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Biology subjects

Mou, Z.

Publications and source records attributed to Mou, Z..

At least 19 recordsLinked to original sources

Mutational fitness landscapes of diverse human influenza H1N1 neuraminidases

While neuraminidase (NA) is emerging as a promising influenza vaccine target, it evolves rapidly and undergoes antigenic drift. However, our understanding of its evolutionary constraints remains limited. Here, we systematically quantified the replication fitness effects of >6,000 mutations for each of three antigenically diverse H1N1 NAs using deep mutational scanning. Moderate correlations among H1N1 NA fitness landscapes revealed mutations with strain-dependent replication fitness effects. Additionally, cross-subtype comparison between N1 and N2 NAs uncovered similar epistatic effects that were enriched in the C-terminal interprotomer interface. We also showed that NA mutational fitness strongly correlated between in vivo and in vitro. Characterization of 40 individually constructed NA mutants further demonstrated that NA mutational fitness depended more on its surface protein expression than on its total protein expression or endoplasmic reticulum stress induction. Overall, the large dataset generated in this work provides critical insights into the evolutionary constraints of NA.

microbiology↗

Model Validation Protocols for Machine Learning in Small Molecule Drug Discovery

Machine learning (ML) models for molecular property prediction are increasingly deployed in drug discovery, yet their adoption in real-world scenarios requires an understanding of the conditions in which a model succeeds or fails. While standardized benchmarks are powerful instruments to measure and unlock progress in ML research, they should not be blindly treated as the end goal. Especially static and retrospective benchmarks, in which no true unknown test set is employed, limit our ability to robustly validate a model's performance. Building on the collective expertise of a cross-industry consortium, we present a model validation framework consisting of five recommendations that would enable the community to move beyond aggregate metrics toward understanding where and why molecular property prediction models fail. We connect evaluation choices to real-world applications and case studies encountered in pharmaceutical research. The framework proposes splitting strategies that mimic realistic distribution shifts and expose common failure modes. We apply the recommended framework to a recently released dataset of absorption, distribution, metabolism, and excretion (ADME) properties. Across two complementary model algorithms, our case studies reveal four distinct failure modes (extrapolation, interpolation, representation, and evaluation), showing that model errors arise not only from distribution shift but also from limitations in molecular representations. Our results show that commonly used evaluation protocols can significantly overestimate performance and may not detect important model failure modes. All software and data are released via https://github.com/srijitseal/polaris.

bioinformatics↗

Extracellular NAD(P) activates systemic acquired resistance through LecRK-VI.2-mediated phosphorylation of NPR1

Systemic acquired resistance (SAR) is a long-lasting, broad-spectrum immune response induced in distal tissues by signals generated at primary infection sites. Although numerous mobile immune signals have been implicated in SAR, how these signals are perceived and mechanistically coupled to transcriptional reprogramming in systemic tissues remains poorly understood. Extracellular NAD(P) [eNAD(P)] functions as a key integrative SAR signal that activates immunity through the plasma membrane-localized lectin receptor kinase LecRK-VI.2 and the master immune coactivator NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1). However, the mechanism linking eNAD(P) perception to activation of NPR1 has remained unknown. Here, we show that LecRK-VI.2 constitutively associates with NPR1 and directly phosphorylates NPR1 at T359 and likely S356 upon eNAD(P) perception. NADP+-induced phosphorylation of NPR1 occurs rapidly in vivo and requires LecRK-VI.2. Nonphosphorylatable NPR1 variants abolish eNADP+-induced local and systemic immunity as well as biologically induced SAR, whereas phosphomimetic variants retain NPR1 function. Mechanistically, LecRK-VI.2-mediated phosphorylation promotes NPR1 interaction with TGACG-binding transcription factors (TGAs) and the Mediator subunit MED15, thereby enhancing assembly of a transcriptional activation complex required for defense gene expression. We further demonstrate that NPR1 facilitates TGA-MED15 association in a phosphorylation-dependent manner. Together, these findings establish a receptor-to-coactivator signaling mechanism that directly links extracellular immune signal perception to transcriptional activation. This work closes a major mechanistic gap in the SAR signaling pathway and reveals receptor-mediated coactivator activation as a mechanism for rapid conversion of extracellular immune cues into coordinated transcriptional outputs during systemic immunity.

