CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

Understanding the structure and function of HPI, a rubber tree serine protease inhibitor, and its interaction with subtilisin

Protease inhibitors are crucial in regulating enzymatic activity and have extensive applications in medicine, biotechnology, and agriculture. This study characterizes a recombinant protease inhibitor from Hevea brasiliensis (rHPI), highlighting its unique structural features and inhibitory potential. Using Matrix-Assisted Laser Desorption/Ionization (MALDI) analysis, the inhibitor exhibits one distinct peak around 7.54 kDa. Enzymatic assays using N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as a substrate confirmed the inhibitor's activity against subtilisin Carlsberg, a widely utilized serine protease in industry and biotechnology. The crystal structure of rHPI, resolved at 1.73 Å, reveals a topology closely resembling eglin c, including a single alpha-helix, two parallel beta-strands, and a distinctive binding loop spanning residues 40-51. Disordered regions at the N- and C-termini contribute to its structural uniqueness. Despite lacking disulfide bonds and featuring an Arg residue instead of Trp at the P'8 position, rHPI maintains a high affinity for subtilisin. Isothermal titration calorimetry (ITC) showed that this interaction is entropically driven. Molecular docking and dynamics simulations of the rHPI-subtilisin complex revealed the formation of antiparallel β-sheets, hydrogen bonding involving the protein backbone, and a salt bridge between His64 of subtilisin and Asp47 of rHPI. These findings provide valuable insights into the molecular basis of rHPI's inhibitory activity and offer a framework for the rational design of novel subtilisin inhibitors with potential applications in agricultural and industrial settings.

Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity

During HIV-1 maturation, the matrix (MA) lattice underlying the viral membrane undergoes a structural rearrangement, and the newly released capsid (CA) protein forms a mature CA. While it is well established that CA formation is essential for particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine maturation of an MA triple mutant, L20K/E73K/A82T, which, despite replicating similarly to wild-type (WT) in some cell lines, exhibits distinct biochemical behaviors that suggest altered MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that, although the MA lattice in immature L20K/E73K/A82T virions closely resembles that of the WT, mature L20K/E73K/A82T virions lack a detectable MA lattice. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer MA interactions in mature L20K/E73K/A82T mutant virions. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing insights into the structural requirements for HIV-1 particle maturation and generation of infectious particles.

A basigin antibody modulates MCTs to impact tumor metabolism and immunity

Lactate metabolism and signaling intricately intertwine in the context of cancer and immunity. Basigin, working alongside monocarboxylate transporters MCT1 and MCT4, orchestrates the movement of lactate across cell membranes. Despite their potential in treating formidable tumors, the mechanisms by which basigin antibodies affect basigin and MCTs remain unclear. Our research demonstrated that basigin positively modulates MCT activity. We subsequently developed a basigin antibody that converts basigin into a negative modulator, thereby suppressing lactate transport and enhancing anti-tumor immunity. Additionally, the antibody alters metabolic profiles in NSCLC-PDOs and T cells. Cryo-EM structural analysis and molecular dynamics simulations reveal that the extracellular Ig2 domain and transmembrane domain of basigin regulate MCT1 activity through an allosteric mechanism. The antibody decreases MCT1 transition rate by reducing the flexibility of basigin's Ig2 domain and diminishing interactions between basigin's transmembrane domain and MCT1. These findings underscore the promise of basigin antibodies in combating tumors by modulating metabolism and immunity, and the value of a common therapeutic subunit shared by multiple transporter targets.

In silico characterization of the gating and selectivity mechanism of the human TPC2 cation channel

Two-pore channels (TPCs) are twofold symmetric endolysosomal cation channels forming important drug targets, especially for antiviral drugs. They are activated by calcium, ligand binding, and membrane voltage, and to date, they are the only ion channels shown to alter their ion selectivity depending on the type of bound ligand. However, despite their importance, ligand activation of TPCs and the molecular mechanisms underlying their ion selectivity are still poorly understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PI(3,5)P2. We performed all-atom in silico electrophysiology simulations to study Na+ and Ca2+ permeation across full-length hTPC2 on the timescale of ion conduction and investigated the conformational changes induced by the presence or absence of bound PI(3,5)P2. Our findings reveal that hTPC2 adopts distinct conformations depending on the presence of PI(3,5)P2 and elucidate the allosteric transition pathways between these structures. Additionally, we examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. The results of our simulations explain the experimental observation that hTPC2 is more selective for Na+ over Ca2+ ions in the presence of PI(3,5)P2via a multilayer selectivity mechanism. Importantly, mutations in the selectivity filter region of hTPC2 maintain cation conduction but change the ion selectivity of hTPC2 drastically.

Structural basis of the tarocystatin inhibitory mechanism against papain

Plant pathogens pose a severe threat to global food security by compromising the availability, quality, and safety of crops for human and animal consumption. Given the urgent need for alternatives to chemical pesticides, natural inhibitors of phytopathogenic proteases represent promising biopesticides. Tarocystatin has been characterized in Colocasia esculenta as a defense protein against phytopathogenic nematodes and fungi. Despite its biotechnological potential, few studies describe its mechanical, structural, and energetic properties. In this study, we characterized the inhibitory mechanism of tarocystatin against papain using a computational biophysics approach. Through extensive molecular dynamics (MD) and steered molecular dynamics (SMD) simulations, we explored the dynamic, energetic, structural, and mechanical basis of tarocystatin and its specific binding to papain. Our results suggest that the stability of the complex is characterized by a lack of conformational rearrangements, showing invariability in its secondary structure across all MD replicas. Additionally, electrostatic analysis revealed a high complementarity of the tarocystatin-papain complex, which was later corroborated by the hydrogen-bond network established at the complex interface, explaining its strong inhibitory capacity. Moreover, we determined that the substrate-competitive inhibitory mechanism is due to the binding ability of conserved motifs in tarocystatin, which efficiently interact with the catalytic active site of papain. This was also confirmed through SMD, where we observed that the N-terminal region acts as a spring to prevent the dissociation of the complex under external pulling forces. Overall, our study is the first to provide a comprehensive exploration of the biophysical properties of the tarocystatin-papain complex, offering insights into the tarocystatin's inhibition mechanism. These results lay the foundation for future development of tarocystatin-based antifungal alternatives, as well as for exploring its inhibitory activity in other pathogens or enhancing its efficacy through molecular engineering.

Structural insights into the selective recognition of RF-amide peptides by neuropeptide FF receptor 2

Neuropeptide FF Receptor 2 (NPFFR2), a G-protein-coupled receptor, plays a role in pain modulation and diet-induced thermogenesis. While NPFFR2 is strongly activated by neuropeptides FF (NPFFs), it shows low activity in response to RF-amide-related peptides (RFRPs), despite the peptides belonging to a shared family. In contrast, NPFFR1, which shares high sequence similarity with NPFFR2, is activated by RFRPs and regulates reproductive hormone balance. The molecular basis for these receptor-specific interactions with their RF-amide peptides remains unclear. Here, we present cryo-electron microscopy structures of NPFFR2 in its active state bound to the agonist RF-amide peptide hNPSF, and in its ligand-free state. Structural analysis reveals that the C-terminal RF-amide moiety engages conserved residues in the transmembrane domain, while the N-terminal segment interacts in a receptor subtype-specific manner. Key selectivity-determining residues in NPFFR2 are also identified. A homology model of NPFFR1 bound to RFRP, supported by mutagenesis studies, further validates this selectivity mechanism. Additionally, structural comparison between the inactive and active states of NPFFR2 suggests a TM3-mediated activation mechanism. These findings provide insights into RF-amide peptide recognition by NPFF receptors.

Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations

Residence time is a crucial parameter for assessing the functional efficacy of drugs, quantifying the duration of a drug's binding to its target protein. It is directly related to therapeutic effects and the dosing regimen. Several factors can influence the residence time, including drug-protein binding kinetics and the unbinding pathways. Understanding the efficacy of a drug requires the characterization of both its binding kinetics and unbinding pathways from the drug-protein complex. By employing our previous computational protocol that uses enhanced sampling techniques such as well-tempered metadynamics (WT-MetaD) and classical molecular dynamics (cMD) simulations, it was possible to elucidate the inhibitor unbinding pathways and identify molecular determinants that extend the residence time in a set of cyclin-dependent kinase 2 (CDK2) inhibitors. In this study, using WT-MetaD, the relative residence times of roniciclib and eight derivatives were quantified on the nanosecond timescale. Notably, substituting the R5 position of the aminopyridine core with larger substituents significantly prolonged the computational residence time, which correlated well with experimental data (R 2 = 0.83). Our computational simulations reveal the critical importance of specific amino acids, including Phe80, Lys33, and Asp145, in maintaining the stability of the protein-inhibitor complex. These residues are key in keeping the hydration network around them, affecting the inhibitor binding duration. The hydrogen bond interaction between residue Asp145 and roniciclib and its derivatives is particularly noteworthy, significantly influencing the electrostatic contribution to the binding free energy when the halogen substituent size increases. Furthermore, our analysis of protein flexibility at the C-terminus and N-terminus angles revealed a relationship with the size of the R5 substituent in the bound inhibitor, supported by principal component analysis. Additionally, different unbinding pathways were proposed, where it was found that inhibitors can dissociate from the CDK2 binding site through two principal routes: the α-helix D and β-1 and β-2 segments.

Mycobacterium tuberculosis FtsB and PerM interact via a C-terminal helix in FtsB to modulate cell division

Latent infection by Mycobacterium tuberculosis (Mtb) impedes effective tuberculosis therapy and eradication. The protein PerM is essential for chronic Mtb infections in mice and acts via the divisome protein FtsB to modulate cell division. Using transgenic co-expression in Escherichia coli, we studied the Mtb PerM-FtsB interaction in isolation from other Mtb proteins, engineering PerM to enhance expression in the E. coli membrane. Using fluorescence microscopy in E. coli, we observed that the previously reported PerM-dependent instability of Mtb FtsB required a segment of FtsB predicted to bind cell-division proteins FtsL and FtsQ. Furthermore, we found that the stability of membrane-localized PerM hinged on its interaction with a conserved, C-terminal helix in FtsB. We also observed that removing this helix disrupted PerM-FtsB interaction using single-molecule tracking. Molecular dynamics results supported the observation that FtsB stabilized PerM and suggested that interactions at the PerM-FtsB interface differ from our initial structure prediction in a way that is consistent with PerM sequence conservation. Although narrowly conserved, the PerM-FtsB interaction emerges as a potential therapeutic target for persistent infections by disrupting the regulation of cell division. Integrating protein structure prediction, molecular dynamics, and single-molecule microscopy, our approach is primed to screen potential inhibitors of the PerM-FtsB interaction and can be straightforwardly adapted to explore other putative interactions.IMPORTANCEOur research reveals significant insights into the dynamic interaction between the proteins PerM and FtsB within Mycobacterium tuberculosis, contributing to our understanding of bacterial cell division mechanisms crucial for infection persistence. By combining innovative fluorescence microscopy and molecular dynamics, we established that the stability of these proteins is interdependent; molecular dynamics placing PerM-FtsB in the context of the mycobacterial divisome shows how disrupting PerM-FtsB interactions can plausibly impact bacterial cell wall synthesis. These findings highlight the PerM-FtsB interface as a promising target for novel therapeutics aimed at combating persistent bacterial infections. Importantly, our approach can be adapted for similar studies in other bacterial systems, suggesting broad implications for microbial biology and antibiotic development.

Active Site Plasticity of the Bacterial Sliding Clamp

The rise of antibiotic resistance poses a severe global threat, specifically due to the emergence of multiresistant bacteria (ESKAPE pathogens), which are responsible for countless deaths globally. Consequently, the development of novel antibiotics is in dire need. Targeting proteins essential to DNA replication is a promising pathway, making the β-sliding clamp (β-SC) an attractive target. Currently, there are no antibiotics on the market that target the β-SC. However, numerous compounds are being investigated to create an antibiotic with high potency against a broad range of bacterial species. Interestingly, most proposed compounds do not bind to the entire active site, which may reduce their potential as high-potency inhibitors. This is due to the active site residue Met at position 362, adopting a "closed" conformation, preventing inhibitors access into Subsite II of the active site. This study explored the effect of key residues on the plasticity of the β-SC active site using molecular dynamics and metadynamics simulations under different physiological states. Our results show that the Met gate exhibits flexibility and both open and closed states are thermodynamically and kinetically accessible.

Role of Cre Dynamics in Autoinhibition and Priming

Cre recombinase, a powerful tool for genome engineering, associates into an intasome, a tetrameric complex of alternate active and inactive monomers that bring together two loxP sequences, stabilized by key protein-protein and protein-DNA interactions. High-resolution structural information for free Cre is still missing, in contrast to the many structures found for Cre-DNA complexes in the Protein Data Bank, hindering understanding of the initial steps in intasome formation. To approach Cre structure and dynamics, we carried out 100 μs of molecular dynamics simulations of free Cre, starting from five Cre structures from different stages of intasome assembly. In the generated ensemble, the linker connecting the CBD and CAT domains is an intrinsically disordered region (IDR) that promotes different orientations of the two domains. The domains remain folded and interact with each other through short-lived interactions, retaining ∼70% of their surface available for interaction with loxP. The C-terminal Helix N in the CAT domain is also an IDR that interacts with the entire protein, including the active site, transiently forming an autoinhibited complex. The active site can be assembled in the absence of DNA, albeit inefficiently. The CAT domain has a clam-like motion, opening and closing the cavity where helix N docks, establishing protein-protein interactions in the intasome. Helix A in the CBD domain slides over the domain like a windshield wiper, sampling intasome-like conformations, among others. The wide range of intramolecular motion sampled by free Cre suggests that it uses conformational selection, using primed DNA-binding surfaces in both domains while assembling into the intasome.

