Structural insights into outer membrane protein biogenesis in pathogenic Neisseria.

N. gonorrhoeae (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, infertility, and blindness.

Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules.

Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached across a wide range of disciplines. In this tutorial, we present a cursory introduction to three widely used ML techniques─logistic regression, random forest, and multilayer perceptron─applied toward analyzing molecular dynamics (MD) trajectory data.

Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly.

An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nucleocapsid assembly, retaining its structure, or misdirect it into noncapsid-like particles. Previous molecular dynamics (MD) simulations of early capsid-assembly intermediates showed differences in protein conformations for the apo and bound states.

The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes.

Proper codon/anticodon pairing within the ribosome necessitates linearity of the transcript. Any structures formed within a messenger RNA (mRNA) must be unwound before the respective codon is interpreted. Linearity, however, is not always the norm; some intricate structures within mRNA are able to exert unique ribosome/mRNA interactions to regulate translation.

Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.

Molecular dynamics (MD) simulations provide a detailed description of biophysical processes allowing mechanistic questions to be addressed at the atomic level. The promise of such approaches is partly hampered by well known sampling issues of typical simulations, where time scales available are significantly shorter than the process of interest. For the system of interest here, the binding of modulators of Hepatitis B virus capsid self-assembly, the binding site is at a flexible protein-protein interface.

DeepPath: Overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.

The structural dynamics of proteins play a crucial role in their function, yet most experimental and deep learning methods produce only static models. While molecular dynamics (MD) simulations provide atomistic insight into conformational transitions, they remain computationally prohibitive, particularly for large-scale motions. Here, we introduce DeepPath, a deep-learning-based framework that rapidly generates physically realistic transition pathways between known protein states.

Probing the Dynamics of Yersinia Adhesin A (YadA) in Outer Membranes Hints at Requirements for β-Barrel Membrane Insertion.

The vast majority of cells are protected and functionalized by a dense surface layer of glycans, proteoglycans, and glycolipids. This surface represents an underexplored space in structural biology that is exceedingly challenging to recreate in vitro. Here, we investigate β-barrel protein dynamics within an asymmetric outer membrane environment, with the trimeric autotransporter Yersinia adhesin A (YadA) as an example.

Conserved lipid-facing basic residues promote the insertion of the porin OmpC into the outer membrane.

Almost all integral membrane proteins that reside in the outer membrane (OM) of gram-negative bacteria contain a closed amphipathic β sheet ("β barrel") that serves as a membrane anchor. The membrane integration of β barrel structures is catalyzed by a highly conserved heterooligomer called the arrel ssembly achine (BAM). Although charged residues that are exposed to the lipid bilayer are infrequently found in outer membrane protein β barrels, the β barrels of OmpC/OmpF-type trimeric porins produced by Enterobacterales contain multiple conserved lipid-facing basic residues located near the extracellular side of the OM.

Machine learning of molecular dynamics simulations provides insights into modulation of viral capsid assembly.

An effective approach in the development of novel antivirals is to target the assembly of viral capsids using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nucleocapsid assembly, retaining its structure, or misdirect it into non-capsid-like particles. Previous molecular dynamics (MD) simulations of early capsid-assembly intermediates showed differences in protein conformations for apo and bound states.

Mg-dependent mechanism of environmental versatility in a multidrug efflux pump.

Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are major drivers of multidrug resistance among gram-negative bacteria. Cations, such as Mg, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg and pH in modulating the structural dynamics of the periplasmic adapter protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug pump from Escherichia coli.

Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA.

Recent studies have demonstrated BamA, the central component of the β-barrel assembly machinery (BAM), as an important therapeutic target to combat infections caused by Acinetobacter baumannii and other Gram-negative pathogens. Homology modeling indicates BamA in A. baumannii consists of five polypeptide transport-associated (POTRA) domains and a β-barrel membrane domain.

Molecular Dynamics Reveals Altered Interactions between Belzutifan and HIF-2 with Natural Variant G323E or Proximal Phosphorylation at T324.

In patients with von-Hippel Lindau (VHL) disease, hypoxia-independent accumulation of HIF-2α leads to increased transcriptional activity of HIF-2α:ARNT that drives cancers such as renal cell carcinoma. Belzutifan, a recently FDA-approved drug, is designed to prevent the transcriptional activity of HIF-2α:ARNT, thereby overcoming the consequences of its unnatural accumulation in VHL-dependent cancers. Emerging evidence suggests that the naturally occurring variant G323E located in the HIF-2α drug binding pocket prevents inhibitory activity of belzutifan analogs, though the mechanism of inhibition remains unclear.

Allosteric coupling of substrate binding and proton translocation in MmpL3 transporter from .

Infections caused by spp. are very challenging to treat, and multidrug-resistant strains rapidly spread in human populations. Major contributing factors include the unique physiological features of these bacteria, drug efflux, and the low permeability barrier of their outer membrane.

Broadening access to small-molecule parameterization with the force field toolkit.

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g.

Mg-dependent mechanism of environmental versatility in a multidrug efflux pump.

Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell.

SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii.

Reactions that occur within the lipid membrane involve, at minimum, ternary complexes among the enzyme, substrate, and lipid. For many systems, the impact of the lipid in regulating activity or oligomerization state is poorly understood. Here, we used small-angle neutron scattering (SANS) to structurally characterize an intramembrane aspartyl protease (IAP), a class of membrane-bound enzymes that use membrane-embedded aspartate residues to hydrolyze transmembrane segments of biologically relevant substrates.

Thicket and Mesh: How the Outer Membrane Can Resist Tension Imposed by the Cell Wall.

The cell envelope of Gram-negative bacteria is composed of an outer membrane (OM) and an inner membrane (IM) and a peptidoglycan cell wall (CW) between them. Combined with Braun's lipoprotein (Lpp), which connects the OM and the CW, and numerous membrane proteins that exist in both OM and IM, the cell envelope creates a mechanically stable environment that resists various physical and chemical perturbations to the cell, including turgor pressure caused by the solute concentration difference between the cytoplasm of the cell and the extracellular environment. Previous computational studies have explored how individual components (OM, IM, and CW) can resist turgor pressure although combinations of them have been less well studied.

Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile.

SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding in proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics and disulfide bonding of recombinant spike proteins derived from the SARS-CoV-2 Omicron variant (B.1.

Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations.

Recent advances in molecular dynamics (MD) simulations have led to rapid improvement in our understanding of the molecular details of the outer membranes (OMs) of Gram-negative bacteria. In this review, we highlight the latest discoveries from MD simulations of OMs, shedding light on the dynamic nature of these bacteria's first line of defense. With the focus on cutting-edge approaches, we explore the OM's sensitivity to structural features, including divalent cations and membrane composition, which have emerged as crucial determinants of antimicrobial passage.

Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10.

Doa10 (MARCHF6 in metazoans) is a large polytopic membrane-embedded E3 ubiquitin ligase in the endoplasmic reticulum (ER) that plays an important role in quality control of cytosolic and ER proteins. Although Doa10 is highly conserved across eukaryotes, it is not understood how Doa10 recognizes its substrates. Here, we define the substrate recognition mechanism of Doa10 by structural and functional analyses on Saccharomyces cerevisiae Doa10 and its model substrates.

Generative β-hairpin design using a residue-based physicochemical property landscape.

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe.

From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all.

In this issue of Structure, Heo and Feig present cg2all, a novel deep-learning model capable of efficiently predicting all-atom protein structures from coarse-grained (CG) representations. The model maintains high accuracy, even when the CG model is simplified to a single bead per residue, and has a number of promising applications.