynamic Basis

AbstractAnalysis of calorimetric and crystallographic information shows that the α-helix is maintained not only by the hydrogen bonds between its polar peptide groups, as originally supposed, but also by van der Waals interactions between tightly packed apolar groups in the interior of the helix. These apolar contacts are responsible for about 60% of the forces stabilizing the folded conformation of the α-helix and their exposure to water on unfolding results in the observed heat capacity increment, i.e. the temperature dependence of the melting enthalpy. The folding process is also favoured by an entropy increase resulting from the release of water from the peptide groups. A similar situation holds for the DNA double helix: calorimetry shows that the hydrogen bonding between conjugate base pairs provides a purely entropic contribution of about 40% to the Gibbs energy while the enthalpic van der Waals interactions between the tightly packed apolar parts of the base pairs provide the remaining 60%. Despite very different structures, the thermodynamic basis of α-helix and B-form duplex stability are strikingly similar. The general conclusion follows that the stability of protein folds is primarily dependent on internal atomic close contacts rather than the hydrogen bonds they contain.

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