Multiple Pendants-Bearing Triglucosides for Membrane Protein Studies: Effects of Pendant Length and Number on Micelle Interior Hydration and Protein Stability

Membrane proteins play central roles in cell physiology and are the targets of over 50% of FDA-approved drugs. In the present study, we prepared single alkyl-chained triglucosides decorated with multiple pendants, designated multiple pendant-bearing glucosides (MPGs), to enhance membrane protein stability. The new detergents feature two and four pendants of varying size at the hydrophilic-lipophilic interfaces, designated MPG-Ds and MPG-Ts, respectively. When tested with model membrane proteins, including the human adrenergic receptor (β2AR), the tetra-pendant-bearing MPGs (MPG-Ts) demonstrated superior performance compared to the dipendant analogs (MPG-Ds) and the gold standard DDM. All-atom molecular dynamics (MD) simulations results reveal that the four-pendant configuration of this detergent is remarkably effective in excluding water from the hydrophobic micelle interiors compared to the dipendant MPGs and DDM, an unprecedented feature of this new detergent. Our findings provide a novel strategy for designing water-resistant detergents, advancing the field of membrane protein research.

Molecular interaction assays in silico of crotapotin from Crotalus durissus terrificus against the molecular target trypanothione reductase from Leishmania braziliensis

Background

Leishmaniasis is a neglected disease that mainly affects impoverished populations and receives limited attention from governments and research institutions. Current treatments are based on antimonial therapies, which present high toxicity and cause significant side effects, such as cardiotoxicity and hepatotoxicity. This study proposes using crotapotin, isolated from Crotalus durissus terrificus venom, as a potential inhibitor of the enzyme trypanothione reductase from Leishmania braziliensis (LbTR).

Methods

In silico assays were conducted to evaluate the interaction of crotapotin with LbTR using molecular docking and molecular dynamics techniques. Recombinant LbTR was expressed in E. coli, and its enzymatic activity was confirmed. The inhibitory action of crotapotin on LbTR was then tested in enzymatic assays.

Results

The stability of these interactions was confirmed over 200 ns molecular dynamics simulations, with a clustering analysis using the GROMACS method revealing a total of 12 distinct clusters. The five most representative clusters showed low RMSD values, indicating high structural stability of the LbTR-crotapotin complex. In particular, cluster 1, with 3,398 frames and an average RMSD of 0.189 nm from the centroid, suggests a dominant stable conformation of the complex. Additional clusters maintained average RMSD values between 0.173 nm and 0.193 nm, further reinforcing the robustness of the complex under physiological conditions. Recombinant LbTR expression was successful, yielding 4.8 mg/L with high purity, as verified by SDS-PAGE. In the enzymatic assays, crotapotin partially inhibited LbTR activity, with an IC50 of 223.4 μM.

Conclusion

The in silico findings suggest a stable and structured interaction between crotapotin and LbTR, with low structural fluctuation, although the inhibition observed in in vitro assays was moderate. These results indicate the potential of crotapotin as a promising basis for developing specific LbTR inhibitors, contributing to the bioprospecting of new antiparasitic agents.

Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence

Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the biological milieu. Studying such structural changes in membrane-embedded proteins and understanding the associated topological signatures in membrane leaflets, therefore, remain relatively unexplored. Herein, we first aim to estimate the free energy barrier and the minimum free energy path (MFEP) connecting the membrane-embedded fully and partially inserted states of the bacteriorhodopsin fragment. To achieve this, we have considered independent sets of simulations from membrane-mimicking and membrane-embedded environments, respectively. An autoencoder model is used to elicit state-distinguishable collective variables for the system utilizing membrane-mimicking simulations. Our in-house Expectation Maximized Molecular Dynamics algorithm is initially used to deduce the barrier height between the two membrane-embedded states. Next, we develop the Geometry Optimized Local Direction search as a post-processing algorithm to identify the MFEP and the corresponding peptide conformations from the autoencoder-projected trajectories. Finally, we apply a graph attention neural network (GAT) model to learn the membrane surface topology as a function of the associated peptide structure, supervised by the membrane-embedded simulations. The resultant GAT model is then utilized to predict the membrane leaflet topology for the peptide structures along MFEP, obtained from membrane-mimicking simulations. The combined framework is expected to be useful in capturing key phenomena accompanying folding transitions in membranes. We discuss opportunities and avenues for further development.

In Slico Screening and In Vitro Identification of Hyperuricemia-Inhibiting Peptides from Trachurus japonicus

Hyperuricemia arises from imbalanced uric acid metabolism, contributing to gout and related chronic diseases. When traditional drugs are used to treat hyperuricemia, side effects are inevitable, which promotes the exploration of new bioactive compounds. Protein hydrolysates and peptides are gradually showing potential in the treatment of hyperuricemia. This study investigated the uric acid inhibitory activity of peptides extracted from Trachurus japonicus using in silico and in vitro methods. We employed in silico virtual enzymolysis and experimental validation to identify bioactive peptides from Trachurus japonicus proteins. Four peptides (DF, AGF, QPSF, and AGDDAPR) were comprehensively screened by molecular docking and database analysis. After solid-phase synthesis, the inhibitory effects of these peptides on hyperuricemia were further verified in vitro and at the cellular level. The results showed that all four peptides have good hyperuricemia-inhibiting activities. Molecular docking and molecular dynamics revealed that peptides DF and AGDDAPR affect the production of uric acid by binding to the active sites of urate transporter 1 (URAT1), glucose transporter 9 (GLUT9), and xanthine oxidase (XOD), while peptides QPSF and AGF mainly influence the XOD active site, confirming that it is feasible to rapidly screen hyperuricemia-inhibiting peptides by molecular docking.

Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases

Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain Acinetobacter baumannii. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, in vitro reconstitution, molecular modeling, and molecular dynamics simulation. Our findings clarify the roles of the fimsbactin NRPS enzymes, uncovering catalytically redundant domains and identifying the multifunctional nature of the FbsF cyclization (Cy) domain. We demonstrate the dynamic interplay between l-serine and 2,3-dihydroxybenzoic acid derived dipeptides, partitioning between amide and ester forms via a 1,2-N-to-O-acyl shift orchestrated by the noncanonical, multichannel FbsF Cy domain. The branching event occurs in a secondary condensation event facilitated by this Cy domain with two dipeptidyl intermediates, which generates a branched tetrapeptide thioester. Finally, the terminal condensation domain of FbsG recruits a soluble nucleophile to release the final product. This study advances our understanding of the intricate biosynthetic pathways and chemical logic employed by NRPSs, shedding light on the mechanisms underlying the synthesis of complex branched peptides.