plant biology↗

Extracellular salicylic acid activates immune signaling through cell-surface receptors

Salicylic acid (SA) is a central immune hormone that accumulates in both intracellular and extracellular compartments during pathogen infection. While intracellular SA signaling is well established, whether extracellular SA (eSA) directly activates immune responses remains unknown. Here we show that eSA functions as an extracellular signal potentially perceived by the plasma membrane-localized lectin receptor kinases LecRK-I.8 and LecRK-VI.2 in Arabidopsis. The extracellular domains of both receptors bind SA with micromolar affinity, SA rapidly induces LecRK-I.8 phosphorylation, and the kinase activities of LecRK-I.8 and LecRK-VI.2 are required for downstream signaling. Moreover, mutagenesis of a computationally predicted binding pocket in LecRK-VI.2 abolishes SA binding and immune function, providing evidence for receptor-mediated perception. Genetic analyses further demonstrate that LecRK receptors are required for SA-induced resistance, transcriptional reprogramming, and phosphoproteomic responses. Together, these findings expand current models of SA signaling by revealing a potential receptor-mediated cell-surface perception mechanism for a classical immune hormone.

plant biology↗

Structural Mechanisms of SAMD9 Autoinhibition and Pathogenic Dysregulation

SAMD9 and SAMD9L (SAMD9/9L) are large cytosolic proteins essential for hematopoietic homeostasis and antiviral defense1-3. Germline gain-of-function (GoF) mutations in SAMD9/9L cause severe multisystem disorders and predisposition to leukemia, yet the mechanisms that regulate SAMD9/9L activity and how pathogenic mutations disrupt these processes, remain poorly understood. Here, we determine cryo-electron microscopy structures of human SAMD9 in multiple conformational and oligomeric states. We show that SAMD9 predominantly adopts a closed, autoinhibited conformation stabilized by a central ATP-bound nucleotide-binding oligomerization domain (NOD) and an extensive network of intramolecular interactions. Recurrent patient-derived GoF mutations localize to and destabilize these intramolecular interfaces, and restoring the disrupted interactions through compensatory mutations reinstates autoinhibition. We further identify low-abundance asymmetric SAMD9 dimers in which one protomer undergoes large conformational changes and establishes intermolecular interactions that are essential for SAMD9 activation. Together, these findings define the structural basis of SAMD9 autoinhibition and explain how human GoF mutations subvert this regulatory mechanism to drive disease.

biophysics↗

Extracellular NAD(P) links hypersensitive response to localized acquired resistance

Effector-triggered immunity (ETI) generates cell non-autonomous signals that activate localized acquired resistance (LAR) in neighboring cells and systemic acquired resistance (SAR) in distant tissues. While SAR signaling has been extensively characterized, the molecular basis of LAR remains poorly understood. Here, we identify extracellular nicotinamide adenine dinucleotide (eNAD(P)) as a key damage-associated molecular pattern (DAMP) that mediates LAR. Using genetic, physiological, and cell death assays, we show that eNAD(P) and its receptor complex restrict hypersensitive response (HR)-associated cell death, promote cell survival, and are required for avirulent pathogen-induced LAR. In contrast, LAR is independent of the major SAR mobile signals N-hydroxypipecolic acid and azelaic acid, as well as certain other characterized DAMP pathways. Notably, ETI-mediated resistance remains largely intact in eNAD(P) pathway mutants, indicating that ETI directly restricts pathogens while simultaneously generating eNAD(P) signals to activate LAR. Our findings establish LAR as a mechanistically distinct immune layer and link HR-associated damage to eNAD(P)-dependent local immune reinforcement.

plant biology↗

Repressed expression of nucleoporins and importins impairs plant defense against an infectious noncoding RNA

