Dataset Information

Combined Adsorption and Reaction in the Ternary Mixture N₂, N₂O₄, NO₂ on MIL-127 Examined by Computer Simulations.

ABSTRACT: A high selectivity of NO _x over N₂ (simulating air) is found in silico when studying the adsorption of the ternary mixture N₂O₄/NO₂/N₂ on the metal-organic framework MIL-127(Fe) by molecular simulations under consideration of the recombination reaction N₂O₄ ? 2NO₂. The number of N atoms in nitrogen oxides NO _x and that in N₂ is used to define a selectivity of the combined adsorption and chemical recombination that can reach values of about 1000.

SUBMITTER: Fritzsche S

PROVIDER: S-EPMC7288586 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Publications

Combined Adsorption and Reaction in the Ternary Mixture N2, N2O4, NO2 on MIL-127 Examined by Computer Simulations.

Fritzsche Siegfried S Chokbunpiam Tatiya T Caro Jürgen J Hannongbua Supot S Janke Wolfhard W Remsungnen Tawun T

ACS omega 20200527 22

A high selectivity of NO x over N2 (simulating air) is found in silico when studying the adsorption of the ternary mixture N2O4/NO2/N2 on the metal-organic framework MIL-127(Fe) by molecular simulations under consideration of the recombination reaction N2O4 ↔ 2NO2. The number of N atoms in nitrogen oxides NO x and that in N2 is used to define a selectivity of the ...[more]

PMID: 32548487

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Project description:The relative orientation of the two variable domains, VH and VL , influences the shape of the antigen binding site, that is, the paratope, and is essential to understand antigen specificity. ABangle characterizes the VH -VL orientation by using five angles and a distance and compares it to other known structures. Molecular dynamics simulations of antibody variable domains (Fvs) reveal fluctuations in the relative domain orientations. The observed dynamics between these domains are confirmed by NMR experiments on a single-chain variable fragment antibody (scFv) in complex with IL-1β and an antigen-binding fragment (Fab). The variability of these relative domain orientations can be interpreted as a structural feature of antibodies, which increases the antibody repertoire significantly and can enlarge the number of possible binding partners substantially. The movements of the VH and VL domains are well sampled with molecular dynamics simulations and are in agreement with the NMR ensemble. Fast Fourier transformation of the ABangle metrics allows to assign timescales of 0.1-10 GHz to the fastest collective interdomain movements. The results clearly show the necessity of dynamics to understand and characterize the favorable orientations of the VH and VL domains implying a considerable binding interface flexibility and reveal in all antibody fragments (Fab, scFv, and Fv) very similar VH -VL interdomain variations comparable to the distributions observed for known X-ray structures of antibodies. SIGNIFICANCE STATEMENT: Antibodies have become key players as therapeutic agents. The binding ability of antibodies is determined by the antigen-binding fragment (Fab), in particular the variable fragment region (Fv). Antigen-binding is mediated by the complementarity-determining regions consisting of six loops, each three of the heavy and light chain variable domain VH and VL . The relative orientation of the VH and VL domains influences the shape of the antigen-binding site and is a major objective in antibody design. In agreement with NMR experiments and molecular dynamics simulations, we show a considerable binding site flexibility in the low nanosecond timescale. Thus we suggest that this flexibility and its implications for binding and specificity should be considered when designing and optimizing therapeutic antibodies.

Dataset Information

Combined Adsorption and Reaction in the Ternary Mixture N₂, N₂O₄, NO₂ on MIL-127 Examined by Computer Simulations.

Publications

Combined Adsorption and Reaction in the Ternary Mixture N<sub>2</sub>, N<sub>2</sub>O<sub>4</sub>, NO<sub>2</sub> on MIL-127 Examined by Computer Simulations.

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