Understanding Folding of bFGF and Potential Cellular Protective Mechanisms of Neural Cells

Traumatic brain injury (TBI) is a serious health condition that affects an increasing number of people, especially veterans and athletes. TBI causes serious consequences because of its long-lasting impact on the brain and its alarming frequency of occurrence. Although the brain has some natural protective mechanisms, the processes that trigger them are poorly understood. Fibroblast growth factor (FGF) proteins interact with receptor proteins to protect cells. Gaps in the literature include how basic-FGF (bFGF) is activated by heparin, can heparin-like molecules induce neural protection, and the effect of allosteric binding on bFGF activity. To fill the gap in our understanding, we applied temperature replica exchange to study the influence of heparin binding to bFGF and how mutations in bFGF influence stability. A new favorable binding site was identified by comparing free energies computed from the potential of mean force (PMF). Although the varied sugars studied resulted in different interactions with bFGF compared to heparin, they each produced structural effects similar to those of bFGF that likely facilitate receptor binding and signaling. Our results also demonstrate how point mutations can trigger the same conformational change that is believed to promote favorable interactions with the receptor. A deeper atomic-level understanding of how chemicals are released during TBI is needed to improve the development of new treatments for TBI and could contribute to a better understanding of other diseases.

Molecular basis of neurosteroid and anticonvulsant regulation of TRPM3

Transient receptor potential channel subfamily M member 3 (TRPM3) is a Ca2+-permeable cation channel activated by the neurosteroid pregnenolone sulfate (PregS) or heat, serving as a nociceptor in the peripheral sensory system. Recent discoveries of autosomal dominant neurodevelopmental disorders caused by gain-of-function mutations in TRPM3 highlight its role in the central nervous system. Notably, the TRPM3 inhibitor primidone, an anticonvulsant, has proven effective in treating patients with TRPM3-linked neurological disorders and in mouse models of thermal nociception. However, our understanding of neurosteroids, inhibitors and disease mutations on TRPM3 is limited. Here we present cryogenic electron microscopy structures of the mouse TRPM3 in complex with cholesteryl hemisuccinate, primidone and PregS with the synthetic agonist CIM 0216. Our studies identify the binding sites for the neurosteroid, synthetic agonist and inhibitor and offer insights into their effects and disease mutations on TRPM3 gating, aiding future drug development.

Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity

HIV-1 assembly is initiated by the binding of Gag polyproteins to the inner leaflet of the plasma membrane, mediated by the myristylated matrix (MA) domain of Gag. Subsequent to membrane binding, Gag oligomerizes and buds as an immature, non-infectious virus particle, which, upon cleavage of the Gag precursor by the viral protease, transforms into a mature, infectious virion. During maturation, the MA lattice underlying the viral membrane undergoes a structural rearrangement and the newly released capsid (CA) protein forms a mature capsid that encloses the viral genome. While it is well established that formation of the mature capsid is essential to particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine MA maturation of an MA triple mutant, L20K/E73K/A82T, which exhibits distinct biochemical behaviours. The L20K/E73K/A82T mutant is a revertant derived by propagating the L20K mutant, which exhibits reduced infectivity and increased association of the Gag polyprotein with membranes. L20K/E73K/A82T replicates similarly to wild type but retains the increased Gag membrane binding properties of L20K. L20K/E73K/A82T MA also sediments to high-density fractions in sucrose gradients after detergent treatment under conditions that fully solubilize WT MA, suggesting enhanced MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that the immature MA lattice of L20K/E73K/A82T closely resembles the wild type. However, mature virions of the triple mutant lack a detectable MA lattice, in stark contrast to both the wild type and L20K mutant. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer interactions in the mature L20K/E73K/A82T MA. Furthermore, introducing additional mutations designed to disrupt the mature MA lattice does not impair particle infectivity. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing new insights into the structural plasticity of the matrix during maturation and its functional role in the viral lifecycle.

Atherosclerotic Oxidized Lipids Affect Formation and Biophysical Properties of Supported Lipid Bilayers and Simulated Membranes

Oxidized lipids arising from oxidative stress are associated with many serious health conditions, including cardiovascular diseases. For example, KDdiA-PC and KOdiA-PC are two oxidized phosphatidylcholines (oxPC) directly linked to atherosclerosis, which precipitate heart failure, stroke, aneurysms, and chronic kidney disease. These oxPCs are well-characterized in small particles such as low-density lipoprotein, but how their presence affects the biophysical properties of larger bilayer membranes is unclear. It is also unclear how membrane mediators, such as cholesterol, affect lipid bilayers containing these oxPCs. Here, we characterize supported lipid bilayers (SLBs) containing POPC, KDdiA-PC, or KOdiA-PC, and cholesterol. We used a quartz crystal microbalance with dissipation monitoring (QCM-D), fluorescence microscopy, and all-atom molecular dynamics (MD) to examine the formation process, biophysical properties, and specific lipid conformations in simulated bilayers. Experimentally, we show that liposomes containing either oxPC form SLBs by rupturing on contact with SiO2 substrates, which differs from the typical adsorption-rupture pathway observed with nonoxidized liposomes. We also show that increasing the oxPC concentration in SLBs results in thinner bilayers that contain defects. Simulations reveal that the oxidized sn-2 tails of KDdiA-PC and KOdiA-PC bend out of the hydrophobic membrane core into the hydrophilic headgroup region and beyond. The altered conformations of these oxPC, which are affected by cholesterol content and protonation state of the oxidized functional groups, contribute to trends of decreasing membrane thickness and increasing membrane area with increasing oxPC concentration. This combined approach provides a comprehensive view of the biophysical properties of membranes containing KDdiA-PC and KOdiA-PC at the molecular level, which is crucial to understanding the role of lipid oxidation in cardiovascular disease and related immune responses.

Physicochemical Properties of Seed Oil Blends and Their Potential for the Creation of Synthetic Oleosomes with Modulated Polarities

There is an increasing demand within the pharmaceutical and cosmetic industries for biofriendly lipid-based active ingredient delivery systems. Micelles, liposomes, and lipid nanoparticles are currently the most used systems despite their limitations. Oleosomes, also known as lipid droplets, are promising alternatives to the existing strategies. Oleosomes are typically found in plant cells and are characterized by a nonpolar triacylglycerol core surrounded by a phospholipid monolayer punctuated with the protein oleosin. Producing oleosomes synthetically allows the customization of their lipid content, size, protein content, and oil core characteristics, expanding their versatility. Herein we demonstrate a proof of concept for the use of synthetic oleosomes to sequester polar molecules by modulating their core polarity with blends of sunflower and castor oils. The physical properties (density, refractive index, and permittivity) of the oil blends are characterized and demonstrate ideal mixing of the oils, which is supported by molecular dynamics simulations. Spectroscopic examination of the oil blends using fluorescent probes shows that the polarity of oil blends increases as the fraction of castor oil increases. Finally, we show that the uptake of a polar fluorescent probe (NBD-glucose) into synthetic oleosomes is enhanced by increasing the polarity of the oil core, but large charged molecules are excluded from the core regardless of polarity. These experiments show that synthetic oleosomes with tunable oil cores can expand the range of molecules that can be loaded into a biofriendly package as desired for biotechnology applications.