Plant pathogens threaten global food security and cause substantial annual economic losses. Of particular concern are host jumps, in which pathogens expand their host range to new species, often resulting in sudden and difficult-to-control disease outbreaks. However, the ability to anticipate such events remains limited by an incomplete understanding of pathogen adaptability and the mechanisms governing nonhost resistance. Here, we show that temperature modulates the infectivity and host range of potato spindle tuber viroid (PSTVd), a pathogenic noncoding RNA that severely impacts solanaceous crops such as potato and tomato. Using in vivo single-molecule RNA structure probing, we found that higher temperatures drive PSTVd into a more uniform RNA conformation associated with enhanced infectivity in tomato. Concurrently, elevated temperature suppresses key host defense pathways, including RNA silencing and NPR1-mediated immunity. Notably, these conditions enable PSTVd to overcome nonhost resistance and establish infection in Arabidopsis thaliana. Our findings reveal that elevated temperature promotes PSTVd host expansion through multiple coordinated mechanisms, linking changes in pathogen behavior with increased host susceptibility, and suggest that ongoing climate warming may heighten the risk of viroid host jumps.

plant biology↗

Persistent antigen is essential for sustaining Leishmania-specific memory CD4+ T cells and long-term immunity

Memory T cells are critical for secondary immunity against pathogens, yet their persistence in the absence of antigen remains unclear. While memory CD8+ T cells are known to persist independently of their cognate antigen, the durability of memory CD4+ T cells in the absence of antigen remains controversial. Recovery from cutaneous leishmaniasis confers lifelong immunity, largely mediated by CD4+ T cells, but the necessity of persistent parasites for sustaining this immunity has not been empirically confirmed. We investigated immunity in mice infected with a dihydrofolate reductase-thymidylate synthase (dhfr-ts)-deficient Leishmania major, which cannot persist due to their thymidine salvage deficiency. These mice lost protection against wild-type challenge, correlating with a decline in Leishmania (PEPCK)-specific CD4+ T cells. To further dissect this relationship, we generated PEPCK-specific CD4+ TCR transgenic (PEG) mice, enabling precise tracking of Leishmania-specific memory CD4+ T cells. Both in vitro and in vivo-generated memory PEG cells gradually disappeared over time in the absence of antigen, irrespective of the hosts MHC II status, and this loss paralleled the erosion of infection-induced immunity. PEG and endogenous PEPCK-specific memory cells were not maintained in mice infected with dhfr-ts- or PEPCK-deficient L. major, resulting in loss of recall responses and secondary immunity. These findings demonstrate that continuous antigen presence is crucial for maintaining Leishmania-specific memory CD4+ T cells and highlight the role of persistent antigen in sustaining long-term immunity against chronic infections.

immunology↗

Rapid synthesis and screening of natively paired antibodies against influenza hemagglutinin stem via oPool+ display

Antibody discovery is crucial for developing therapeutics and vaccines as well as understanding adaptive immunity. However, the lack of approaches to synthesize antibodies with defined sequences in a high-throughput manner represents a major bottleneck in antibody discovery. Here, we presented oPool+ display, a high-throughput cell-free platform that combined oligo pool synthesis and mRNA display to rapidly construct and characterize many natively paired antibodies in parallel. As a proof-of-concept, we applied oPool+ display to probe the binding specificity of >300 uncommon influenza hemagglutinin (HA) antibodies against 9 HA variants through 16 different screens. Over 5,000 binding tests were performed in 3-5 days with further scaling potential. Follow-up structural analysis of two HA stem antibodies revealed the previously unknown versatility of IGHD3-3 gene segment in recognizing the HA stem. Overall, this study established an experimental platform that not only accelerate antibody characterization, but also enable unbiased discovery of antibody molecular signatures.

immunology↗

Immunological correlates of protection mediated by a whole organism Cryptococcus neoformans vaccine deficient in chitosan

