Institute of Fundamental Technological Research

Rational design of novel antibody therapeutics against viral infections such as coronavirus relies on surface complementarity and high affinity for their effectiveness. Here, we explore an additional property of protein complexes, the intrinsic mechanical stability, in SARS-CoV-2 variants when complexed with a potent antibody. In this study, we utilized a recent implementation of the GōMartini 3 approach to investigate large conformational changes in protein complexes with a focus on the mechanostability of the receptor-binding domain (RBD) from WT, Alpha, Delta, and XBB.1.5 variants in complex with the H11-H4 nanobody. The analysis revealed moderate differences in mechanical stability among these variants. Also, we identified crucial residues in both the RBD and certain protein segments in the nanobody that contribute to this property. By performing pulling simulations and monitoring the presence of specific native and non-native contacts across the protein complex interface, we provided mechanistic insights into the dissociation process. Force-displacement profiles indicate a tensile force clamp mechanism associated with the type of protein complex. Our computational approach not only highlights the key mechanostable interactions that are necessary to maintain overall stability, but it also paves the way for the rational design of potent antibodies that are mechanostable and effective against emergent SARS-CoV-2 variants.

SARS-CoV-2, GōMartini 3, Nanomechanics, Protein complexes, protein engineering, MD, native contacts

The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.

COVID-19, SARS-CoV-2, spike protein, RBD, structural stability, large conformational changes, protein complexes, free energy, molecular dynamics, dynamics contact analysis

We report on the novel observation about the gain in mechanical stability of the SARS-CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our findings have several biological implications in the subfamily of coronaviruses, as they suggest that the receptor binding domain (RBD) (~200 amino acids) plays a fundamental role as a damping element of the massive viral particle's motion prior to cell-recognition, while also facilitating viral attachment, fusion and entry. The mechanical stability via pulling of the RBD is 250 pN and 200 pN for CoV2 and CoV1 respectively, and the additional stability observed for CoV2 (~50 pN) might play a role in the increasing spread of COVID-19.

Type IV pili (T4P) are biopolymers comprised of many protein subunits called pilin. These pilin subunits are not covalently bonded to one another, however remarkably T4P filaments are very strong and flexible. T4P emanate from the surface of prokaryotic cells and are utilized for many functions, including biofilm formation, surface adhesion, motility, and infection. The recent cryo-EM based structures for T4P from Escherichia coli, Neisseria meningitidis, Pseudomonas aeruginosa, and Neisseria gonorrhoeae have provided unprecedented insights into the structures of these filaments. However, although the structures of T4P are known, the dynamics of these filaments at the molecular scale at equilibrium and under tensile forces is not well characterized. In this work we provide an overview of our research into these various T4P filaments and their constituent pilin monomers under force. Specifically we carried out steered molecular dynamics simulations using a multiscale approach encompassing all-atom simulations and two levels of coarse-grained simulation. We have analyzed the changes in secondary structure of pilin subunits, global changes in filament architecture, and calculated the Young's modulus of each of the different T4P filaments. By drawing comparisons between all of these filament systems, we are able to obtain a broader picture of T4P dynamics than experimental structures alone can provide. In particular, we observe elongation of the alpha helix region of pilin subunits in each of these systems, which has been previously attributed to T4P flexibility and strength.

filament, molecular dynamics, coarse graining, T4P