CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Plasmin cleavage of β2-glycoprotein I alters its structure and ability to bind to pathogenic antibodies

BACKGROUND

β2-Glycoprotein I (β2GPI) is the main autoantigenic target of antiphospholipid syndrome, with antibodies leading to clinical manifestations. There are 2 known structural isomers of β2GPI: a J shape and a circular shape. The transition between these structures is incompletely understood, with the functional implications unknown. β2GPI is a substrate of the protease plasmin, which cleaves within the fifth domain of β2GPI, leading to altered cellular binding. Very little is currently known regarding the structure and function of this protein variant. We present the first comprehensive structural characterization of plasmin-clipped β2GPI and the associated implications for pathogenic antibody binding to this protein.

AIM

To determine if cleavage of B2GPI by plasmin triggers structural change, and what this change may mean for antibody reactivity.

METHODS

β2GPI was purified using an adapted acid-free process from healthy control plasma and cleaved with plasmin. Cleavage was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Structural characterization was undertaken using dynamic light scattering, small-angle X-ray scattering, ion mobility mass spectrometry, and molecular dynamics simulation. Activity was tested using inhibition of β2GPI enzyme-linked immunosorbent assays with patient samples and cleaved β2GPI in the fluid phase and cellular binding by flow cytometry using human umbilical vein endothelial cells.

RESULTS

Dynamic light scattering revealed a significantly smaller hydrodynamic radius for plasmin-clipped β2GPI (P = .0043). Small-angle X-ray scattering and molecular dynamics analysis indicated a novel S-like structure of β2GPI only present in the plasmin-clipped sample, while ion mobility mass spectrometry showed different structure distributions in plasmin-clipped compared with nonclipped β2GPI. The increased binding of autoantibodies was shown for plasmin-clipped β2GPI (P = .056), implying a greater exposure of pathogenic epitopes following cleavage.

CONCLUSION

Cleavage of β2GPI by plasmin results in the production of a unique S-shaped structural conformation and higher patient antibody binding. This novel structure may increase the production of antibodies and explain the loss of binding to phospholipids described previously for plasmin-clipped β2GPI.

An integrated multiscale computational framework deciphers SARS-CoV-2 resistance to sotrovimab

The emergence of resistance mutations in the SARS-CoV-2 spike (S) protein presents a challenge for monoclonal antibody treatments like sotrovimab. Understanding the structural, dynamic, and molecular features of these mutations is essential for therapeutic advancements. However, the intricate landscape of potential mutations and critical residues conferring resistance to mAbs like sotrovimab remains elusive. This study introduces an integrated framework that combines interface protein design, machine learning, hybrid quantum mechanics/molecular mechanics methodologies, all-atom and coarse-grained molecular dynamics simulations, and correlation analysis. Beginning with the interface-based design and analysis, this framework elucidates the interaction between sotrovimab and the S-protein, identifying pivotal residues and plausible resistance mutations. Machine learning algorithms then facilitate the identification of potential resistance mutations using structural-sequence-binding affinity-energetics features. The hybrid quantum mechanics/molecular mechanics approach subsequently evaluates the role of mutational residues as quantum regions, assessing their impact on stabilizing the macromolecular complex. To gain a deeper understanding of the dynamic behavior of these mutations, multiscale simulations comprising all-atom and coarse-grained molecular dynamics simulations were performed, revealing their structural, biophysical and energetic impacts. These simulations complemented the static predictions, capturing the conformational dynamics and stability of the mutants in presence of glycan in the S-protein. The accuracy of the predictions is validated by correlating identified resistance mutations with clinical-sequencing data and empirical evidence from sotrovimab-treated patients. Notably, two residues, E340 at the S-protein-sotrovimab interface and Y508 distal from it, and their designs, align with clinically observed resistance mutations. Furthermore, machine learning approaches predict novel S-protein sequences with enhanced/reduced affinity for sotrovimab, validated structurally using AlphaFold. This integrated framework showcases its effectiveness in identifying potential resistance mutations, corroborated with clinical insights and offering a multidimensional strategy for decoding resistance mutations in SARS-CoV-2. Its translational relevance extends to understanding resistance mechanisms and designing novel antibody therapeutics in other systems.

Viral fusion proteins of classes II and III recognize and reorganize complex biological membranes

Viral infection requires stable binding of viral fusion proteins to host membranes, which contain hundreds of lipid species. The mechanisms by which fusion proteins utilize specific host lipids to drive virus-host membrane fusion remains elusive. We conducted molecular simulations of classes I, II, and III fusion proteins interacting with membranes of diverse lipid compositions. Free energy calculations reveal that class I fusion proteins generally exhibit stronger membrane binding compared to classes II and III - a trend consistent across 74 fusion proteins from 13 viral families as suggested by sequence analysis. Class II fusion proteins utilize a lipid binding pocket formed by fusion protein monomers, stabilizing the initial binding of monomers to the host membrane prior to assembling into fusogenic trimers. In contrast, class III fusion proteins form a lipid binding pocket at the monomer-monomer interface through a unique fusion loop crossover. The distinct lipid binding modes correlate with the differing maturation pathways of classes II and III proteins. Binding affinity was predominantly controlled by cholesterol and gangliosides as well as via local enrichment of polyunsaturated lipids, thereby locally enhancing membrane disorder. Our study reveals energetics and atomic details underlying lipid recognition and reorganization by different viral fusion protein classes, offering insights into their specialized membrane fusion pathways.

All-atom virus simulations to tackle airborne disease

We briefly review the latest computational studies focused on modeling viruses with classical all-atom (AA) molecular dynamics. We report on the challenges, current solutions, and ongoing developments in constructing and simulating whole viruses, and discuss unique insights derived from AA mesoscale simulations that cannot be achieved by other means. Finally, we present new opportunities in computational virology to understand viral aerostability within the context of respiratory disease transmission. Overall, we highlight the value of large-scale AA simulation and champion the need for increased interdisciplinary collaboration to generate novel insights and guide future research in respiratory disease.

Wood Biomolecules as Agricultural Adjuvants for Effective Suppression of Droplet Rebound from Plant Foliage

The agrochemical run-off associated with crop control is an unintended consequence of droplet rebound from plant foliage, which negatively affects crop performance and the environment. This is most critical in water-based formulations delivered on plant surfaces that are typically waxy and nonwetting. This study introduces an alternative to synthetic surfactants and high molecular weight polymers that are used as spreading agents for agrochemicals. Specifically, biopolymeric adjuvants (hemicelluloses and oligomeric lignin) extracted from wood by pressurized hot water are shown for their synergistic pinning capacity and surface activity that can effectively suppress droplet rebound from hydrophobic surfaces. Hemicellulose and lignin mixtures, alongside several model compounds, are investigated for understanding the dynamics of droplet impact and its correlation with biomacromolecule formations. The benefit of utilizing lean solutions (0.1 wt.% concentration) is highlighted for reducing droplet rebounding from leaves, outperforming synthetic systems in current use. For instance, a tenfold deposition improvement is demonstrated on citrus leaves, because of a significantly suppressed droplet roll-off. These results establish the excellent prospects of wood extracts to improve crop performance.

