In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold.

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface.

Thermodynamic control of the polymerizability of five-, six-, and seven-membered lactones.

The thermodynamics of polymerization of epsilon-caprolactone and 1,4-dioxan-2-one has been investigated theoretically and compared with that recently reported for delta-valerolactone and gamma-butyrolactone. Specifically, the ability of these monomers to polymerize has been related to the strain of the rings, the Gibbs free energy of simple models for ring-opening reactions of the cyclic lactones, and the conformational preferences of linear model compounds of the corresponding homopolyesters. The results are fully consistent with the lack of polymerizability of gamma-butyrolactone, while the ring openings of epsilon-caprolactone and delta-valerolactone have been found to be exergonic processes.

Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: a molecular dynamics investigation.

The conformational tendencies of C(alpha,alpha)-diethylglycine (Deg)-based peptides have been studied in solution using all atom molecular dynamics simulations. Specifically, the conformational effects of breaking the symmetry of the host Tfa-(Deg)(5)-OtBu (Tfa, trifluoroacetyl; OtBu, tert-butoxy) pentapeptide with punctual replacements at different sequence positions of one Deg residue by its corresponding guest chiral analogue, L-alpha-aminobutyric acid (L-Abu), have been examined by simulating the following peptides: Tfa-(Deg)(5)-OtBu, Tfa-(Deg)(2)-L-Abu-(Deg)(2)-OtBu, Tfa-(Deg)(3)-L-Abu-Deg-OtBu, and Tfa-(Deg)(4)-L-Abu-OtBu. Simulations show that only the Deg homopeptide is able to stabilize a 2.