Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2.

The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We have previously reported the design and characterization of a mammalian cell expressed RBD derivative, mRBD1-3.2, that has higher thermal stability and greatly enhanced immunogenicity relative to the wild type mRBD. The protein is highly thermotolerant and immunogenic and is being explored for use in room temperature stable Covid-19 vaccine formulations. In the current study, we have investigated the folding pathway of both WT and stabilized RBD. It was found that chemical denaturation of RBD proceeds through a stable equilibrium intermediate. Thermal and chemical denaturation is reversible, as assayed by binding to the receptor ACE2. Unusually, in its native state, RBD binds to the hydrophobic probe ANS, and enhanced ANS binding is observed for the equilibrium intermediate state. Further characterization of the folding of mRBD1-3.2, both in solution and after reconstitution of lyophilized protein stored for a month at 37 °C, revealed a higher stability represented by higher Cm, faster refolding, slower unfolding, and enhanced resistance to proteolytic cleavage relative to WT. In contrast to WT RBD, the mutant showed decreased interaction with the hydrophobic moiety linoleic acid. Collectively, these data suggest that the enhanced immunogenicity results from reduced conformational fluctuations that likely enhance in vivo half-life as well as reduce the exposure of irrelevant non-neutralizing epitopes to the immune system.

News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting.

Since the formalization of the Central Dogma of molecular biology, the relevance of RNA in modulating the flow of information from DNA to proteins has been clear. More recently, the discovery of a vast set of non-coding transcripts involved in crucial aspects of cellular biology has renewed the enthusiasm of the RNA community. Moreover, the remarkable impact of RNA therapies in facing the COVID19 pandemics has bolstered interest in the translational opportunities provided by this incredible molecule. For all these reasons, the Italian Society of Biophysics and Molecular Biology (SIBBM) decided to dedicate its 17th yearly meeting, held in June 2022 in Rome, to the many fascinating aspects of RNA biology. More than thirty national and international speakers covered the properties, modes of action and applications of RNA, from its role in the control of development and cell differentiation to its involvement in disease. Here, we summarize the scientific content of the conference, highlighting the take-home message of each presentation, and we stress the directions the community is currently exploring to push forward our comprehension of the RNA World 3.0.

Electrostatics in Computational Biophysics and Its Implications for Disease Effects.

This review outlines the role of electrostatics in computational molecular biophysics and its implication in altering wild-type characteristics of biological macromolecules, and thus the contribution of electrostatics to disease mechanisms. The work is not intended to review existing computational approaches or to propose further developments. Instead, it summarizes the outcomes of relevant studies and provides a generalized classification of major mechanisms that involve electrostatic effects in both wild-type and mutant biological macromolecules. It emphasizes the complex role of electrostatics in molecular biophysics, such that the long range of electrostatic interactions causes them to dominate all other forces at distances larger than several Angstroms, while at the same time, the alteration of short-range wild-type electrostatic pairwise interactions can have pronounced effects as well. Because of this dual nature of electrostatic interactions, being dominant at long-range and being very specific at short-range, their implications for wild-type structure and function are quite pronounced. Therefore, any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could be the dominant factor contributing to pathogenicity. However, we also outline that due to the plasticity of biological macromolecules, the effect of amino acid mutation may be reduced, and thus a charge deletion or insertion may not necessarily be deleterious.

Highlights from Faraday discussion 232: Peptide-membrane interactions, 8th-10th September 2021 (online).

The Faraday discussions meeting on peptide-membrane interactions was designed with the goal of repositioning peptides as powerful model systems that are indispensable in contemporary membrane biophysics and biology research. The meeting, originally scheduled for September 2020, was finally held in a virtual format during September 8th-10th, 2021 due to the COVID-19 pandemic. The meeting saw enthusiastic participation by ∼120 scientists from 23 countries. There were 23 talks delivered during the four sessions and 25 posters presented in two poster sessions (the published volume can be accessed online). The meeting drew attention to the multitude of open questions that persist in our understanding of the behavior of membrane peptides and proteins in spite of nearly half-a-century of intensive interdisciplinary research, and was beyond successful in throwing into sharp relief the enduring relevance of exploring membrane biophysics and biology through the looking glass of peptide-membrane interactions.

Strategies adopted by undergraduate teaching assistants in physiology and biophysics education during the COVID-19 pandemic.