Short-Term Exposure to Foodborne Xenoestrogens Affects Breast Cancer Cell Morphology and Motility Relevant for Metastatic Behavior In Vitro

Breast cancer is highly susceptible to metastasis formation. During the time of disease progression, tumor pathophysiology can be impacted by endogenous factors, like hormonal status, as well as by environmental exposures, such as those related to diet and lifestyle. New lines of evidence point toward a potential role for foodborne endocrine disruptive chemicals in this respect; however, mechanistic understanding remains limited. At the molecular level, crucial steps toward metastasis formation include cell structural changes, alteration of adhesion, and reorganization of cytoskeletal proteins involved in motility. Hence, this study investigates the potential of dietary xenoestrogens to impact selected aspects of breast cancer cell mechanotransduction. Taking the onset of the metastatic cascade as a model, experiments focused on cell-matrix adhesion, single-cell migration, and adaptation of cell morphology. Dietary mycoestrogens alternariol (AOH, 1 μM) and α-zearalenol (α-ZEL, 10 nM), soy isoflavone genistein (GEN, 1 μM), and food packaging plasticizer bisphenol A (BPA, 10 nM) were applied as single compounds or in mixtures. Pursuing the hypothesis that endocrine active molecules could affect cell functions beyond the estrogen receptor-dependent cascade, experiments were performed comparing the MCF-7 cell line to the triple negative breast cancer cells MDA MB-231. Indeed, the four compounds functionally affected the motility and the adhesion of both cell types. These responses were coherent with rearrangements of the actin cytoskeleton and with the modulation of the expression of integrin β1 and cathepsin D. Mechanistically, molecular dynamics simulations confirmed a potential interaction with fragments of the α1 and β1 integrin subunits. In sum, dietary xenoestrogens proved effective in modifying the motility and adhesion of breast cancer cells, as predictive end points for metastatic behavior in vitro. These effects were measurable after short incubation times (1 or 8 h) and contribute to shed novel light on the activity of compounds with hormonal mimicry potential in breast cancer progression.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Microfluidic measurement of the size and shape of lipid-anchored proteins

The surface of a cell is crowded with membrane proteins. The size, shape, density, and mobility of extracellular surface proteins mediate cell surface accessibility to external molecules, viral particles, and other cells. However, predicting these qualities is not always straightforward, even when protein structures are known. We previously developed an experimental method for measuring flow-driven lateral transport of neutravidin bound to biotinylated lipids in supported lipid bilayers. Here, we use this method to detect hydrodynamic force applied to a series of lipid-anchored proteins with increasing size. We find that the measured force reflects both protein size and shape, making it possible to distinguish these features of intact, folded proteins in their undisturbed orientation and proximity to the lipid membrane. In addition, our results demonstrate that individual proteins are transported large distances by flow forces on the order of femtoNewtons, similar in magnitude to the shear forces resulting from blood circulation or from the swimming motion of microorganisms. Similar protein transport across living cells by hydrodynamic force may contribute to biological flow sensing.

Molecular basis of the urate transporter URAT1 inhibition by gout drugs

Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood1. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population2-4. The human urate transporter 1 (URAT1) is responsible for the reabsorption of ~90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout5. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown5. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the novel compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.

The Endocannabinoid Peptide RVD-Hemopressin Is a TRPV1 Channel Blocker

Neurotransmission is critical for brain function, allowing neurons to communicate through neurotransmitters and neuropeptides. RVD-hemopressin (RVD-Hp), a novel peptide identified in noradrenergic neurons, modulates cannabinoid receptors CB1 and CB2. Unlike hemopressin (Hp), which induces anxiogenic behaviors via transient receptor potential vanilloid 1 (TRPV1) activation, RVD-Hp counteracts these effects, suggesting that it may block TRPV1. This study investigates RVD-Hp's role as a TRPV1 channel blocker using HEK293 cells expressing TRPV1-GFP. Calcium imaging and patch-clamp recordings demonstrated that RVD-Hp reduces TRPV1-mediated calcium influx and TRPV1 ion currents. Molecular docking and dynamics simulations indicated that RVD-Hp interacts with TRPV1's selectivity filter, forming stable hydrogen bonds and van der Waals contacts, thus preventing ion permeation. These findings highlight RVD-Hp's potential as a therapeutic agent for conditions involving TRPV1 activation, such as pain and anxiety.

Remodelling of the translatome controls diet and its impact on tumorigenesis

Fasting is associated with a range of health benefits1-6. How fasting signals elicit changes in the proteome to establish metabolic programmes remains poorly understood. Here we show that hepatocytes selectively remodel the translatome while global translation is paradoxically downregulated during fasting7,8. We discover that phosphorylation of eukaryotic translation initiation factor 4E (P-eIF4E) is induced during fasting. We show that P-eIF4E is responsible for controlling the translation of genes involved in lipid catabolism and the production of ketone bodies. Inhibiting P-eIF4E impairs ketogenesis in response to fasting and a ketogenic diet. P-eIF4E regulates those messenger RNAs through a specific translation regulatory element within their 5' untranslated regions (5' UTRs). Our findings reveal a new signalling property of fatty acids, which are elevated during fasting. We found that fatty acids bind and induce AMP-activated protein kinase (AMPK) kinase activity that in turn enhances the phosphorylation of MAP kinase-interacting protein kinase (MNK), the kinase that phosphorylates eIF4E. The AMPK-MNK-eIF4E axis controls ketogenesis, revealing a new lipid-mediated kinase signalling pathway that links ketogenesis to translation control. Certain types of cancer use ketone bodies as an energy source9,10 that may rely on P-eIF4E. Our findings reveal that on a ketogenic diet, treatment with eFT508 (also known as tomivosertib; a P-eIF4E inhibitor) restrains pancreatic tumour growth. Thus, our findings unveil a new fatty acid-induced signalling pathway that activates selective translation, which underlies ketogenesis and provides a tailored diet intervention therapy for cancer.

Insights into dynamic changes in ADC-7 and P99 cephalosporinases using small angle x-ray scattering (SAXS)

To counter the emergence of β-lactamase (BL) mediated resistance, design of new β-lactamase inhibitors (BLIs) is critical. Many high-resolution crystallographic structures of BL complexed with BLIs are available. However, their impact on BLI design is struggling to keep pace with novel and emerging variants. Small angle x-ray scattering (SAXS) in combination with molecular modeling is a useful tool to determine dynamic structures of macromolecules in solution. An important application of SAXS is to determine the conformational changes that occur when BLI bind to BL. To probe if conformational dynamics occur in class C cephalosporinases, we studied SAXS profiles of two clinically relevant class C β-lactamases, Acinetobacter baumannii ADC-7 and Enterobacter cloacae P99 in apo format complexed with BLIs. Importantly, SAXS data analysis demonstrated that in solution, these representative class C enzymes remain monomeric and did not show the associated assemblies that were seen in various crystal structures. SAXS data acquired for ADC-7 and P99, in apo and inhibitor bound states, clearly showed that these enzymes undergo detectable conformational changes, and these class C β-lactamases also close upon binding inhibitors as does BlaC. Further analysis revealed that addition of inhibitor led to the compacting of a range of residues around the active site, indicating that the conformational changes that both P99 and ADC-7 undergo are central to inhibitor recognition and efficacy. Our findings support the importance of exploring conformational changes using SAXS analysis in the design of future BLIs.Communicated by Ramaswamy H. Sarma.

Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein

The human StAR-related lipid transfer domain protein 2 (STARD2), also known as phosphatidylcholine (PC) transfer protein, is a single-domain lipid transfer protein thought to transfer PC lipids between intracellular membranes. We performed extensive μs-long molecular dynamics simulations of STARD2 of its apo and holo forms in the presence or absence of complex lipid bilayers. The simulations in water reveal ligand-dependent conformational changes. In the 2 μs-long simulations of apo STARD2 in the presence of a lipid bilayer, we observed spontaneous reproducible PC lipid uptake into the protein hydrophobic cavity. We propose that the lipid extraction mechanism involves one to two metastable states stabilized by choline-tyrosine or choline-tryptophane cation-π interactions. Using free energy perturbation, we evaluate that PC-tyrosine cation-π interactions contribute 1.8 and 2.5 kcal/mol to the affinity of a PC-STARD2 metastable state, thus potentially providing a significant decrease of the energy barrier required for lipid desorption.

Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants

Cardiovascular diseases are a major global health concern, responsible for a significant number of deaths each year, often linked to cardiac arrhythmias resulting from dysfunction in ion channels. Hereditary Long QT Syndrome (LQTS) is a condition characterized by a prolonged QT interval on ECG, increasing the risk of sudden cardiac death. The most common type of LQTS, LQT2, is caused by mutations in the hERG gene, affecting a potassium ion channel. The majority of these mutations disrupt the channel's trafficking to the cell membrane, leading to intracellular retention. Specific high-affinity hERG blockers (e.g., E-4031) can rescue this mutant phenotype, but the exact mechanism is unknown. This study used accelerated molecular dynamics simulations to investigate how these mutations affect the hERG channel's structure, folding, endoplasmic reticulum (ER) retention, and trafficking. We reveal that these mutations induce structural changes in the channel, narrowing its central pore and altering the conformation of the intracellular domains. These changes expose internalization signals that contribute to ER retention and degradation of the mutant hERG channels. Moreover, the study found that the trafficking rescue drug E-4031 can inhibit these structural changes, potentially rescuing the mutant channels. This research offers valuable insights into the structural issues responsible for the degradation of rescuable transmembrane trafficking mutants. Understanding the defective trafficking structure of the hERG channel could help identify binding sites for small molecules capable of restoring proper folding and facilitating channel trafficking. This knowledge has the potential to lead to mechanism-based therapies that address the condition at the cellular level, which may prove more effective than treating clinical symptoms, ultimately offering hope for individuals with hereditary Long QT Syndrome.

Fedor J, Feng S, Suo Y, Im W, Lee SY. Mechanisms of sensory adaptation and inhibition of the cold and menthol receptor TRPM8

Our sensory adaptation to cold and chemically induced coolness is mediated by the intrinsic property of TRPM8 channels to desensitize. TRPM8 is also implicated in cold-evoked pain disorders and migraine, highlighting its inhibitors as an avenue for pain relief. Despite the importance, the mechanisms of TRPM8 desensitization and inhibition remained unclear. We found, using cryo-electron microscopy, electrophysiology, and molecular dynamics simulations, that TRPM8 inhibitors bind selectively to the desensitized state of the channel. These inhibitors were used to reveal the overlapping mechanisms of desensitization and inhibition and that cold and cooling agonists share a common desensitization pathway. Furthermore, we identified the structural determinants crucial for the conformational change in TRPM8 desensitization. Our study illustrates how receptor-level conformational changes alter cold sensation, providing insights into therapeutic development.

CHARMM-GUI Membrane Builder for Lipid Droplet Modeling and Simulation

Lipid droplets (LDs) are organelles that are necessary for eukaryotic and prokaryotic metabolism and energy storage. They have a unique structure consisting of a spherical phospholipid monolayer encasing neutral lipids such as triacylglycerol (TAG). LDs have garnered increased interest for their implications in disease and for drug delivery applications. Consequently, there is an increased need for tools to study their structure, composition, and dynamics in biological contexts. In this work, we utilize CHARMM-GUI Membrane Builder to simulate and analyze LDs with and without a plant LD protein, oleosin. The results show that Membrane Builder can generate biologically relevant all-atom LD systems with relatively short equilibration times using a new TAG library having optimized headgroup parameters. TAG molecules originally inserted into a lipid bilayer aggregate in the membrane center, forming a TAG-only core flanked by two monolayers. The TAG-only core thickness stably grows with increasing TAG mole fraction. A 70 % TAG system has a core that is thick enough to house oleosin without its interactions with the distal leaflet or disruption of its secondary structure. We hope that Membrane Builder can aid in the future study of LD systems, including their structure and dynamics with and without proteins.

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods

Alchemical relative binding free energy (ΔΔG) calculations have shown high accuracy in predicting ligand binding affinity and have been used as important tools in computer-aided drug discovery and design. However, there has been limited research on the application of ΔΔG methods to membrane proteins despite the fact that these proteins represent a significant proportion of drug targets, play crucial roles in biological processes, and are implicated in numerous diseases. In this study, to predict the binding affinity of ligands to G protein-coupled receptors (GPCRs), we employed two ΔΔG calculation methods: thermodynamic integration (TI) with AMBER and the alchemical transfer method (AToM) with OpenMM. We calculated ΔΔG values for 53 transformations involving four class A GPCRs and evaluated the performance of AMBER-TI and AToM-OpenMM. In addition, we conducted tests using different numbers of windows and varying simulation times to achieve reliable ΔΔG results and to optimize resource utilization. Overall, both AMBER-TI and AToM-OpenMM show good agreement with the experimental data. Our results validate the applicability of AMBER-TI and AToM-OpenMM for optimization of lead compounds targeting membrane proteins.

CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.

Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations

The accurate experimental estimation of protein-ligand systems' residence time (τ) has become very relevant in drug design projects due to its importance in the last stages of refinement of the drug's pharmacodynamics and pharmacokinetics. It is now well-known that it is not sufficient to estimate the affinity of a protein-drug complex in the thermodynamic equilibrium process in in vitro experiments (closed systems), where the concentrations of the drug and protein remain constant. On the contrary, it is mandatory to consider the conformational dynamics of the system in terms of the binding and unbinding processes between protein and drugs in in vivo experiments (open systems), where their concentrations are in constant flux. This last model has been proven to dictate much of several drugs' pharmacological activities in vivo. At the atomistic level, molecular dynamics simulations can explain why some drugs are more effective than others or unveil the molecular aspects that make some drugs work better in one molecular target. Here, the protein kinases Aurora A/B, complexed with its inhibitor Danusertib, were studied using conventional and enhanced molecular dynamics (MD) simulations to estimate the dissociation paths and, therefore, the computational τ values and their comparison with experimental ones. Using classical molecular dynamics (cMD), three differential residues within the Aurora A/B active site, which seems to play an essential role in the observed experimental Danusertib's residence time against these kinases, were characterized. Then, using WT-MetaD, the relative Danusertib's residence times against Aurora A/B kinases were measured in a nanosecond time scale and were compared to those τ values observed experimentally. In addition, the potential dissociation paths of Danusertib in Aurora A and B were characterized, and differences that might be explained by the differential residues in the enzyme's active sites were found. In perspective, it is expected that this computational protocol can be applied to other protein-ligand complexes to understand, at the molecular level, the differences in residence times and amino acids that may contribute to it.

