Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.

Modeling membranes in situ

Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

In the last quarter-century, the field of molecular dynamics (MD) has undergone a remarkable transformation, propelled by substantial enhancements in software, hardware, and underlying methodologies. In this Perspective, we contemplate the future trajectory of MD simulations and their possible look at the year 2050. We spotlight the pivotal role of artificial intelligence (AI) in shaping the future of MD and the broader field of computational physical chemistry. We outline critical strategies and initiatives that are essential for the seamless integration of such technologies. Our discussion delves into topics like multiscale modeling, adept management of ever-increasing data deluge, the establishment of centralized simulation databases, and the autonomous refinement, cross-validation, and self-expansion of these repositories. The successful implementation of these advancements requires scientific transparency, a cautiously optimistic approach to interpreting AI-driven simulations and their analysis, and a mindset that prioritizes knowledge-motivated research alongside AI-enhanced big data exploration. While history reminds us that the trajectory of technological progress can be unpredictable, this Perspective offers guidance on preparedness and proactive measures, aiming to steer future advancements in the most beneficial and successful direction.

There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning

We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.

Reconstruction of the real 3D shape of the SARS-CoV-2 virus

The photographs of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus taken by electron transmission microscopy and cryoelectron microscopy provide only a 2D silhouette. The viruses appear to look like distorted circles. The present paper questions the real shape of the SARS-CoV-2 virus and makes an attempt to give an answer. Is this a general ellipsoid, a spheroid with rotational symmetry, a sphere, or something else? The answer requires the application of tools from three different disciplines: structural mechanics, microbiology, and statistics. A total of 590 virus photographs taken from 22 recently published papers were examined. From this experimental data pool, the histogram of diameter ratios was built from the 283 measurements where the virus images could be approximated as ellipses. The curve peaks at the diameter ratio of 1.22. The transformation equation for the spatial shape to the planar shade was derived for a fixed light source of the microscope. This equation involves an unknown orientation of the viruses with respect to the microscope. Two sets of models were developed, one with a uniform distribution of the virus orientation and the other with the orientation defined by the normalized beta distribution. In both sets of models, the unknown diameter ratio of the spheroidal virus was regarded as a random realization from translated gamma distributions. The parameters of the distribution of the kernel functions were determined by minimizing the mean square difference between the predicted and measured 2D histograms. The information included in the measured histograms was found to be insufficient to find an unknown distribution of the virus's orientation. Simply too many unknown parameters render the solution physically unrealistic. The minimization procedure with a uniform probability of virus orientation predicted the peak of the aspect ratio of the 3D spheroid at 1.32. Based on this result, models of the virus will be developed in the continuation of this research for a full dynamic analysis.

Glycans modulate lipid binding in Lili-Mip lipocalin protein: insights from molecular simulations and protein network analyses

The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.

When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases

Biomolecular research traditionally revolves around comprehending the mechanisms through which peptides or proteins facilitate specific functions, often driven by their relevance to clinical ailments. This conventional approach assumes that unraveling mechanisms is a prerequisite for wielding control over functionality, which stands as the ultimate research goal. However, an alternative perspective emerges from physics-based inverse design, shifting the focus from mechanisms to the direct acquisition of functional control strategies. By embracing this methodology, we can uncover solutions that might not have direct parallels in natural systems, yet yield crucial insights into the isolated molecular elements dictating functionality. This provides a distinctive comprehension of the underlying mechanisms.In this context, we elucidate how physics-based inverse design, facilitated by evolutionary algorithms and coarse-grained molecular simulations, charts a promising course for innovating the reverse engineering of biopolymers interacting with intricate fluid phases such as lipid membranes and liquid protein phases. We introduce evolutionary molecular dynamics (Evo-MD) simulations, an approach that merges evolutionary algorithms with the Martini coarse-grained force field. This method directs the evolutionary process from random amino acid sequences toward peptides interacting with complex fluid phases such as biological lipid membranes, offering significant promises in the development of peptide-based sensors and drugs. This approach can be tailored to recognize or selectively target specific attributes such as membrane curvature, lipid composition, membrane phase (e.g., lipid rafts), and protein fluid phases. Although the resulting optimal solutions may not perfectly align with biological norms, physics-based inverse design excels at isolating relevant physicochemical principles and thermodynamic driving forces governing optimal biopolymer interaction within complex fluidic environments. In addition, we expound upon how physics-based evolution using the Evo-MD approach can be harnessed to extract the evolutionary optimization fingerprints of protein-lipid interactions from native proteins. Finally, we outline how such an approach is uniquely able to generate strategic training data for predictive neural network models that cover the whole relevant physicochemical domain. Exploring challenges, we address key considerations such as choosing a fitting fitness function to delineate the desired functionality. Additionally, we scrutinize assumptions tied to system setup, the targeted protein structure, and limitations posed by the utilized (coarse-grained) force fields and explore potential strategies for guiding evolution with limited experimental data. This discourse encapsulates the potential and remaining obstacles of physics-based inverse design, paving the way for an exciting frontier in biomolecular research.

