Transient hydrophobic exposure in the molecular dynamics of Abeta peptide at low water concentration

Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We subjected Abeta40 to 100 different simulations with variable water cell size. We show that even for this disordered aggregation-prone peptide, many properties are not cell-size dependent, i.e. a small cell is easily justified. The radius of gyration, intra-peptide, and peptide-water hydrogen bonds are well-sampled by short (50 ns) time scales at any cell size. Abeta is mainly disordered with 0-30% alpha helix but undergoes consistent alpha-beta transitions up to 14% strand in 5-10% of the simulations regardless of cell size. The similar prevalence in long and short simulations indicate small diffusion barriers for structural transitions in contrast to folded globular proteins, which we suggest is a defining hallmark of intrinsically disordered proteins. Importantly, the hydrophobic surface increases significantly in small cells (confidence level 95%, two-tailed t-test), as does the variation in exposure and backbone conformations (>40% and >27% increased standard deviations). Whereas hydrophilic exposure dominates hydrophobic exposure in large cells, this tendency breaks down at low water concentration. We interpret these findings as a concentration-dependent hydrophobic effect, with the small water layer unable to keep the protein unexposed, an effect mainly caused by the layered water-water interactions, not by the peptide dynamics. The exposure correlates with radius of gyration (R2 0.35-0.50) and could be important in crowded environments, e.g. the synaptic cleft

Molecular dynamics derived life times of active substrate binding poses explain K_M of laccase mutants

Fungal laccases (EC 1.10.3.2) are important multi-copper oxidases with broad substrate specificity. Laccases from Trametes versicolor (TvL) are among the best-characterized of these enzymes. Mutations in the substrate-binding site of TvL substantially affect K(M), but a molecular understanding of this effect is missing. We explored the effect of TvL mutations on K(M) for the standard laccase substrate 2,6-dimethoxyphenol using 4500 ns of molecular dynamics, docking, and MMGBSA free energy computations. We show that changes in K(M) due to mutation consistently correlate with the dynamics of the substrates within the substrate-binding site. We find that K(M) depends on the lifetime (“dynamic stability”) of the enzyme-substrate complex as commonly assumed. We then further show that MMGBSA-derived free energies of substrate binding in the active pose consistently reproduce large vs. small experimental K(M) values. Our results indicate that hydrophobic packing of the substrate near the T1 binding site of the laccase is instrumental for high turnover via K(M). We also address the more general question of how enzymes such as laccases gain advantage of lower K(M) despite the Sabatier principle, which disfavors a stable enzyme–substrate complex. Our data suggest that the observed K(M) relates directly to the lifetime of the active substrate pose within a protein. In contrast, the thermochemical stability of the enzyme–substrate complex reflects an ensemble average of all enzyme–substrate binding poses. This distinction may explain how enzymes work by favoring longer residence time in the active pose without too favorable general enzyme–substrate interactions, a principle that may aid the rational design of enzymes

Anti-bacterial activity of neoandrographolide derivatives: In silico interaction with the bacterial target

157-164Natural products and their semi synthesized molecules have been used as efficient antibiotics since a long time. The present global health scenario has raised the demand for novel antimicrobial agents and drug targets that are effective against drug resistant pathogens, emerging infections etc. The current study has promoted the antibacterial activity of the glucoside labdane ‘neoandrographolide’, isolated from the methanolic extract of the medicinal plant Andrographis paniculata. Further modification at its glucoside hydroxyl groups to generate ester and acetonide derivatives was done and the antibacterial potential of these compounds was screened against common bacterial pathogens. Among various derivatives, 4,6-O-(4-methoxybenzylidene) neoandrographolide exhibited promising results. In addition, molecular modeling study of the active compound was also explored to identify its probable binding mode on the bacterial target. The present study reported antibacterial activity of neoandrographolide derivatives for first time and also the bioactive molecule, 4,6-O-(4-methoxybenzylidene) neoandrographolide was examined as a potent antibacterial agent against different strains

Structure and Mutations of SARS-CoV‑2 Spike Protein:A Focused Overview

[Image: see text] The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure–function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure–function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure–function relationships

Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures:SARS-CoV-2 spike-protein mutations as a test case

Protein structures may be used to draw functional implications at the residue level, but how sensitive are these implications to the exact structure used? Calculation of the effects of SARS-CoV-2 S-protein mutations based on experimental cryo-electron microscopy structures have been abundant during the pandemic. To understand the precision of such estimates, we studied three distinct methods to estimate stability changes for all possible mutations in 23 different S-protein structures (3.69 million ΔΔG values in total) and explored how random and systematic errors can be remedied by structure-averaged mutation group comparisons. We show that computational estimates have low precision, due to method and structure heterogeneity making results for single mutations uninformative. However, structure-averaged differences in mean effects for groups of substitutions can yield significant results. Illustrating this protocol, functionally important natural mutations, despite individual variations, average to a smaller stability impact compared to other possible mutations, independent of conformational state (open, closed). In summary, we document substantial issues with precision in structure-based protein modeling and recommend sensitivity tests to quantify these effects, but also suggest partial solutions to the problem in the form of structure-averaged “ensemble” estimates for groups of residues when multiple structures are available. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00249-022-01619-8

Predicting virus Fitness: Towards a structure-based computational model

Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host