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. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

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. Polymerizability of 1,4-dioxan-2-one has been found to be favored, even though less than that of epsilon-caprolactone and delta-valerolactone. Two factors explain these features: (i) the strain of the ester group in the lactones increases with the exergonic character of the ring-opening process, and (ii) the stability of coiled conformations in model compounds follows this order: poly-4-hydroxybutyrate > poly(1,4-dioxan-2-one) > poly-6-hydroxycaproate approximately poly-5-hydroxyvalerate. Finally, the influence of the environment on the polymerizability of the three cyclic lactones is discussed in detail.

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 2.0(5) helix, even though a kinked arrangement with all the Deg residues adopting a fully-extended conformation was found to be stable when the L-Abu residue is introduced in the middle of the sequence. On the other hand, when the L-Abu residue is closer to the C-end of the sequence, the peptide chain prefers a partially folded 3(10)-helix. Additional simulations on Tfa-(Deg)(3)-L-Abu-(Deg)(3)-OtBu highlighted that, when the size of the Deg segments increases, their tendency to adopt a 2.0(5) helix predominates over the preferred folded conformation of L-Abu. The overall picture extracted after more than 300 ns of molecular dynamics simulation is that breaking the alpha-carbon symmetry of achiral C(alpha)-tetrasubstituted amino acids is a promising strategy to build up polypeptides with modulated conformational tendencies.