SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern.

The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.

Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences.

SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.

Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations.

Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.

Stability and reactivity of ϵ-χ-θ iron carbide catalyst phases in Fischer-Tropsch synthesis: controlling µ(C).

The stability and reactivity of ϵ, χ, and θ iron carbide phases in Fischer-Tropsch synthesis (FTS) catalysts as a function of relevant reaction conditions was investigated by a synergistic combination of experimental and theoretical methods. Combined in situ X-ray Absorption Fine Structure Spectroscopy/X-ray Diffraction/Raman Spectroscopy was applied to study Fe-based catalysts during pretreatment and, for the first time, at relevant high pressure Fischer-Tropsch synthesis conditions, while Density Functional Theory calculations formed a fundamental basis for understanding the influence of pretreatment and FTS conditions on the formation of bulk iron carbide phases. By combining theory and experiment, it was found that the formation of θ-Fe(3)C, χ-Fe(5)C(2), and ϵ-carbides can be explained by their relative thermodynamic stability as imposed by gas phase composition and temperature. Furthermore, it was shown that a significant part of the Fe phases was present as amorphous carbide phases during high pressure FTS, sometimes in an equivalent amount to the crystalline iron carbide fraction. A catalyst containing mainly crystalline χ-Fe(5)C(2) was highly susceptible to oxidation during FTS conditions, while a catalyst containing θ-Fe(3)C and amorphous carbide phases showed a lower activity and selectivity, mainly due to the buildup of carbonaceous deposits on the catalyst surface, suggesting that amorphous phases and the resulting textural properties play an important role in determining final catalyst performance. The findings further uncovered the thermodynamic and kinetic factors inducing the ϵ-χ-θ carbide transformation as a function of the carbon chemical potential µ(C).

Charging of Au atoms on TiO2 thin films from CO vibrational spectroscopy and DFT calculations.

Au atoms have been deposited on oxidized and reduced TiO2 thin films grown on Mo(110). The gold binding sites and the occurrence of Au-TiO2 charge transfer were identified by measuring infrared spectra as a function of temperature and substrate preparation. The results have been interpreted by slab model DFT calculations. Au binds weakly to regular TiO2 sites (De < 0.5 eV) where it remains neutral, and diffuses easily even at low temperature until it gets trapped at strong binding sites such as oxygen vacancies (De = 1.7 eV). Here, a charge transfer from TiO2 to Au occurs. Au(delta-)CO complexes formed on oxygen vacancies easily lose CO (De = 0.4 eV), and the CO stretching frequency is red-shifted. On nondefective surfaces, CO adsorption induces a charge transfer from Au to TiO2 with formation of strongly bound Audelta+CO complexes (De = 2.4 eV); the corresponding CO frequency is blue-shifted with respect to free CO. We propose possible mechanisms to reconcile the observed CO desorption around 380 K with the unusually high stability of Au-CO complexes formed on regular sites predicted by the calculations. This implies: (a) diffusion of AuCO complexes above 150 K; (b) formation of gold dimers when the diffusing AuCO complex encounters a Au atom bound to an oxygen vacancy (reduced TiO2) or a second AuCO unit (oxidized TiO2); and (c) CO desorption from the resulting dimer, occurring around 350-400 K.

Cationic and anionic vacancies on the NiO(100) surface: DFT+U and hybrid functional density functional theory calculations.

The electronic structure of oxygen and nickel vacancies at the surface of NiO(100) has been investigated theoretically by means of density functional theory (DFT) comparing plane wave density functional theory with the Hubbard correction DFT+U with atomic-orbital-hybrid-functional (20% exact-exchange) calculations. The two approaches provide a similar description of the nature of the oxygen vacancy. At variance with the same defect center in MgO, where two electrons are trapped in the vacancy, on NiO the charge is more delocalized, partly over the Ni ions around the vacancy, the rest either trapped in the vacancy or delocalized over other Ni ions. Concerning the nickel vacancy, both methods clearly show that the removal of a neutral Ni atom does not result in the oxidation of other nickel ions from Ni2+ to Ni3+ but rather in the formation of two holes in the O 2p valence band. However, the description is slightly different with the approaches, the hybrid functional indicates that the holes are essentially localized on the oxygen ions nearest to the vacancy, while they result much more delocalized from the DFT+U calculation. Comparison with the corresponding results, obtained with the two methods for the case of the Mg vacancy in MgO, suggests that the DFT+U approach does not adequately correct for the self-interaction of the unpaired electrons in this case. However, the overall picture that emerges clearly from the present calculations is that both defects affect the electronic structure in a much wider region in NiO than in MgO.