Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach.

Redox processes are an important step in many chemical and biochemical reactions. One simple approach to calculate the free energy change of a redox process is linear response approximation (LRA). However, variability in conformational and energy-gap sampling poses a challenge in balancing computational cost and accuracy.

Impact of Native Environment in Multiheme-Cytochrome Chains of the MtrCAB Complex.

MtrCAB protein complex plays a crucial role in exporting electrons through the outer membrane (OM) to external acceptors. This complex consists of three proteins and contains 20 hemes. Optimal protein-protein interactions and, consequently, heme-heme interactions facilitate efficient electron transfer through the conduit of hemes.

Scalable One-Pot Production of Geranylgeranylated Proteins in Engineered Prokaryotes.

Geranylgeranylation is a critical post-translational modification essential for various cellular functions. However, current methods for synthesizing geranylgeranylated proteins are complex and costly, which hinders access to these proteins for both biophysical and biomaterials applications. Here, we present a method for the one-pot production of geranylgeranylated proteins in .

Machine Learning Approach to Vertical Energy Gap in Redox Processes.

A straightforward approach to calculating the free energy change (Δ) and reorganization energy of a redox process is linear response approximation (LRA). However, accurate prediction of redox properties is still challenging due to difficulties in conformational sampling and vertical energy-gap sampling. Expensive hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are typically employed in sampling energy gaps using conformations from simulations.

Variable Non-Gaussian Transport of Nanoplastic on Supported Lipid Bilayers in Saline Conditions.

Nanoplastic-lipid interaction is vital to understanding the nanoscale mechanism of plastic adsorption and aggregation on a lipid membrane surface. However, a single-particle mechanistic picture of the nanoplastic transport process on a lipid surface remains unclear. Here, we report a salt-dependent non-Gaussian transport mechanism of polystyrene particles on a supported 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer surface.

A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation.

Lymphocyte-specific protein tyrosine kinase (LCK) is essential for T cell antigen receptor (TCR)-mediated signal transduction. Here, we report two siblings homozygous for a novel LCK variant (c.1318C>T; P440S) characterized by T cell lymphopenia with skewed memory phenotype, infant-onset recurrent infections, failure to thrive, and protracted diarrhea.

A General Strategy Toward pH-Resistant Phenolic Fluorophores for High-Fidelity Sensing and Bioimaging Applications.

Aryl alcohol-type or phenolic fluorophores offer diverse opportunities for developing bioimaging agents and fluorescence probes. Due to the inherently acidic hydroxyl functionality, phenolic fluorophores provide pH-dependent emission signals. Therefore, except for developing pH probes, the pH-dependent nature of phenolic fluorophores should be considered in bioimaging applications but has been neglected.

Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding.

Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope".

Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3.

Mycobacteria, such as Mycobacterium tuberculosis, are characterized by a uniquely thick and waxy cell envelope that consists of two membranes, with a variety of mycolates comprising their outer membrane (OM). The protein Mycobacterial membrane protein Large 3 (MmpL3) is responsible for the transport of a primary OM component, trehalose monomycolate (TMM), from the inner (cytoplasmic) membrane (IM) to the periplasmic space, a process driven by the proton gradient. Although multiple structures of MmpL3 with bound substrates have been solved, the exact pathway(s) for TMM or proton transport remains elusive.

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.

The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state.

Proton transfer activity of the reconstituted MmpL3 is modulated by substrate mimics and inhibitors.

Transporters belonging to the Resistance-Nodulation-cell Division (RND) superfamily of proteins such as MmpL3 and its analogs are the focus of intense investigations due to their importance in the physiology of species and antimycobacterial drug discovery. These transporters deliver trehalose monomycolates, the precursors of major lipids of the outer membrane, to the periplasm by a proton motive force-dependent mechanism. In this study, we successfully purified, from native membranes, the full-length and the C-terminal truncated MmpL3 and CmpL1 proteins and reconstituted them into proteoliposomes.

Restoring and Enhancing the Potency of Existing Antibiotics against Drug-Resistant Gram-Negative Bacteria through the Development of Potent Small-Molecule Adjuvants.