IgG4 and IgG1 undergo common acid-induced compaction into an alternatively folded state

Immunoglobulin G1 (IgG1) antibodies undergo denaturation in acidic conditions, resulting in an alternatively folded state (AFS). The AFS structure is more compact than the native state. However, the prevalence of AFS in other subclasses remains largely unexplored. This study provides evidence that humanized IgG4 can also adopt the AFS structure, as demonstrated through size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis. These findings suggest that the anomalous compaction of immunoglobulins G (IgGs) is resilient to variations in sequence and structure among subclasses.

Physical insights guided rational design of anti-EGFR antibody to reverse the acquired resistance

Cetuximab (Ctx), a monoclonal antibody targeting the epidermal growth factor receptor (EGFR) for colorectal cancer treatment, often faces diminished clinical efficacy due to acquired resistance driven by EGFR mutations. Here, we investigated the molecular mechanisms underlying this mutation-induced drug resistance and developed a mechanism-based strategy to restore the binding affinity of Ctx to EGFR mutants. Through molecular dynamics simulations and free energy perturbation calculations, we discovered that most resistant mutations primarily alter the electrostatic properties of the binding interface. Focusing on two key mutations, EGFR K489E and I491M, we rationally designed two Ctx variants-CtxD103R for EGFRK489E and CtxD103E_E105D for EGFRI491M-using electrostatic compensation and steric hindrance adjustment strategies. Surface plasmon resonance measurements verified that the two designed Ctx variants exhibit improved binding affinity to the corresponding EGFR mutants compared with wild-type Ctx. Additionally, western blot experiments using HEK-293T cells showed that the designed CtxD103R effectively inhibits EGF-stimulated phosphorylation of EGFRK489E. Our findings highlight a rational design approach, empowered by interaction landscape at atomic detail, as a promising and cost-effective strategy to combat mutation-driven resistance in antibody therapies.

Impact of SARS-CoV-2 RBM Mutations N501Y and E484K on ACE2 Binding: A Combined Computational and Experimental Study

The SARS-CoV-2 spike receptor-binding motif is crucial for viral entry via interaction with the human ACE2 receptor. Mutations N501Y and E484K, found in several variants of concern, impact viral transmissibility and immune escape, but experimental data on their binding effects remain inconsistent. Using isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations, we analyzed the thermodynamic and structural effects of these mutations. ITC confirmed that N501Y increases ACE2 affinity by 2.2-fold, while E484K enhances binding by 5.8-fold. The Beta/Gamma variant (carrying both mutations) showed the strongest affinity, with a 15-fold increase. E484K was enthalpy-driven, while N501Y introduced entropy-driven effects, suggesting hydrophobic interactions and conformational changes. MD simulations revealed distinct binding poses, with Beta/Gamma peptides interacting with a secondary ACE2 site. A strong correlation was found between entropy contributions and hydrophobic contacts. Additionally, a convolutional neural network was used to estimate the free binding energy of these complexes. Our findings confirm that N501Y and E484K enhance ACE2 binding, with the greatest effect when combined, providing insights into SARS-CoV-2 variant evolution and potential therapeutic strategies.

Heparan-6-O-endosulfatase 2, a cancer-related proteoglycan enzyme, is effectively inhibited by a specific sea cucumber fucosylated glycosaminoglycan

Heparan-6-O-endosulfatase 2 (Sulf-2) is a proteoglycan enzyme that modifies sulfation of heparan sulfate proteoglycans. Dysregulation of Sulf-2 is associated with various pathological conditions, including cancer, which makes Sulf-2 a potential therapeutic target. Despite the key pathophysiological roles of Sulf-2, inhibitors remain insufficiently developed. In previous work, a fucosylated chondroitin sulfate from the sea cucumber Holothuria floridana (HfFucCS) exhibited potent Sulf-2 inhibition. This study investigates the structural basis of HfFucCS-mediated Sulf-2 inhibition, examines the binding profile of HfFucCS to Sulf-2, and explores the mode of inhibition. Additionally, a structurally diverse library of sulfated poly/oligosaccharides, including common glycosaminoglycans and unique marine sulfated glycans, was screened for Sulf-2 inhibition. Results from a high-throughput arylsulfatase assay and specific 6-O-desulfation assay have proved that HfFucCS is the most potent among the tested sulfated glycans, likely due to the presence of the unique 3,4-disulfated fucose structural motif. HfFucCS demonstrated non-competitive inhibition, and inhibitory analysis of its low-molecular-weight fragments suggests a minimum length of ~7.5 kDa for effective inhibition. Surface plasmon resonance analyses revealed that Sulf-2 binds to surface heparin with high affinity (KD of 0.817 nM). HfFucCS and its derivatives effectively disrupt this interaction. Results from mass spectrometry-hydroxyl radical protein footprinting and repulsive scaling replica exchange molecular dynamics indicate similarities in the binding of heparin and HfFucCS oligosaccharides to both the catalytic and hydrophilic domains of Sulf-2. These findings reveal the unique inhibitory properties of a structurally distinct marine glycosaminoglycan, supporting its further investigation as a selective and effective inhibitor for Sulf-2-associated cancer events.

Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding

The von Willebrand factor (VWF), a multimeric plasma glycoprotein, binds to the platelet glycoprotein (GPIbα) to initiate the process of primary hemostasis as a response to blood flow alteration in the site of vascular injury. The GPIbα binding site located on the A1 domain of VWF is exposed during the activation of the VWF multimer when it changes from a coiled form to a thread-like, extended form. Though experimental studies have demonstrated that the autoinhibitory module (AIM) connected to the N-/C-termini of the A1 domain is a regulator of VWF activity, the molecular mechanism underlying the regulation of A1-GPIbα binding remains unclear. We modeled the structures of the A1 domain having full-length N-terminal AIM (NAIM) and C-terminal AIM (CAIM) with different types of O-linked glycans. The conventional and steered molecular dynamics simulations were conducted to investigate the dynamics of the AIM and O-glycans under different conditions and elucidate how they affect the binding of GPIbα. Our results indicate that the NAIM alone with no glycan is sufficient to shield the GPIbα binding site under static conditions. However, when the AIM is unfolded with external forces applied, the O-glycans on both NAIM and CAIM increase the shielding of the binding site. These findings suggest a potential mechanism by which the AIM and O-glycans regulate the interaction of the VWF A1 domain and GPIbα.

MGAT1-Guided complex N-Glycans on CD73 regulate immune evasion in triple-negative breast cancer

Despite the widespread application of immunotherapy, treating immune-cold tumors remains a significant challenge in cancer therapy. Using multiomic spatial analyses and experimental validation, we identify MGAT1, a glycosyltransferase, as a pivotal factor governing tumor immune response. Overexpression of MGAT1 leads to immune evasion due to aberrant elevation of CD73 membrane translocation, which suppresses CD8+ T cell function, especially in immune-cold triple-negative breast cancer (TNBC). Mechanistically, addition of N-acetylglucosamine to CD73 by MGAT1 enables the CD73 dimerization necessary for CD73 loading onto VAMP3, ensuring membrane fusion. We further show that THBS1 is an upstream etiological factor orchestrating the MGAT1-CD73-VAMP3-adenosine axis in suppressing CD8+ T cell antitumor activity. Spatial transcriptomic profiling reveals spatially resolved features of interacting malignant and immune cells pertaining to expression levels of MGAT1 and CD73. In preclinical models of TNBC, W-GTF01, an inhibitor specifically blocked the MGAT1-catalyzed CD73 glycosylation, sensitizing refractory tumors to anti-PD-L1 therapy via restoring capacity to elicit a CD8+ IFNγ-producing T cell response. Collectively, our findings uncover a strategy for targeting the immunosuppressive molecule CD73 by inhibiting MGAT1.

Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study

The SARS-CoV-2 Omicron variants show different behavior compared to the previous variants, especially with respect to the Delta variant, which promotes a lower morbidity despite being much more contagious. In this perspective, we performed molecular dynamics (MD) simulations of the different spike RBD/hACE2 complexes corresponding to the WT, Delta and four Omicron variants. Carrying out a comprehensive analysis of residue interactions within and between the two partners allowed us to draw the profile of each variant by using complementary methods (PairInt, hydrophobic potential, contact PCA). PairInt calculations highlighted the residues most involved in electrostatic interactions, which make a strong contribution to the binding with highly stable interactions between spike RBD and hACE2. Apolar contacts made a substantial and complementary contribution in Omicron with the detection of two hydrophobic patches. Contact networks and cross-correlation matrices were able to detect subtle changes at point mutations as the S375F mutation occurring in all Omicron variants, which is likely to confer an advantage in binding stability. This study brings new highlights on the dynamic binding of spike RBD to hACE2, which may explain the final persistence of Omicron over Delta.

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining region (CDR) grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein's structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high-affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.

Molecular Basis of High-Blood-Pressure-Enhanced and High-Fever-Temperature-Weakened Receptor-Binding Domain/Peptidase Domain Binding: A Molecular Dynamics Simulation Study

The entry and infection of the Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) involve recognition and binding of the receptor-binding domain (RBD) of the virus surface spike protein to the peptidase domain (PD) of the host cellular Angiotensin-Converting Enzyme-2 (ACE2) receptor. ACE2 is also involved in normal blood pressure control. An association between hypertension and COVID-19 severity and fatality is evident, but how hypertension predisposes patients diagnosed with COVID-19 to unfavorable outcomes remains unclear. High temperature early during SARS-CoV-2 infection impairs binding to human cells and retards viral progression. Low body temperature can prelude poor prognosis. In this study, all-atom molecular dynamics simulations were performed to examine the effects of high pressure and temperature on RBD/PD binding. A high blood pressure of 940 mmHg enhanced RBD/PD binding. A high temperature above 315 K significantly weakened RBD/PD binding, while a low temperature of 305 K enhanced binding. The curvature of the PD α1-helix and proximity of the PD β3β4-hairpin tip to the RBM motif affected the compactness of the binding interface and, hence, binding affinity. These findings provide novel insights into the underlying mechanisms by which hypertension predisposes patients to unfavorable outcomes in COVID-19 and how an initial high temperature retards viral progression.

Effect of Acetylation Patterns of Xylan on Interactions with Cellulose

The present study demonstrates that the change in the degree of xylan acetylation significantly alters the 2-fold screw population that effectively interacts with the (100) hydrophobic cellulose, while such effects are less prominent for the (110) hydrophilic surface. All of the acetylated xylans reveal an ≈10-40% higher 2-fold population on the hydrophobic cellulose due to higher xylan-cellulose contacts. Deviations from periodic acetylation result in much lower 2-fold conformations, despite a comparable number of xylan-cellulose hydrogen bonds and contacts. Thus, it can be hypothesized that a specific and unique set of xylan: cellulose interactions mediate the formation of 2-fold xylan to interact with cellulose, which is also a 2-fold screw. Highly acetylated xylans desorb from cellulose, while low acetylated xylans show dependence on the topology of the cellulose surface. These findings provide additional insights into plant cell wall microstructure dynamics and inform future strategies for efficient biomass deconstruction in biofuel production.

Extending the Martini 3 Coarse-Grained Force Field to Hyaluronic Acid

Hyaluronan, also known as hyaluronic acid, is a large glycosaminoglycan composed of repeating disaccharide units. It plays a crucial role in providing structural support, hydration, and facilitating cellular processes in connective tissue, skin, and the extracellular matrix in biological systems. We present a coarse-grained (CG) model of hyaluronic acid (HA) and its constituent residues, N-acetyl-d-glucosamine (GlcNAc) and glucuronic acid (GlcA), designed to be compatible with the Martini 3 force field. The model was validated against atomistic molecular dynamics simulations following standard procedures to ensure the accuracy of bonded interactions and, in the case of GlcNAc, the free energies of transfer between octanol and water. For the final HA model, we investigated its properties by simulating the self-assembly of HA chains at varying ion concentrations in solution and comparing the persistence length of single-chain HA with experimental data. We also studied the interactions of HA with lipid bilayers and various HA-binding proteins, demonstrating the ability of the model to accurately reproduce interactions with other biomolecules characteristic of natural biological systems. This extension of the carbohydrate-dedicated branch of the CG Martini 3 force field enables large-scale molecular dynamics simulations of HA-containing systems and contributes to a better understanding of the roles and functions of hyaluronan in natural biomolecular systems.

Pharmacological Dissection Identifies Retatrutide Overcomes the Therapeutic Barrier of Obese TNBC Treatments through Suppressing the Interplay between Glycosylation and Ubiquitylation of YAP

Triple-negative breast cancer (TNBC) in obese patients remains challenging. Recent studies have linked obesity to an increased risk of TNBC and malignancies. Through multiomic analysis and experimental validation, a dysfunctional Eukaryotic Translation Initiation Factor 3 Subunit H (EIF3H)/Yes-associated protein (YAP) proteolytic axis is identified as a pivotal junction mediating the interplay between cancer-associated adipocytes and the response to anti-cancer drugs in TNBC. Mechanistically, cancer-associated adipocytes drive metabolic reprogramming resulting in an upregulated hexosamine biosynthetic pathway (HBP). This aberrant upregulation of HBP promotes YAP O-GlcNAcylation and the subsequent recruitment of EIF3H deubiquitinase, which stabilizes YAP, thus promoting tumor growth and chemotherapy resistance. It is found that Retatrutide, an anti-obesity agent, inhibits HBP and YAP O-GlcNAcylation leading to increased YAP degradation through the deprivation of EIF3H-mediated deubiquitylation of YAP. In preclinical models of obese TNBC, Retatrutide downregulates HBP, decreases YAP protein levels, and consequently decreases tumor size and enhances chemotherapy efficacy. This effect is particularly pronounced in obese mice bearing TNBC tumors. Overall, these findings reveal a critical interplay between adipocyte-mediated metabolic reprogramming and EIF3H-mediated YAP proteolytic control, offering promising therapeutic strategies to mitigate the adverse effects of obesity on TNBC progression.