Helical reorganization in the context of membrane protein folding: Insights from simulations with bacteriorhodopsin (BR) fragments

Membrane protein folding is distinct from folding of soluble proteins. Conformational acquisition in major membrane protein subclasses can be delineated into insertion and folding processes. An exception to the "two stage" folding, later developed to "three stage" folding, is observed within the last two helices in bacteriorhodopsin (BR), a system that serves as a model membrane protein. We employ a reductionist approach to understand interplay of molecular factors underlying the apparent defiance. Leveraging available solution NMR structures, we construct, sample in silico, and analyze partially (PIn) and fully inserted (FIn) BR membrane states. The membrane lateral C-terminal helix (CH) in PIn is markedly prone to transient structural distortions over microsecond timescales; a disorder prone region (DPR) is thereby identified. While clear transmembrane propensities are not acquired, the distortions induce alterations in local membrane curvature and area per lipid. Importantly, energetic decompositions reveal that overall, the N-terminal helix (NH) is thermodynamically more stable in the PIn. Higher overall stability of the FIn arises from favorable interactions between the NH and the CH. Our results establish lack of spontaneous transition of the PIn to the FIn, and attributes their partitioning to barriers that exceed those accessible with thermal fluctuations. This work paves the way for further detailed studies aimed at determining the thermo-kinetic roles of the initial five helices, or complementary external factors, in complete helical folding and insertion in BR. We comment that complementing such efforts with the growing field of machine learning assisted energy landscape searches may offer unprecedented insights.

Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA

The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.

Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

Lecithin:cholesterol acyltransferase (LCAT) exhibits α-activity on high-density and β-activity on low-density lipoproteins. However, the molecular determinants governing LCAT activation by different apolipoproteins remain elusive. Uncovering these determinants would offer the opportunity to design and explore advanced therapies against dyslipidemias. Here, we have conducted coarse-grained and all-atom molecular dynamics simulations of LCAT with nanodiscs made with α-helical amphiphilic peptides either derived from apolipoproteins A1 and E (apoA1 and apoE) or apoA1 mimetic peptide 22A that was optimized to activate LCAT. This study aims to explore what drives the binding of peptides to our previously identified interaction site in LCAT. We hypothesized that this approach could be used to screen for binding sites of LCAT in different apolipoproteins and would provide insights to differently localized LCAT activities. Our screening approach was able to discriminate apoA1 helixes 4, 6, and 7 as key contributors to the interaction with LCAT supporting the previous research data. The simulations provided detailed molecular determinants driving the interaction with LCAT: the formation of hydrogen bonds or salt bridges between peptides E4 or D4 and LCAT S236 or K238 residues. Additionally, salt bridging between R7 and D73 was observed, depending on the availability of R7. Expanding our investigation to diverse plasma proteins, we detected novel LCAT binding helixes in apoL1, apoB100, and serum amyloid A. Our findings suggest that the same binding determinants, involving E4 or D4 -S236 and R7-D73 interactions, influence LCAT β-activity on low-density lipoproteins, where apoE and or apoB100 are hypothesized to interact with LCAT.

Stepwise activation of a metabotropic glutamate receptor

Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain1. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain2. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding.

Binary bilayer simulations for partitioning within membranes

Membrane proteins (MPs) often show preference for one phase over the other, which is characterized by the partition coefficient, Kp. The physical mechanisms underlying Kp have been only inferred indirectly from experiments due to the unavailability of detailed structures and compositions of ordered phases. Molecular dynamics (MD) simulations can complement these details and thus, in principle, provide further insights into the partitioning of MPs between two phases. However, the application of MD has remained difficult due to long time scales required for equilibration and large system size for the phase stability, which have not been fully resolved even in free energy simulations. This chapter describes the recently developed binary bilayer simulation method, where the membrane is composed of two laterally attached membrane patches. The binary bilayer system (BBS) is designed to preserve the lateral packing of both phases in a significantly smaller size compared to that required for macroscopic phase separation. These characteristics are advantageous in partitioning simulations, as the length scale for diffusion across the system can be significantly smaller. Hence the BBS can be efficiently employed in both conventional MD and free energy simulations, though sampling in ordered phases remains difficult due to slow diffusion. Development of efficient lipid swapping methods and its combination with the BBS would be a useful approach for partitioning in coexisting phases.

Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations: Comparison to Crystal Structures

Glycans are central to information content and regulation in biological systems. These carbohydrate molecules are active either as oligo- or polysaccharides, often in the form of glycoconjugates. The monosaccharide entities are joined by glycosidic linkages and stereochemical arrangements are of utmost importance in determining conformation and flexibility of saccharides. The conformational preferences and population distributions at the glycosidic torsion angles φ and ψ have been investigated for O-methyl glycosides of three disaccharides where the substitution takes place at a secondary alcohol, viz., in α-l-Fucp-(1→3)-β-d-Glcp-OMe, α-l-Fucp-(1→3)-α-d-Galp-OMe and α-d-Glcp-(1→4)-α-d-Galp-OMe, corresponding to disaccharide structural elements present in bacterial polysaccharides. Stereochemical differences at or adjacent to the glycosidic linkage were explored by solution state NMR spectroscopy using one-dimensional 1 H,1 H-NOESY NMR experiments to obtain transglycosidic proton-proton distances and one- and two-dimensional heteronuclear NMR experiments to obtain 3 JCH transglycosidic coupling constants related to torsion angles φ and ψ. Computed effective proton-proton distances from molecular dynamics (MD) simulations showed excellent agreement to experimentally derived distances for the α-(1→3)-linked disaccharides and revealed that for the bimodal distribution at the ψ torsion angle for the α-(1→4)-linked disaccharide experiment and simulation were at variance with each other, calling for further force field developments. The MD simulations disclosed a highly intricate inter-residue hydrogen bonding pattern for the α-(1→4)-linked disaccharide, including a nonconventional hydrogen bond between H5' in the glucosyl residue and O3 in the galactosyl residue, supported by a large downfield 1 H NMR chemical shift displacement compared to α-d-Glcp-OMe. Comparison of population distributions of the glycosidic torsion angles φ and ψ in the disaccharide entities to those of corresponding crystal structures highlighted the potential importance of solvation on the preferred conformation.

Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CLPro and PLPro) by Molecular Docking and Dynamic Simulation Studies

We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.

Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study

Cytokinesis of animal and fungi cells depends crucially on the anillin scaffold proteins. Fission yeast anillin-related Mid1 anchors cytokinetic ring precursor nodes to the membrane. However, it is unclear if both of its Pleckstrin Homology (PH) and C2 C-terminal domains bind to the membrane as monomers or dimers, and if one domain plays a dominant role. We studied Mid1 membrane binding with all-atom molecular dynamics near a membrane with yeast-like lipid composition. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the disordered L3 loop of C2 in a vertical orientation, with the PH away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. Simulations of C2-PH dimers show extensive asymmetric membrane contacts. These multiple modes of binding may reflect Mid1's multiple interactions with membranes, node proteins, and ability to sustain mechanical forces.

Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.

Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities

Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages. In recent years, this has been facilitated further by the implementation of workflows that enable non-experts to quickly and consistently set up the required simulations. Given the correct input structures, workflows handle the difficult aspects of setting up perturbations, including consistently defining the perturbable molecule, its atom mapping and topology generation, perturbation network generation, running of the simulations via different sampling methods, and analysis of the results. Different academic and commercial workflows are discussed, including FEW, FESetup, FEPrepare, CHARMM-GUI, Transformato, PMX, QLigFEP, TIES, ProFESSA, PyAutoFEP, BioSimSpace, FEP+, Flare, and Orion. These workflows differ in various aspects, such as mapping algorithms or enhanced sampling methods. Some workflows can accommodate more than one molecular dynamics (MD) engine and use external libraries for tasks. Differences between workflows can present advantages for different use cases, however a lack of interoperability of the workflows' components hinders systematic comparisons.

Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family

Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52cs), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52cs reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52cs demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.

Novel peptide inhibitors targeting CD40 and CD40L interaction: A potential for atherosclerosis therapy

Atherosclerosis is a chronic inflammatory disease characterized by plaque build-up in the arteries, leading to the obstruction of blood flow. Macrophages are the primary immune cells found in the atherosclerotic lesions and are directly involved in atherosclerosis progression. Macrophages are derived from extravasating blood monocytes. The monocytic CD40 receptor is important for monocyte recruitment on the endothelium expressing the CD40 ligand (CD40L). Thus, targeting monocyte/macrophage interaction with the endothelium by inhibiting CD40-CD40L interaction may be a promising strategy for attenuating atherosclerosis. Monoclonal antibodies have been used against this target but shows various complications. We used an array of computer-aided drug discovery tools and molecular docking approaches to design a therapeutic inhibitory peptide that could efficiently bind to the critical residues (82Y, 84D, and 86N) on the CD40 receptor essential for the receptor's binding to CD40L. The initial screen identified a parent peptide with a high binding affinity to CD40, but the peptide exhibited a positive hepatotoxicity score. We then designed several novel peptidomimetic derivatives with higher binding affinities to CD40, good physicochemical properties, and negative hepatotoxicity as compared to the parent peptide. Furthermore, we conducted molecular dynamics simulations for both the apo and complexed forms of the receptor with ligand, and screened peptides to evaluate their stability. The designed peptidomimetic derivatives are promising therapeutics targeting the CD40-CD40L interaction and may potentially be used to attenuate atherosclerosis.

The GET insertase exhibits conformational plasticity and induces membrane thinning

The eukaryotic guided entry of tail-anchored proteins (GET) pathway mediates the biogenesis of tail-anchored (TA) membrane proteins at the endoplasmic reticulum. In the cytosol, the Get3 chaperone captures the TA protein substrate and delivers it to the Get1/Get2 membrane protein complex (GET insertase), which then inserts the substrate via a membrane-embedded hydrophilic groove. Here, we present structures, atomistic simulations and functional data of human and Chaetomium thermophilum Get1/Get2/Get3. The core fold of the GET insertase is conserved throughout eukaryotes, whilst thinning of the lipid bilayer occurs in the vicinity of the hydrophilic groove to presumably lower the energetic barrier of membrane insertion. We show that the gating interaction between Get2 helix α3' and Get3 drives conformational changes in both Get3 and the Get1/Get2 membrane heterotetramer. Thus, we provide a framework to understand the conformational plasticity of the GET insertase and how it remodels its membrane environment to promote substrate insertion.

Zika virus prM protein contains cholesterol binding motifs required for virus entry and assembly

For successful infection of host cells and virion production, enveloped viruses, including Zika virus (ZIKV), extensively rely on cellular lipids. However, how virus protein-lipid interactions contribute to the viral life cycle remains unclear. Here, we employ a chemo-proteomics approach with a bifunctional cholesterol probe and show that cholesterol is closely associated with the ZIKV structural protein prM. Bioinformatic analyses, reverse genetics alongside with photoaffinity labeling assays, and atomistic molecular dynamics simulations identified two functional cholesterol binding motifs within the prM transmembrane domain. Loss of prM-cholesterol association has a bipartite effect reducing ZIKV entry and leading to assembly defects. We propose a model in which membrane-resident M facilitates cholesterol-supported lipid exchange during endosomal entry and, together with cholesterol, creates a platform promoting virion assembly. In summary, we identify a bifunctional role of prM in the ZIKV life cycle by mediating viral entry and virus assembly in a cholesterol-dependent manner.

One-step site-specific S-alkylation of full-length caveolin-1: Lipidation modulates the topology of its C-terminal domain

Caveolin-1 is an integral membrane protein that is known to acquire a number of posttranslational modifications upon trafficking to the plasma membrane. In particular, caveolin-1 is palmitoylated at three cysteine residues (C133, C143, and C156) located within the C-terminal domain of the protein which could have structural and topological implications. Herein, a reliable preparation of full-length S-alkylated caveolin-1, which closely mimics the palmitoylation observed in vivo, is described. HPLC and ESI-LC-MS analyses verified the addition of the C16 alkyl groups to caveolin-1 constructs containing one (C133), two (C133 and C143), and three (C133, C143, and C156) cysteine residues. Circular dichroism spectroscopy analysis of the constructs revealed that S-alkylation does not significantly affect the global helicity of the protein; however, molecular dynamics simulations revealed that there were local regions where the helicity was altered positively or negatively by S-alkylation. In addition, the simulations showed that lipidation tames the topological promiscuity of the C-terminal domain, resulting in a disposition within the bilayer characterized by increased depth.

Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms

The dysregulation of retinoid metabolism has been linked to prevalent ocular diseases including age-related macular degeneration and Stargardt disease. Modulating retinoid metabolism through pharmacological approaches holds promise for the treatment of these eye diseases. Cellular retinol-binding protein 1 (CRBP1) is the primary transporter of all-trans-retinol (atROL) in the eye, and its inhibition has recently been shown to protect mouse retinas from light-induced retinal damage. In this report, we employed high-throughput screening to identify new chemical scaffolds for competitive, nonretinoid inhibitors of CRBP1. To understand the mechanisms of interaction between CRBP1 and these inhibitors, we solved high-resolution X-ray crystal structures of the protein in complex with six selected compounds. By combining protein crystallography with hydrogen/deuterium exchange mass spectrometry, we quantified the conformational changes in CRBP1 caused by different inhibitors and correlated their magnitude with apparent binding affinities. Furthermore, using molecular dynamic simulations, we provided evidence for the functional significance of the "closed" conformation of CRBP1 in retaining ligands within the binding pocket. Collectively, our study outlines the molecular foundations for understanding the mechanism of high-affinity interactions between small molecules and CRBPs, offering a framework for the rational design of improved inhibitors for this class of lipid-binding proteins.