The COVID-19 pandemic affected almost all aspects of our lives, including the education sector and the way of teaching and learning. In March 2020, health authorities in Brazil imposed social isolation and the interruption of on-site activities in schools and universities. In this context, the Federal University of Minas Gerais (UFMG), one of the largest universities in Brazil and Latin America, developed an emergency remote learning (ERL) plan that allowed the return of classes in an online format and supported students to obtain access to equipment and internet network. Within this new perspective, the Undergraduate Teaching Assistant (UTA) program of the Department of Physiology and Biophysics (DFIB) explored strategies to minimize the impact of the absence of face-to-face classes. Using different available tools in online platforms and social media such as Microsoft Teams, YouTube animated video classes, and Instagram, the UTA program assisted >500 undergraduate students and strongly supported professors during ERL. In just over a year, our video classes on YouTube Channel reached ∼40,000 views. Most of the students reported that their questions were fully and quickly solved by the UTA program. Collectively, our results indicate that the strategies implemented by the UTA program helped the undergraduate students and professors to adapt to a remote learning format.

Statistical mechanics study of the introduction of a vaccine against COVID-19 disease.

By the end of 2020, a year since the first cases of infection by the Covid-19 virus have been reported; several pharmaceutical companies made significant progress in developing effective vaccines against the Covid-19 virus that has claimed the lives of more than 10^{6} people over the world. On the other hand, there is growing evidence of re-infection by the virus, which can cause further outbreaks. In this paper, we apply statistical physics tools to examine theoretically the vaccination rate required to control the pandemic for three different vaccine efficiency scenarios and five different vaccination rates. Also, we study the effect of temporal restrictions or reliefs on the pandemic's outbreak, assuming that re-infection is possible. When examining the efficiency of the vaccination rate of the general population in preventing an additional outbreak of the disease, we find that a high vaccination rate (where 0.3% of the population is vaccinated daily, which is equivalent to ≈10^{6} vaccine doses in the United States daily) is required to gain control over the spread of the virus without further restrictions.

Evolution of biophysical tools for quantitative protein interactions and drug discovery.

With millions of signalling events occurring simultaneously, cells process a continuous flux of information. The genesis, processing, and regulation of information are dictated by a huge network of protein interactions. This is proven by the fact that alterations in the levels of proteins, single amino acid changes, post-translational modifications, protein products arising out of gene fusions alter the interaction landscape leading to diseases such as congenital disorders, deleterious syndromes like cancer, and crippling diseases like the neurodegenerative disorders which are often fatal. Needless to say, there is an immense effort to understand the biophysical basis of such direct interactions between any two proteins, the structure, domains, and sequence motifs involved in tethering them, their spatio-temporal regulation in cells, the structure of the network, and their eventual manipulation for intervention in diseases. In this chapter, we will deliberate on a few techniques that allow us to dissect the thermodynamic and kinetic aspects of protein interaction, how innovation has rendered some of the traditional techniques applicable for rapid analysis of multiple samples using small amounts of material. These advances coupled with automation are catching up with the genome-wide or proteome-wide studies aimed at identifying new therapeutic targets. The chapter will also summarize how some of these techniques are suited either in the standalone mode or in combination with other biophysical techniques for the drug discovery process.

The Contribution of Biophysics and Structural Biology to Current Advances in COVID-19.

Critical to viral infection are the multiple interactions between viral proteins and host-cell counterparts. The first such interaction is the recognition of viral envelope proteins by surface receptors that normally fulfil other physiological roles, a hijacking mechanism perfected over the course of evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has successfully adopted this strategy using its spike glycoprotein to dock on the membrane-bound metalloprotease angiotensin-converting enzyme 2 (ACE2). The crystal structures of several SARS-CoV-2 proteins alone or in complex with their receptors or other ligands were recently solved at an unprecedented pace. This accomplishment is partly due to the increasing availability of data on other coronaviruses and ACE2 over the past 18 years. Likewise, other key intervening actors and mechanisms of viral infection were elucidated with the aid of biophysical approaches. An understanding of the various structurally important motifs of the interacting partners provides key mechanistic information for the development of structure-based designer drugs able to inhibit various steps of the infective cycle, including neutralizing antibodies, small organic drugs, and vaccines. This review analyzes current progress and the outlook for future structural studies.

Modeling Immunity In Vitro: Slices, Chips, and Engineered Tissues.

Modeling immunity in vitro has the potential to be a powerful tool for investigating fundamental biological questions, informing therapeutics and vaccines, and providing new insight into disease progression. There are two major elements to immunity that are necessary to model: primary immune tissues and peripheral tissues with immune components. Here, we systematically review progress made along three strategies to modeling immunity: ex vivo cultures, which preserve native tissue structure; microfluidic devices, which constitute a versatile approach to providing physiologically relevant fluid flow and environmental control; and engineered tissues, which provide precise control of the 3D microenvironment and biophysical cues. While many models focus on disease modeling, more primary immune tissue models are necessary to advance the field. Moving forward, we anticipate that the expansion of patient-specific models may inform why immunity varies from patient to patient and allow for the rapid comprehension and treatment of emerging diseases, such as coronavirus disease 2019.