Identifying multi-target drugs for prostate cancer using machine learning-assisted transcriptomic analysis

Prostate cancer is a leading cause of cancer death in men, and the development of effective treatments is of great importance. This study explored to identify the candidate drugs for prostate cancer by transcriptomic data and CMap database analysis. After integrating the results of omics analysis, bisoprolol is confirmed as a promising drug. Moreover, cell experiment reveals its potential inhibitory effect on the proliferation of prostate cancer cells. Importantly, machine learning methods are employed to predict the targets of bisoprolol, and the dual-target ADRB3 and hERG are explored by dynamic simulation. The findings of this study demonstrate the potential of bisoprolol as a multi-target drug for prostate cancer treatment and the feasibility of using beta-adrenergic receptor inhibitors in prostate cancer treatment. In addition, the proposed research approach is promising for discovering potential drugs for cancer treatment by leveraging the concept of drug side effects leading to anticancer effects. Further research is necessary to investigate the pharmacological action, potential toxicity, and underlying mechanisms of bisoprolol in treating prostate cancer with ADRB3.Communicated by Ramaswamy H. Sarma.

Structural and functional insights into recombinant β-glucosidase from Thermothelomyces thermophilus: Cello-oligosaccharide hydrolysis and thermostability

β-glucosidases (BGLs) are key enzymes in the depolymerization of cellulosic biomass, catalyzing the conversion of cello-oligosaccharides into glucose. This conversion is pivotal for enhancing the production of second-generation ethanol or other value-added products in biorefineries. However, the process is often cost-prohibitive due to the high enzyme loadings required. Therefore, the discovery of new highly efficient BGLs represents a significant advancement. In this study, a BGL from the glycoside hydrolase family 3 (GH3) of the thermophilic fungus Thermothelomyces thermophilus (TthBgl3A) was heterologously expressed in Aspergillus nidulans. The recombinant enzyme exhibited optimal activity at pH 5.0 and 55 °C, with noteworthy stability for up to 160 h. A distinctive, extensive loop within the catalytic cavity of TthBgl3A facilitates hydrophobic interactions that enhance the binding and hydrolysis of long cello-oligosaccharides. Consequently, TthBgl3A has proven to be an efficient enzyme for the hydrolysis lignocellulosic biomass. These findings are significant for expanding the repertoire of enzymes produced by T. thermophilus and provide new insights into the potential application of TthBgl3A in the degradation of cellulosic materials and the production of valuable compounds.

Unraveling the Structural Basis of Biased Agonism in the β2-Adrenergic Receptor Through Molecular Dynamics Simulations

Biased agonism in G protein-coupled receptors is a phenomenon resulting in the selective activation of distinct intracellular signaling pathways by different agonists, which may exhibit bias toward either Gs, Gi, or arrestin-mediated pathways. This study investigates the structural basis of ligand-induced biased agonism within the context of the β2-adrenergic receptor (β2-AR). Atomistic molecular dynamics simulations were conducted for β2-AR complexes with two stereoisomers of methoxynaphtyl fenoterol (MNFen), that is, compounds eliciting qualitatively different cellular responses. The simulations reveal distinct interaction patterns within the binding cavity, dependent on the stereoisomer. These changes propagate to the intracellular parts of the receptor, triggering various structural responses: the dynamic structure of the intracellular regions of the (R,R)-MNFen complex more closely resembles the "Gs-compatible" and "β-arrestin-compatible" conformation of β2-AR, while both stereoisomers maintain structural responses equidistant from the inactive conformation. These findings are confirmed by independent coarse-grained simulations. In the context of deciphered molecular mechanisms, Trp313 plays a pivotal role, altering its orientation upon interactions with (R,R)-MNFen, along with the Lys305-Asp192 ionic bridge. This effect, accompanied by ligand interactions with residues on TM2, increases the strength of interactions within the extracellular region and the binding cavity, resulting in a slightly more open conformation and a minor (by ca. 0.2 nm) increase in the distance between the TM5-TM7, TM1-TM6, TM6-TM7, and TM1-TM5 pairs. On the other hand, an even slighter decrease in the distance between the TM1-TM4 and TM2-TM4 pairs is observed.

Exploring the effects of N234 and N343 linked glycans to SARS CoV 2 spike protein pocket accessibility using Gaussian accelerated molecular dynamics simulations

The N234 and N343-linked glycans of the SARS-CoV 2 spike protein are known to stabilize the up-conformation of its receptor-binding domains (RBDs), enabling human angiotensin enzyme 2 (hACE2) receptor binding. However, the effect of spike-hACE2 binding on these important glycans remains poorly understood, and these changes could have implications in the development of drugs that inhibit viral entry. In this study, Gaussian accelerated molecular dynamics (GaMD) simulations of the hACE2-free and hACE2-bound spike protein are performed. Biophysical analyses were focused on the accessibility of three previously suggested druggable pockets underneath the three RBD subunits. A shielding effect by N234-linked glycans on the components of their adjacent pockets was observed. Although deshielding of central scaffold residues was observed in the hACE2-bound state, pocket A's accessibility was reduced due to an increase in NTDB-RBDB contacts, restricting entry into the pocket. For pocket B, changes in N234C and N343C expose the central scaffold residues in the bound state, increasing accessibility. In Pocket C, increased shielding due to N234A was found in the bound state, reducing accessibility. Despite these changes, the pockets remain accessible to ligands in both states and are still valid targets for drug development studies.

The effect of cysteine oxidation on conformational changes of SARS-CoV-2 spike protein using atomistic simulations

The SARS-CoV-2 Spike (S) protein plays a central role in viral entry into host cells, making it a key target for therapeutic interventions. Oxidative stress, often triggered during viral infections, can cause oxidation of cysteine in this protein. Here we investigate the impact of cysteine oxidation, specifically the formation of cysteic acid, on the conformational dynamics of the SARS-CoV-2 S protein using atomistic simulations. In particular, we examine how cysteine oxidation influences the transitions of the S protein's receptor-binding domain (RBD) between "down" (inaccessible) and "up" (accessible) states, which are critical for host cell receptor engagement. Using solvent-accessible surface area (SASA) analysis, we identify key cysteine residues susceptible to oxidation. The results of targeted molecular dynamics (TMD) and umbrella sampling (US) simulations reveal that oxidation reduces the energy barrier for RBD transitions by approximately 30 kJ mol-1, facilitating conformational changes and potentially enhancing viral infectivity. Furthermore, we analyze the interactions between oxidized cysteine residues and glycans, as well as alterations in hydrogen bonds and salt bridges. Our results show that oxidation disrupts normal RBD dynamics, influencing the energy landscape of conformational transitions. Our work provides novel insights into the role of cysteine oxidation in modulating the structural dynamics of the SARS-CoV-2 S protein, highlighting potential targets for antiviral strategies aimed at reducing oxidative stress or modifying post-translational changes. These findings contribute to a deeper understanding of viral infectivity and pathogenesis under oxidative conditions.

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field

Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure-dynamics-function relationships of macromolecules to which they are attached, with the exception of nucleic acids. This is largely due to the inherent difficulties of not only studying the conformational dynamics of sugars using experimental methods but indeed also resolving their static structures. Molecular dynamics (MD) simulations offer a route to the prediction of conformational ensembles and the time-dependent behavior of sugars and glycosylated macromolecules. However, at the all-atom level of detail, MD simulations are often too computationally demanding to allow a systematic investigation of molecular interactions in systems of interest. To overcome this, large scale simulations of complex biological systems have profited from advances in coarse-grained (CG) simulations. Perhaps the most widely used CG force field for biomolecular simulations is Martini. Here, we present a parameter set for glucose- and mannose-based disaccharides for Martini 3. The generation of the CG parameters from atomistic trajectories is automated as fully as possible, and where not possible, we provide details of the protocol used for manual intervention.