The global burden of infections due to the pathogenic fungus Cryptococcus is substantial in persons with low CD4+ T cell counts. Previously, we deleted three chitin deacetylase genes from C. neoformans to create a chitosan-deficient, avirulent strain, designated cda1{Delta}2{Delta}3{Delta} which, when used as a vaccine, protected mice from challenge with virulent C. neoformans strain KN99. Here, we explored the immunological basis for protection. Vaccine-mediated protection was maintained in mice lacking B cells or CD8+ T cells. In contrast, protection was lost in mice lacking /{beta} T cells or CD4+ T cells. Moreover, CD4+ T cells from vaccinated mice conferred protection upon adoptive transfer to naive mice. Importantly, while monoclonal antibody-mediated depletion of CD4+ T cells just prior to vaccination resulted in complete loss of protection, significant protection was retained in mice depleted of CD4+ T cells after vaccination, but prior to challenge. Vaccine-mediated protection was lost in mice genetically deficient in IFN{gamma}, TNF, or IL-23p19. A robust influx of leukocytes and IFN{gamma}- and TNF-expressing CD4+ T cells was seen in the lungs of vaccinated and challenged mice. Finally, a higher level of IFN{gamma} production by lung cells stimulated ex vivo correlated with lower fungal burden in the lungs. Thus, while B cells and CD8+ T cells are dispensable, IFN{gamma} and CD4+ T cells have overlapping roles in generating protective immunity prior to cda1{Delta}2{Delta}3{Delta} vaccination. However, once vaccinated, protection becomes less dependent on CD4+ T cells, suggesting a strategy for vaccinating HIV+ persons prior to loss of CD4+ T cells. ImportanceThe fungus Cryptococcus neoformans is responsible for >100,000 deaths annually, mostly in persons with impaired CD4+ T cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain of C. neoformans, designated cda1{Delta}2{Delta}3{Delta}. When used as a vaccine, cda1{Delta}2{Delta}3{Delta} protects mice against a subsequent challenge with a virulent C. neoformans strain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8+ T cells were dispensible, protection was lost in mice genetically deficient in CD4+ T cells, and the cytokines IFN{gamma}, TNF, or IL-23. A robust influx of cytokine-producing CD4+ T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4+ T cells following vaccination, suggesting a strategy to protect persons who are at risk for future CD4+ T cell dysfunction.

immunology↗

Genome-Wide Identification and Expression Pattern of the N-acetylserotonin deacetylase (ASDAC) Gene Family in Orchidaceae

Orchids are a kind of horticultural plant with highly ornamental and medical value. N-acetylserotonin deacetylase (ASDAC) is the only reverse enzyme of the melatonin biosynthesis pathway, and plays an important role in regulating the balance of melatonin. Melatonin as a multifunctional molecule, is typically involved in plant growth and development regulation, as well as abiotic stress tolerance. Here, we aimed at identifying ASDAC genes from the orchid genome to provide valuable information for further study of the role of melatonin in orchids. In this study, a total of 7 ASDAC genes were identified from the 7 orchid genome with one member in each species. The 7 orchid ASDACs have an HDAC functional domain, and cluster together with functionally confirmed OsHDAC10 and AtHDAC14, it shows that these members may have function of N-acetylserotonin deacetylase. Furthermore, based on the phylogenetic, motif, and gene structure analysis, the same clusters orchid ASDAC or ASDAC-like genes generally contained similar introns and motifs, suggesting the distribution pattern of exons/introns and motifs were strongly related to phylogeny on an evolutionary basis. Interestingly, homologous genes of OsHDAC10 and AtHDAC14 in Gastrodia elata have low homology and not cluster together with rice and A.thaliana ASDACs, showing that ASDAC gene family may lost in the holomycoheterotrophic orchids. The Ka/Ks ratios of ASDAC gene pairs from lower plant to higher plant were less than one, suggested that ASDAC genes have undergone purifying selection during the evolution process. Cis-acting element analysis results showed that the promoter regions of orchid ASDAC genes contained plant growth and development, phytohormone, and stress-responsive elements. Moreover, most orchid ASDACs were expressed in the roots, stems, leaves, flowers, and seeds. Combined cis-acting element and tissue expression analysis, indicating orchid ASDAC genes are involved in melatonin regulation of growth and development, as well as melatonin responding to various stresses in orchids. These findings of orchid ASDAC genes may provide valuable information for further study of the role of melatonin in orchids.