Force matching and iterative Boltzmann inversion coarse grained force fields for ZIF-8

Despite the intense activity at electronic and atomistic resolutions, coarse grained (CG) modeling of metal-organic frameworks remains largely unexplored. One of the main reasons for this is the lack of adequate CG force fields. In this work, we present iterative Boltzmann inversion and force matching (FM) force fields for modeling ZIF-8 at three different coarse grained resolutions. Their ability to reproduce structure, elastic tensor, and thermal expansion is evaluated and compared with that of MARTINI force fields considered in previous work [Alvares et al., J. Chem. Phys. 158, 194107 (2023)]. Moreover, MARTINI and FM are evaluated for their ability to depict the swing effect, a subtle phase transition ZIF-8 undergoes when loaded with guest molecules. Overall, we found that all our force fields reproduce structure reasonably well. Elastic constants and volume expansion results are analyzed, and the technical and conceptual challenges of reproducing them are explained. Force matching exhibits promising results for capturing the swing effect. This is the first time these CG methods, widely applied in polymer and biomolecule communities, are deployed to model porous solids. We highlight the challenges of fitting CG force fields for these materials.

Developing inhibitory peptides against SARS-CoV-2 envelope protein

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected approximately 800 million people since the start of the Coronavirus Disease 2019 (COVID-19) pandemic. Because of the high rate of mutagenesis in SARS-CoV-2, it is difficult to develop a sustainable approach for prevention and treatment. The Envelope (E) protein is highly conserved among human coronaviruses. Previous studies reported that SARS-CoV-1 E deficiency reduced viral propagation, suggesting that E inhibition might be an effective therapeutic strategy for SARS-CoV-2. Here, we report inhibitory peptides against SARS-CoV-2 E protein named iPep-SARS2-E. Leveraging E-induced alterations in proton homeostasis and NFAT/AP-1 pathway in mammalian cells, we developed screening platforms to design and optimize the peptides that bind and inhibit E protein. Using Vero-E6 cells, human-induced pluripotent stem cell-derived branching lung organoid and mouse models with SARS-CoV-2, we found that iPep-SARS2-E significantly inhibits virus egress and reduces viral cytotoxicity and propagation in vitro and in vivo. Furthermore, the peptide can be customizable for E protein of other human coronaviruses such as Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The results indicate that E protein can be a potential therapeutic target for human coronaviruses.

Mechanisms of allostery at the viral surface through the eyes of molecular simulation

The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome. A limited number of proteins on the virion surface must perform a multitude of functions in order to orchestrate the viral life cycle, and allostery can regulate their structures at multiple levels of organization, spanning individual molecules, protomers, large oligomeric assemblies, or entire viral surfaces. Here, we review recent contributions from the molecular simulation field to viral surface allostery, with a particular focus on the trimeric spike glycoprotein emerging from the coronavirus surface, and the icosahedral flaviviral envelope complex. As emerging viral pathogens continue to pose a global threat, an improved understanding of viral dynamics and allosteric regulation will prove crucial in developing novel therapeutic strategies.

Mesoscale simulation of biomembranes with FreeDTS

We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.