Energetics of Oligosaccharide Adsorption on Ionic Liquid-Clay Composites

Well-Tempered Metadynamics (WT-MetaD) simulations indicate that composite materials made up of Na-Montmorillonite (Na-MMT) coated with ionic liquids (ILs) having hydrophilic cations serve as good adsorbents for a hexameric (1,4) linked β-D-glucopyranoside (BGLC). Hydrophilic IL cations are effectively coated on the negative charges lining the Na-MMT surface while attracting simultaneously the polar oligosaccharides. In this work we have used two less conventional polyethylene glycol (PEG) based IL cations, [mim2 peg1]2+ and [mim2 peg2]2+, paired with [tf2N]- and Cl- anions. Another strongly hydrophilic ion combination, [C2OHmim][Cl], also showed great promise in effective oligosaccharide adsorption on the Na-MMT surface. The study reveals that the topological polar surface area (TPSA), the octanol-water partition coefficient (log PO/W), the length of the cationic side chain and the Debye screening lengthλ D ${\left({\lambda }_{D}\right)}$ of the IL are some of the most important factors affecting the adsorption of hydrophilic oligosaccharides on the clay-IL composites. Among all the systems studied, [mim2 peg2][tf2N]2 having the highest TPSA and a long screening length emerged as the best adsorbent for the oligosaccharide on the IL-coated clay.

N-linked glycosylation affects catalytic parameters and fluctuation of the active center of Aspergillus awamori exo-inulinase

Heterogeneous expression of enzymes allows large-scale production with reduced costs. Changes in glycosylation often occur due to changes in the expression host. In the study, the catalytic and biochemical properties of Aspergillus awamori exo-inulinase 1 are compared for A. awamori and Penicillium verruculosum expression hosts. The tertiary structure contains seven sites of N-glycosylation, with two of them located near the active center. If expressed in P. verruculosum, the enzyme was four times less glycosylated and two times more active toward sucrose, raffinose, and stachyose due to an increase in kcat. These substrates with a short chain of 2-4 monosaccharide units were used to characterize the interaction of the substrate with the amino acid residues in the active center while preventing the interaction of the substrate with N-linked glycans. Molecular dynamics simulations showed an increase in the fluctuation of the active center with an increase in the length of N-linked glycans. The fluctuation of the residues N40 and Q57, which interact with the hydroxyl group O5 of the fructose unit in the -1 subsite of the active center, was increased by 1.6 times. The fluctuation of the residue W335, which interacts with the hydroxyl group O1 of the fructose unit together with the catalytic residue D41 and affects the torsion angle geometry of the substrate molecules, was increased by 1.5 times. The residue R188, which analogously to W335 affects the torsion angle geometry of the substrate molecules, was also among the affected residues with a 1.2-fold increase in the fluctuation.

Unveiling the Electrical Properties of Hyaluronan-Coated Cancer Extracellular Vesicles Using Correlative Scanning Probe Microscopy-Based Nano-Electrical Modes

Cancer cells produce extracellular vesicles (EVs) coated with an anionic sugar polymer, hyaluronan (HA), in the extracellular matrix. Hyaluronan is an established cancer biomarker in several cancer types. In this work, we thoroughly investigated the electrical properties of HA-coated EVs using advanced scanning probe microscopy (SPM) based nanoelectrical modes, which include EFM (electrostatic force microscopy), KPFM (Kelvin probe force microscopy), PFM (piezoresponse force microscopy) and C-AFM (conductive atomic force microscopy). Analyses revealed distinct properties for different sets of EVs regarding surface potential, charge distribution, and piezoelectric electro-mechanical response at the single-vesicle resolution. The typical electron transport capabilities are primarily driven by ions in sandwiched EV junctions. This correlative approach essentially could distinguish HA-coated cancer EVs (CEVs) from normal EV (NEVs) counterparts. The combined SPM-based nanoelectrical modes offered a multiplexed one-stop label-free solution for EV's electrical property assessments. This strategy is useful in developing EV-based bioelectronic sensors.

Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD

Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics (MD) simulations are utilized to estimate binding poses and binding free energies of small-molecule drugs to proteins, quantitative prediction of the binding thermodynamics of PE-based drugs presents a significant obstacle in computer-aided drug design. This is due to the sluggish dynamics of PEs caused by their size and strong charge-charge correlations. In this paper, we introduce advanced sampling methods based on a force-spectroscopy setup and theoretical modeling to overcome this barrier. We exemplify our method with explicit solvent all-atom MD simulations of the interactions between anionic PEs that show antiviral properties, namely heparin and linear polyglycerol sulfate (LPGS), and the SARS-CoV-2 spike protein receptor binding domain (RBD). Our prediction for the binding free-energy of LPGS to the wild-type RBD matches experimentally measured dissociation constants within thermal energy, k B T, and correctly reproduces the experimental PE-length dependence. We find that LPGS binds to the Delta-variant RBD with an additional free-energy gain of 2.4 k B T, compared to the wild-type RBD, due to the additional presence of two mutated cationic residues contributing to the electrostatic energy gain. We show that the LPGS-RBD binding is solvent dominated and enthalpy driven, though with a large entropy-enthalpy compensation. Our method is applicable to general polymer adsorption phenomena and predicts precise binding free energies and reconfigurational friction as needed for drug and drug-delivery design.

Balancing enthalpy and entropy in inhibitor binding to the prostate-specific membrane antigen (PSMA)

Understanding the molecular mechanism of inhibitor binding to prostate-specific membrane antigen (PSMA) is of fundamental importance for designing targeted drugs for prostate cancer. Here we designed a series of PSMA-targeting inhibitors with distinct molecular structures, which were synthesized and characterized using both experimental and computational approaches. Microsecond molecular dynamics simulations revealed the structural and thermodynamic details of PSMA-inhibitor interactions. Our findings emphasize the pivotal role of the inhibitor's P1 region in modulating binding affinity and selectivity and shed light on the binding-induced conformational shifts of two key loops (the entrance lid and the interface loop). Binding energy calculations demonstrate the enthalpy-entropy balance in the thermodynamic driving force of different inhibitors. The binding of inhibitors in monomeric form is entropy-driven, in which the solvation entropy from the binding-induced water restraints plays a key role, while the binding of inhibitors in dimeric form is enthalpy-driven, due to the promiscuous PSMA-inhibitor interactions. These insights into the molecular driving force of protein-ligand binding offer valuable guidance for rational drug design.

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.

