Influence of C-H...O interactions on the structural stability of β-lactamases

Abstract

β-Lactamases produced by pathogenic bacteria cleave β-lactam antibiotics and render them ineffective. Understanding the principles that govern the structural stability of β-lactamases requires elucidation of the nature of the interactions that are involved in stabilization. In the present study, we systematically analyze the influence of CH...O interactions on determining the specificity and stability of β-lactamases in relation to environmental preferences. It is interesting to note that all the residues located in the active site of β-lactamases are involved in CH...O interactions. A significant percentage of CH...O interactions have a higher conservation score and short-range interactions are the predominant type of interactions in β-lactamases. These results will be useful in understanding the stability patterns of β-lactamases.

In silico structure evaluation of BAG3 and elucidating its association with bacterial infections through protein–protein and host‐pathogen interaction analysis

“…The environmental preferences of different amino acids along with their role and importance in the structural stability of proteins are well documented. [39][40][41][42][43] From the secondary structure prediction, it was observed that 82% of the human BAG3 protein had solvent accessibility, whereas 16% of the residues were buried, which can be correlated from the corresponding secondary structure profile composed primarily of random coils (72.52%) followed by α-helix (14.43%), extended strand (8%), and β-turns (5.04%) of which the BAG domain consisted of α-helices. The 3D modelled structure of the BAG3 protein was refined (Figure 1A) and subjected to multiple validations and optimisations.…”

Aerobactin Seems To Be a Promising Marker Compared With Unstable RmpA2 for the Identification of Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae: In Silico and In Vitro Evidence

“…Although previous studies have reported the correlation of rmpA and rmpA2 as markers for hypervirulent and hypermucoviscous pathotypes, there is a dearth of comprehensive correlations between the constitutive virulence markers for hvKp, viz., rmpA , rmpA2 , and aerobactin , based on “genome-structure” perspectives. Our research group has extensively worked on genomics ( Jacob et al, 2019 ; Shankar et al, 2020a ; Vasudevan et al, 2020 ; Shankar et al, 2021 ) and in silico structural analysis ( Lavanya et al, 2013 ; Lavanya et al, 2014 ; Lavanya et al, 2015 ) to decipher the functional circuitry of various pathogenic proteins. The present study adopted a combination of whole-genome sequencing (WGS), genomic analysis, computational modeling, and structural dynamics studies, which have not been used previously to assess the concerned virulence markers as per our knowledge.…”

C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study

“…4,5 The C-H/O interactions are now accepted as genuine hydrogen bonds [6][7][8][9] which play a significant role in the stability of biomolecules, biomolecular complexes and crystal structures. [10][11][12][13] The importance of C-H/O interactions in proteins is evident from the fact that 20-25% of the total number of water and benzene is −1.28 kcal mol −1 , while the interaction energy for the bifurcated C-H/O interaction is −1.38 kcal mol −1 . 29 The interaction energies for the linear C-H/O interactions between water and pyridine ortho, meta, and para C-H groups are −1.24, −1.94 and −1.97 kcal mol −1 , respectively, whereas the energies for the bifurcated ortho-meta and meta-para interactions are −1.96 and −2.16 kcal mol −1 , respectively.…”