The rapid and persistent emergence of drug-resistant bacteria poses a looming public health crisis. The possible task of developing new sets of antibiotics to replenish the existing ones is daunting to say the least. Searching for adjuvants that restore or even enhance the potency of existing antibiotics against drug-resistant strains of bacteria represents a practical and cost-effective approach.

A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks.

Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>10 s) comparable to synthetic molecular wires, with negligible carrier loss over micrometers.

Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole.

Thiotemplated pyrrole is a prevailing intermediate in the synthesis of numerous natural products in which the pyrrole is tethered to a carrier protein (CP). Biosynthesis of the pyrrole requires oxidation of an l-proline side chain. Herein, we investigate the biocatalytic mechanism of proline-to-pyrrole synthesis by molecular dynamics simulations, quantum mechanics/molecular mechanics simulations, and electronic structure calculations using the recently reported (Thapa, H.

Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.

The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section.

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies.

ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV.

We report a distinct difference in the interactions of the glycans of the host-cell receptor, ACE2, with SARS-CoV-2 and SARS-CoV S-protein receptor-binding domains (RBDs). Our analysis demonstrates that the ACE2 glycan at N322 enhances interactions with the SARS-CoV-2 RBD while the ACE2 glycan at N90 may offer protection against infections of both coronaviruses depending on its composition. The interactions of the ACE2 glycan at N322 with SARS-CoV RBD are blocked by the presence of the RBD glycan at N357 of the SARS-CoV RBD.

Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides.

Assembly line biosynthesis of polyketide natural products involves checkpoints where identities of thiotemplated intermediates are verified before polyketide extension reactions are allowed to proceed. Determining what these checkpoints are and how they operate is critical for reprogramming polyketide assembly lines. Here we demonstrate that ketosynthase (KS) domains can perform this gatekeeping role.

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.

The main protease (M) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M, a cysteine protease, have been determined, facilitating structure-based drug design. M plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins.

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.

The main protease (M ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of M , a cysteine protease, have been determined, facilitating structure-based drug design. M plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins.

Electric field stimulates production of highly conductive microbial OmcZ nanowires.

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S cm) and threefold higher stiffness (1.

The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure.

Amyloid-β (Aβ) is a macromolecular structure of great interest because its misfolding and aggregation, along with changes in the secondary structure, have been correlated with its toxicity in various neurodegenerative diseases. Small drug-like molecules can modulate the amyloid secondary structure and therefore have raised significant interest in applications to active and passive therapies targeting amyloids. In this study, we investigate the interactions of epigallocatechin-3-gallate (EGCG), found in green tea, with Aβ polypeptides, using a combination of in vitro immuno-infrared sensor measurements, docking, molecular dynamics simulations, and ab initio calculations.

Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics.

CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain.

Influence of the First Chromophore-Forming Residue on Photobleaching and Oxidative Photoconversion of EGFP and EYFP.

Enhanced green fluorescent protein (EGFP)-one of the most widely applied genetically encoded fluorescent probes-carries the threonine-tyrosine-glycine (TYG) chromophore. EGFP efficiently undergoes green-to-red oxidative photoconversion ("redding") with electron acceptors. Enhanced yellow fluorescent protein (EYFP), a close EGFP homologue (five amino acid substitutions), has a glycine-tyrosine-glycine (GYG) chromophore and is much less susceptible to redding, requiring halide ions in addition to the oxidants.

Regioselective Ultrafast Photoinduced Electron Transfer from Naphthols to Halocarbon Solvents.

Excited state decay of 2-naphthol (2N) in halocarbon solvents has been observed to be significantly slower when compared to that of 1-naphthol (1N). In this study, we provide new physical insights behind this observation by exploring the regioselective electron transfer (ET) mechanism from photoexcited 1N and 2N to halocarbon solvents at a detailed molecular level. Using state-of-the-art electronic structure calculations, we explore several configurations of naphthol-chloroform complexes and find that the proximity of the electron-accepting chloroform molecule to the electron-rich -OH group of the naphthol is the dominant factor affecting electron transfer rates.