Development of a Sustainable Flexible Humidity Sensor Based on Tenebrio molitor Larvae Biomass-Derived Chitosan

This study presents the fabrication of a sustainable flexible humidity sensor utilizing chitosan derived from mealworm biomass as the primary sensing material. The chitosan-based humidity sensor was fabricated by casting chitosan and polyvinyl alcohol (PVA) films with interdigitated copper electrodes, forming a laminate composite suitable for real-time, resistive-type humidity detection. Comprehensive characterization of the chitosan film was performed using Fourier-transform infrared (FTIR) spectroscopy, contact angle measurements, and tensile testing, which confirmed its chemical structure, wettability, and mechanical stability. The developed sensor exhibited a broad range of measurements from 6% to 97% relative humidity (RH), a high sensitivity of 2.43 kΩ/%RH, and a rapid response time of 18.22 s with a corresponding recovery time of 22.39 s. Moreover, the chitosan-based humidity sensor also demonstrated high selectivity for water vapor when tested against various volatile organic compounds (VOCs). The superior performance of the sensor is attributed to the structural properties of chitosan, particularly its ability to form reversible hydrogen bonds with water molecules. This mechanism was further elucidated through molecular dynamics simulations, revealing that the conductivity in the sensor is modulated by proton mobility, which operates via the Grotthuss mechanism under high-humidity and the packed-acid mechanism under low-humidity conditions. Additionally, the chitosan-based humidity sensor was further seamlessly integrated into an Internet of Things (IoT) framework, enabling wireless humidity monitoring and real-time data visualization on a mobile device. Comparative analysis with existing polymer-based resistive-type sensors further highlighted the superior sensing range, rapid dynamic response, and environmental sustainability of the developed sensor. This eco-friendly, biomass-derived, eco-friendly sensor shows potential for applications in environmental monitoring, smart agriculture, and industrial process control.

Isoform-specific N-linked glycosylation of NaV channel α-subunits alters β-subunit binding sites

Voltage-gated sodium channel α-subunits (NaV1.1-1.9) initiate and propagate action potentials in neurons and myocytes. The NaV β-subunits (β1-4) have been shown to modulate α-subunit properties. Homo-oligomerization of β-subunits on neighboring or opposing plasma membranes has been suggested to facilitate cis or trans interactions, respectively. The interactions between several NaV channel isoforms and β-subunits have been determined using cryogenic electron microscopy (cryo-EM). Interestingly, the NaV cryo-EM structures reveal the presence of N-linked glycosylation sites. However, only the first glycan moieties are typically resolved at each site due to the flexibility of mature glycan trees. Thus, existing cryo-EM structures may risk de-emphasizing the structural implications of glycans on the NaV channels. Herein, molecular modeling and all-atom molecular dynamics simulations were applied to investigate the conformational landscape of N-linked glycans on NaV channel surfaces. The simulations revealed that negatively charged sialic acid residues of two glycan sites may interact with voltage-sensing domains. Notably, two NaV1.5 isoform-specific glycans extensively cover the α-subunit region that, in other NaV channel α-subunit isoforms, corresponds to the binding site for the β1- (and likely β3-) subunit immunoglobulin (Ig) domain. NaV1.8 contains a unique N-linked glycosylation site that likely prevents its interaction with the β2 and β4-subunit Ig-domain. These isoform-specific glycans may have evolved to facilitate specific functional interactions, for example, by redirecting β-subunit Ig-domains outward to permit cis or trans supraclustering within specialized cellular compartments such as the cardiomyocyte perinexal space. Further experimental work is necessary to validate these predictions.

Mapping O- and N-Glycosylation in Transmembrane and Interface Regions of Proteins: Insights from a Database Search Study

Glycosylation is a critical post-translational modification that influences protein folding, stability and function. While extensively studied in extracellular and intracellular regions, glycosylation within transmembrane (TM) regions and at membrane interfaces remains poorly understood. This study aimed to map O- and N-glycosylation sites in these regions using a comprehensive database search and structural validation where possible. Extensive database searches revealed glycosylation sites in a range of membrane proteins. Only the sites falling in the TM regions and at the membrane interface (according to Uniprot annotations) were retained. The location of these sites was confirmed based on available 3D structures. We identified 32 O-glycosylation sites and 7 N-glycosylation sites in the TM domains of 29 proteins. O-GlcNAc sites validated as located within TM regions presented side chains either oriented toward the lipid bilayer or buried within the protein. N-glycosylation sites predicted in protein TM regions were largely confined to interface or extracellular domains. The results obtained here highlight the occurrence of glycosylation in TM regions of proteins and at membrane interfaces. This dataset provides a valuable foundation for the further exploration of structural and functional roles of glycosylation in membrane-associated regions.

3D structural insights into the effect of N-glycosylation in human chitotriosidase variant G102S

BACKGROUND

N-glycosylation is a key post-translational modification critical for protein function and stability. Chitotriosidase-1 (CHIT1), belonging to glycoside hydrolase family 18, is clinically utilized as a biomarker of Gaucher disease. A G102S variant is common in some populations, but the implications of this missense mutation on CHIT1 function and in disease pathology are unknown. We have investigated the effects of the G102S mutation on the N-glycosylation, structure, and activity of CHIT1.

METHODS

Three recombinant CHIT1 proteins, wild-type (WT), G102S, and N100Q+G102S double mutants, were expressed, purified, and analyzed for glycosylation using SDS-PAGE, MALDI-MS, PNGase F treatment, and lectin blotting. NMR and LC-MS/MS were employed to characterize glycan structures. Enzymatic assays and molecular dynamics simulations were used to assess the effects of mutations on CHIT1 function and dynamics.

RESULTS

The G102S mutation introduced a new N-glycosylation site at N100, confirmed by SDS-PAGE and MALDI-MS, and the composition of the N-glycan structures was verified by lectin blotting, NMR, and MS. Both G102S and N100Q+G102S proteins exhibited reduced catalytic efficiency compared to WT. Molecular dynamics simulations suggested that G102S mutation induces significant structural changes and reduces stability, particularly without N-glycan, likely impairing substrate binding and enzymatic activity.

CONCLUSION

Our findings indicate that the common G102S mutation affects the structure and function of CHIT1, partially by introducing a new N-glycosylation site. They provide a foundation for further research on the impact of N-glycosylation on its hydrolase activity and structural dynamics, with potential implications for understanding the role of CHIT1 in Gaucher disease.

Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A

Amyloid diseases feature pathologic deposition of normally soluble proteins and peptides as insoluble fibrils in vital organs. Amyloid fibrils co-deposit with various nonfibrillar components including heparan sulfate (HS), a glycosaminoglycan that promotes amyloid formation in vitro for many unrelated proteins. HS-amyloid interactions have been proposed as a therapeutic target for inflammation-linked amyloidosis wherein N-terminal fragments of serum amyloid A (SAA) protein deposit in the kidney and liver. The structural basis for these interactions is unclear. Here, we exploit the high-resolution cryoelectron microscopy (cryo-EM) structures of ex vivo murine and human SAA fibrils in a computational study employing molecular docking, Brownian dynamics simulations, and molecular dynamics simulations to elucidate how heparin, a highly sulfated HS mimetic, recognizes and binds to amyloid protein fibrils. Our results demonstrate that negatively charged heparin chains bind to linear arrays of uncompensated positively charged basic residues along the spines of amyloid fibrils facilitated by electrostatic steering. The predicted heparin binding sites match the location of unidentified densities observed in cryo-EM maps of SAA amyloids, suggesting that these extra densities represent bound HS. Since HS is constitutively found in various amyloid deposits, our results suggest a common mechanism for HS-amyloid recognition and binding.