Inferring mechanical properties of the SARS-CoV-2 virus particle with nano-indentation tests and numerical simulations

The pandemic caused by the SARS-CoV-2 virus has claimed more than 6.5 million lives worldwide. This global challenge has led to accelerated development of highly effective vaccines tied to their ability to elicit a sustained immune response. While numerous studies have focused primarily on the spike (S) protein, less is known about the interior of the virus. Here we propose a methodology that combines several experimental and simulation techniques to elucidate the internal structure and mechanical properties of the SARS-CoV-2 virus. The mechanical response of the virus was analyzed by nanoindentation tests using a novel flat indenter and evaluated in comparison to a conventional sharp tip indentation. The elastic properties of the viral membrane were estimated by analytical solutions, molecular dynamics (MD) simulations on a membrane patch and by a 3D Finite Element (FE)-beam model of the virion's spike protein and membrane molecular structure. The FE-based inverse engineering approach provided a reasonable reproduction of the mechanical response of the virus from the sharp tip indentation and was successfully verified against the flat tip indentation results. The elastic modulus of the viral membrane was estimated in the range of 7-20 MPa. MD simulations showed that the presence of proteins significantly reduces the fracture strength of the membrane patch. However, FE simulations revealed an overall high fracture strength of the virus, with a mechanical behavior similar to the highly ductile behavior of engineering metallic materials. The failure mechanics of the membrane during sharp tip indentation includes progressive damage combined with localized collapse of the membrane due to severe bending. Furthermore, the results support the hypothesis of a close association of the long membrane proteins (M) with membrane-bound hexagonally packed ribonucleoproteins (RNPs). Beyond improved understanding of coronavirus structure, the present findings offer a knowledge base for the development of novel prevention and treatment methods that are independent of the immune system.

Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling

Methylene blue has multiple antiviral properties against Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2). The ability of methylene blue to inhibit different stages of the virus life cycle, both in light-independent and photodynamic processes, is used in clinical practice. At the same time, the molecular aspects of the interactions of methylene blue with molecular components of coronaviruses are not fully understood. Here, we use Brownian dynamics to identify methylene blue binding sites on the SARS-CoV-2 envelope. The local lipid and protein composition of the coronavirus envelope plays a crucial role in the binding of this cationic dye. Viral structures targeted by methylene blue include the S and E proteins and negatively charged lipids. We compare the obtained results with known experimental data on the antiviral effects of methylene blue to elucidate the molecular basis of its activity against coronaviruses.

Pragmatic Coarse-Graining of Proteins: Models and Applications

The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.

Self-Association of ACE-2 with Different RBD Amounts: A Dynamic Simulation Perspective on SARS-CoV-2 Infection

Transmissibility of SARS-CoV-2 initially relies on its trimeric Spike-RBDs to tether the ACE-2 on host cells, and enhanced self-association of ACE-2 engaged with Spike facilitates the viral infection. Two primary packing modes of Spike-ACE2 heteroproteins exist potentially due to discrepant amounts of RBDs loading on ACE-2, but the resultant self-association difference is inherently unclear. We used extensive coarse-grained dynamic simulations to characterize the self-association efficiency, the conformation relevance, and the molecular mechanism of ACE-2 with different RBD amounts. It was revealed that the ACE-2 hanging two/full RBDs (Mode-A) rapidly dimerized into the heteroprotein complex in a compact "linear" conformation, while the bare ACE-2 showed weakened self-association and a protein complex. The RBD-tethered ectodomains of ACE-2 presented a more upright conformation relative to the membrane, and the intermolecular ectodomains were predominantly packed by the neck domains, which was obligated to the rapid protein self-association in a compact pattern. Noted is the fact that the ACE-2 tethered by a single RBD (Mode-B) retained considerable self-association efficiency and clustering capability, which unravels the interrelation of ACE-2 colocalization and protein cross-linkage. The molecular perspectives in this study expound the self-association potency of ACE-2 with different RBD amounts and the viral activity implications, which can greatly enhance our comprehension of SARS-CoV-2 infection details.

Understanding Virus Structure and Dynamics through Molecular Simulations

Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.