Journal: The journal of physical chemistry. B

Article Title: Ewald summation approach to potential models of aqueous electrolytes involving gaussian charges and induced dipoles: formal and simulation results.

doi: 10.1021/jp509074p

Figure Lengend Snippet: Figure 1. Schematic representation of the split between real- and reciprocal-space contributions in the Ewald summation approach involving Gaussian smeared electrostatic charges and induced dipoles.

Article Snippet: A.; Horita, J. Polarization Behavior of Water in Extreme Aqueous Environments: A Molecular Dynamics Study Based on the Gaussian Charge Polarizable Water Model. J. Chem.

Techniques:

Journal: Microorganisms

Article Title: Cross-Kingdom Enzymatic Strategies for Deoxynivalenol Detoxification: Computational Analysis of Structural Mechanisms and Evolutionary Adaptations

doi: 10.3390/microorganisms13102384

Figure Lengend Snippet: Structural characterization of the NADP-binding site and dynamic coupling in DepB. ( A ) Overall structure of DepB highlighting the NADP-binding pocket. The enzyme is shown in ribbon representation (yellow) with the molecular surface displayed in transparent gray, while the bound NADP molecule is depicted as spheres (carbon, gray; oxygen, red; nitrogen, blue; phosphate, orange). The cofactor is positioned within a deep hydrophobic cleft at the interface of several α-helices and β-strands. ( B ) Covariance matrix obtained from normal mode analysis using iMODS, showing residue–residue dynamic correlations within DepB. Positive correlations (red) indicate coordinated motions, particularly within the NADP-binding region, whereas anti-correlated motions (blue) correspond to distal structural domains, suggesting functional compartmentalization of the enzyme. ( C ) Detailed two-dimensional interaction map of the amino acid residues involved in NADP binding. Solvent accessibility, backbone and side-chain contacts, and various π-interactions are indicated according to the legend.

Article Snippet: Normal mode analysis (NMA) was performed using the iModS (internal coordinates-based Molecular Dynamics and normal Modes for Structures) protocol to investigate the conformational flexibility of the protein structures [ ]. iModS integrates elastic network modeling and normal mode calculations to efficiently explore large-scale structural dynamics.

Techniques: Binding Assay, Residue, Functional Assay, Solvent