Fc-FcγRI Complexes: Molecular Dynamics Simulations Shed Light on Ectodomain D3's Potential Role in IgG Binding

FcγRI plays a crucial role in the effector function of IgG antibodies, interacting with the lower hinge region of IgG1 with nanomolar affinity. Binding occurs specifically in domain 2 (D2) of the FcγRI ectodomain, while domain 3 (D3) is a flexible linker. The D3 domain is positioned away from the IgG binding site on the FcγRI and does not directly contact the Fc region. This study investigates the structural and functional properties of FcγRI D3 using 200 ns classical MD simulations of two models: (1) a full FcγRI ectodomain complex with Fc and (2) a truncated model excluding D3. Our findings suggest that the D3 ectodomain provides additional structural flexibility to the FcγRI-Fc complex without altering the C backbone motion or flexibility of the KHR binding motif in the FG loop. Critical residues involved in binding and contributing to complex stability were evaluated regarding changes in intramolecular interactions and destabilization tendency upon D3 truncation. Truncation did not significantly alter interactions around glycan-interacting residues in Fc chains or FcγRI-Fc binding interfaces. These findings provide valuable insights into the role of FcγRI D3 in modulating the structural dynamics of the FcγRI-Fc complex. While D3 does not directly contact Fc, its mobility and positioning may modulate the receptor's affinity, accessibility, and ability to bind IgG immune complexes. We suggest that a truncated FcγRI construct lacking the D3 domain may be a promising candidate for biosensor or capturing agents' development and optimization, offering improved performance in IgG capture assays without compromising critical binding interactions.

Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques

An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID50] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC50] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.

Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation

Ligand-induced receptor and co-receptor heterodimerization is a common mechanism in receptor kinase (RK) signalling activation. SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) mediate the complex formation of Arabidopsis RK MIK2 and co-receptor BAK1, triggering immune responses. Through structural, biochemical and genetic analyses, we demonstrate that SCOOPs use their SxS motif and adjacent residues to bind MIK2 and the carboxy-terminal GGR residues to link MIK2 to BAK1. While N-glycosylation of plant RKs is typically associated with protein maturation, plasma membrane targeting and conformation maintenance, a surprising revelation emerges from our crystal structural analysis of MIK2-SCOOP-BAK1 complexes. Specific N-glycans on MIK2 directly interact with BAK1 upon SCOOP sensing. The absence of N-glycosylation at the specific site in MIK2 neither affects its subcellular localization and protein accumulation in plant cells nor alters its structural conformation, but markedly reduces its affinity for BAK1, abolishing SCOOP-triggered immune responses. This N-glycan-mediated receptor and co-receptor heterodimerization occurs in both Arabidopsis and Brassica napus. Our findings elucidate the molecular basis of SCOOP perception by the MIK2-BAK1 immune complex and underscore the crucial role of N-glycans in plant receptor-coreceptor interactions and signalling activation, shaping immune responses.

Theoretical Investigations of a point mutation affecting H5 Hemagglutinin's receptor binding preference

The avian influenza A H5N1 virus is a subtype of influenza A virus (IAV) that causes a highly infectious and severe respiratory illness in birds and poses significant economic losses in poultry farming. To infect host cell, the virus uses its surface glycoprotein named Hemagglutinin (HA) to recognize and to interact with the host cell receptor containing either α2,6- (SAα2,6 Gal) or α2,3-linked Sialic Acid (SAα2,3 Gal). The H5N1 virus has not yet acquired the capability for efficient human-to-human transmission. However, studies have demonstrated that even a single amino acid substitution in the HA can switch its glycan receptor preference from the avian-type SAα2,3 Gal to the human-type SAα2,6 Gal. The present study aims to explain the underlying mechanism of a mutation (D94N) on the H5 HA that causes the protein to change its glycan receptor-binding preference using molecular dynamics (MD) simulations. Our results reveal that the mutation alters the electrostatic interactions pattern near the HA receptor binding pocket, leading to a reduced stability for the HA-avian-type SAα2,3 Gal complex. On the other hand, the detrimental effect of the mutation D94N is not observed in the HA-human-type SAα2,6 Gal complex due to the glycan's capability to switch its topology.

HIV-1-envelope trimer transitions from prefusion-closed to CD4-bound-open conformations through an occluded-intermediate state

HIV-1 infection is initiated by the interaction between the gp120 subunit in the envelope (Env) trimer and the cellular receptor CD4 on host cells. This interaction induces substantial structural rearrangement of the Env trimer. Currently, static structural information for prefusion-closed trimers, CD4-bound prefusion-open trimers, and various antibody-bound trimers is available. However, dynamic features between these static states (e.g., transition structures) are not well understood. Here, we investigate the full transition pathway of a site-specific glycosylated Env trimer between prefusion-closed and CD4-bound-open conformations by collective molecular dynamics and single-molecule Förster resonance energy transfer (smFRET). Our investigations reveal and confirm important features of the transition pathway, including movement of variable loops to generate a glycan hole at the trimer apex and formation or rearrangements of α-helices and β-strands. Notably, by comparing the transition pathway to known Env structures, we uncover evidence for a transition intermediate, with four antibodies, Ab1303, Ab1573, b12, and DH851.3, recognizing this intermediate. Each of these four antibodies induced population shifts of Env to occupy a newly observed smFRET state: the "occluded-intermediate" state. We propose this occluded-intermediate state to be both a prevalent state of Env and a neutralization-relevant conformation between prefusion-closed and CD4-bound-open states, previously overlooked in smFRET analyses.

Towards a molecular picture of the archaeal cell surface

Archaea produce various protein filaments with specialised functions. While some archaea produce only one type of filament, the archaeal model species Sulfolobus acidocaldarius generates four. These include rotary swimming propellers analogous to bacterial flagella (archaella), pili for twitching motility (Aap), adhesive fibres (threads), and filaments facilitating homologous recombination upon UV stress (UV pili). Here, we use cryo-electron microscopy to describe the structure of the S. acidocaldarius archaellum at 2.0 Å resolution, and update the structures of the thread and the Aap pilus at 2.7 Å and 2.6 Å resolution, respectively. We define features unique to archaella of the order Sulfolobales and compare their structure to those of Aap and threads in the context of the S-layer. We define distinct N-glycan patterns in the three filaments and identify a putative O-glycosylation site in the thread. Finally, we ascertain whether N-glycan truncation leads to structural changes in archaella and Aap.

Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide

Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1 fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with substitutions to negatively charged amino acids at residue positions 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV-1; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structural analysis of the naturally elicited ACS202 antibody in complex with the HIV-1 Env trimer with an alanine 517 to glutamine substitution suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence, perhaps reflecting the immunization with fusion peptide of the vaccine-elicited antibodies.

Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies

Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. Here, to precisely engineer bnAb boosting immunogens, we use molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identify Env mutations predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encode antibody affinity gains and select for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.

Restoring protein glycosylation with GlycoShape

Despite ground-breaking innovations in experimental structural biology and protein structure prediction techniques, capturing the structure of the glycans that functionalize proteins remains a challenge. Here we introduce GlycoShape ( https://glycoshape.org ), an open-access glycan structure database and toolbox designed to restore glycoproteins to their native and functional form in seconds. The GlycoShape database counts over 500 unique glycans so far, covering the human glycome and augmented by elements from a wide range of organisms, obtained from 1 ms of cumulative sampling from molecular dynamics simulations. These structures can be linked to proteins with a robust algorithm named Re-Glyco, directly compatible with structural data in open-access repositories, such as the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and AlphaFold Protein Structure Database, or own. The quality, performance and broad applicability of GlycoShape is demonstrated by its ability to predict N-glycosylation occupancy, scoring a 93% agreement with experiment, based on screening all proteins in the PDB with a corresponding glycoproteomics profile, for a total of 4,259 N-glycosylation sequons.

Maltose gradient-induced biosensor-based high-throughput screening for directed evolution of maltogenic amylase from Bacillus stearothermophilus

Maltogenic amylase is a starch-hydrolyzing enzyme commonly used in bread baking and high-concentration maltose syrup production. However, low catalytic activity limits its industrial application. Improving catalytic activity based on molecular modification and directed evolution requires a High-Throughput Screening (HTS) method. In this study, a maltose gradient-induced (MaGI) biosensor was designed and applied for the directed evolution of maltogenic amylase AmyM, showing a good positive correlation between enzyme activity and fluorescence. The MaGI biosensor detected maltose and maltogenic amylase activity efficiently and specifically. Two mutants, Q440N and S442N/Q661L, were identified through the screening of 3000 mutants using the MaGI biosensor, showing a significant increase in catalytic activity of 35.56 % and 24.51 %, respectively, compared to the wild-type. Meanwhile, the t1/2 of Q440N and S442N/Q661L at 60 °C increased by 58.53 % and 66.66 %, respectively. In industrial applications, the enhancement of catalytic activity and stability is conducive to improving production efficiency and reducing costs. MD simulation has found that when modifying multidomain enzymes, distal mutations can enhance catalytic activity. In conclusion, the developed MaGI biosensor is a promising tool for high-throughput and specific detection of maltose.

Unlocking the potential of biocompatible chitosan-hyaluronic acid nanogels labeled with fluorochromes: A promising step toward enhanced FRET bioimaging

Chitosan is a natural polysaccharide widely used in medical formulations as nanoparticles due to their special properties. Our work aimed to assess the biocompatibility of chitosan-hyaluronic acid nanogels labeled with fluorochromes for use in biomedical applications, based on the FRET effect. The preparation method included the ionic gelation, grafting rhodamine or fluorescein isothiocyanate molecules onto the chitosan backbone. To assess the potential applications as fluorescence imaging tools of chitosan-fluorophores conjugates in diagnostics and therapies, SVEC4-10 cells (simian virus 40-transformed mouse microvascular endothelial cell line) and RAW264.7 murine macrophages were used within this study. Good biocompatibility was observed after 6 and 24 h of incubation with nanogels, with no increase in cell death or membrane damage for concentrations up to 120 μg/mL. Both types of fluorescent nanogels presented the tendency to agglomerate on the cell membrane's surface, and few cells were internalized, especially at the periphery of cells. Molecular dynamics simulations showed that distances between fluorophores fitted at values close to those calculated based on FRET experiments. These formulations can further incorporate gadolinium for better nanomedicine tools.

Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins

Mucins, the biomolecular components of mucus, are glycoproteins that form a thick physical barrier at all tissue-air interfaces, forming a first line of defense against pathogens. Structural features of mucins and their interactions with other biomolecules remain largely unexplored due to the challenges associated with their high-resolution characterization. Combining limited mass spectrometry glycomics and protein sequencing data, we present all-atom, explicitly solvated molecular dynamics simulations of a major respiratory mucin, MUC5B. We detail key forces and degrees of freedom imposed by the extensive O-glycosylation, which imbue the canonically observed bottlebrush-like structures to these otherwise intrinsically disordered protein backbones. We compare our simulation results to static structures observed in recent scanning tunneling microscopy experiments as well as other published experimental efforts. Our work represents the demonstration of a workflow applied to a mucin example, which we hope will be employed by other groups to investigate the dynamics and interactions of other mucins, which can inform on structural details currently inaccessible to experimental techniques.

Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations

Carbohydrates are key biological mediators of molecular recognition and signaling processes. In this case study, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in the binding free energy of -0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively -0.14, -0.22, and -0.41 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be -0.14 ± 0.02, -0.24 ± 0.03, and -0.46 ± 0.06 kcal/mol per heavy atom, respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible, and weakly bound ligands, we nevertheless find that the ABFE method performs well for this lectin system. The approach shows promise as a quantitative tool for predicting and deconvoluting carbohydrate-protein interactions, with potential application to design of therapeutics, vaccines, and diagnostics.

Freeze-drying-induced mutarotation of lactose detected by Raman spectroscopy

Freeze-drying enables delicate, heat-sensitive biomaterials to be stored in a dry form even at room temperature. However, exposure to physicochemical stress induced by freeze-drying presents challenges for maintaining material characteristics and functionality upon reconstitution, for which reason excipients are required. Although wide variety of different excipients are available for pharmaceutical applications, their protective role in the freeze-drying is not yet fully understood. In this study our aim was to use molecular dynamics simulations to screen the properties of different sugars and amino acids, which could be combined with plant-based nanofibrillated cellulose (NFC) hydrogel to provide protective matrix system for future freeze-drying for pharmaceuticals and biologics. The changes in the NFC-based formulations before and after freeze-drying and reconstitution were evaluated using non-invasive Timegate PicoRaman spectroscopy and traditional characterization methods. We continued to the freeze-drying with the NFC hydrogel formulations including lactose with and without glycine, which showed the highest attraction preferences on NFC surface in silico. This formulation enabled successful freeze-drying and subsequent reconstitution with preserved physicochemical and rheological properties. Raman spectroscopy gave us insights of the molecular-level changes during freeze-drying, especially the mutarotation of lactose. This research showed the potential of integrating in silico screening and non-invasive spectroscopical method to design novel biomaterial-based formulations for freeze-drying. The research provided insights of the molecular-level interactions and orientational changes of the excipients, which might be crucial in future freeze-drying applications of pharmaceuticals and biologics.

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.

Ligand modelling of Trachyspermum ammi phytocompounds for Aeromonas hydrophila cell wall synthesis enzyme in Labeo rohita

Aquaculture faces challenges from Aeromonas hydrophila, causing Motile Aeromonas Septicaemia, particularly affecting Labeo rohita (Rohu) in Pakistan. This study explores potential herbal antibacterials targeting A. hydrophila, molecular docking of Trachyspermum ammi (ajwain) phytocompounds against pathogen. The cell wall synthesis ligase, D-alanine-D-alanine ligase (PDB ID 6ll9) was processed in BIOVIA Discovery Studio and docked with 13 antibacterial phytocompounds found after QSAR analysis of T. ammi. Binding energies were calculated using PyRx to assess complex stability. ADME-TOX assessment for selected phytocompounds and parameterisation in CHARMM-GUI were performed. Docking the two best ligands with highest binding energies and ADME-TOX compliance, we found carvacrol and limonene formed most stable protein-ligand complexes, with raw and processed protein. Our findings suggest these herbal compounds can inhibit D-alanine-D-alanine ligase. These in-silico results support the potential of 'ajwain' in managing A. hydrophila, further in-vivo experiments are necessary to validate these inhibitory properties.