bioinformatics↗

NONEXPRESSOR OF PATHOGENESIS-RELATED GENES control Huanglongbing tolerance by regulating immune balance in citrus plants

Huanglongbing (HLB) is a devastating citrus disease caused by the phloem-resident bacterial pathogen Candidatus liberibacter asiaticus (CLas). CLas infection of susceptible varieties triggers unbalanced immune responses, leading to overaccumulation of callose and reactive oxygen species (ROS), which in turn causes phloem plugging and HLB symptom development. Interestingly, some citrus relatives exhibit little or no symptoms in the presence of CLas, a phenomenon termed HLB tolerance. Moreover, overexpression of the Arabidopsis thaliana NPR1 (AtNPR1) gene in susceptible varieties has been shown to confer robust HLB tolerance. However, the mechanisms underlying HLB tolerance remain enigmatic. Here, we show that overexpression of AtNPR1 suppresses CLas- and Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced overaccumulation of callose and ROS in citrus and Arabidopsis, respectively. Importantly, we found that knocking out of the Arabidopsis negative immune regulators, AtNPR3 and AtNPR4, and silencing of their Citrus sinensis ortholog CsNPR3, similarly suppress Psm- and CLas-induced callose and ROS overaccumulation, respectively, and that silencing of CsNPR3 also enhances HLB tolerance. These results reveal a conserved role of the NPR1/NPR3/NPR4-mediated signaling pathway in regulating plant immune balances and provide mechanistic support for overexpression of AtNPR1 or silencing of AtNPR3/AtNPR4 orthologs in citrus as a long-term solution to the HLB disease.

plant biology↗

Genome organization in double-stranded DNA viruses observed by cryoET

Double-stranded DNA (dsDNA) viruses package their genetic material into protein cages with diameters usually a few hundred times smaller than the length of their genome. Compressing the relatively stiff and highly negatively charged dsDNA into a small volume is energetically costly and mechanistically enigmatic. Multiple models of dsDNA packaging have been proposed based on various experimental evidence and simulation methods, but direct observation of any viral genome organization is lacking. Here, using cryoET and an improved data processing scheme that utilizes information from the encaging protein shell, we present 3D views of dsDNA genome inside individual viral particles at resolution that densities of neighboring DNA duplexes are readily separable. These cryoET observations reveal a "rod-and-coil" fold of the dsDNA that is conserved among herpes simplex virus type 1 (HSV-1) with a spherical capsid, bacteriophage T4 with a prolate capsid, and bacteriophage T7 with a proteinaceous core inside the capsid. Finally, inspired by the genome arrangement in partially packaged T4 particles, we propose a mechanism for the genome packaging process in dsDNA viruses.

molecular biology↗

Multiplexed gene editing with a multi-intron containing Cas9 gene in citrus

The citrus industry holds significant economic importance in Florida, being one of the leading producers of oranges and grapefruits in the United States. However, several diseases, such as canker and huanglongbing along with natural disasters like hurricanes have rigorously affected citrus production, quality, and yield. Improving citrus through traditional breeding methods requires significant challenges due to time constraints and complexity in genetic enhancements. To overcome these limitations, several expression systems have been developed in clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) framework allowing for gene editing of disease-associated genes across diverse citrus varieties. In this study, we present a new approach employing a multi-intron containing Cas9 gene plus multiple gRNAs separated with tRNA sequences to target the phytoene desaturase (PDS) gene in both Carrizo citrange and Duncan grapefruit. Notably, using this unified vector significantly boosted editing efficiency in both citrus varieties, showcasing mutations in all three designated targets. The implementation of this multiplex gene editing system with a multi-intron-containing Cas9 plus a gRNA-tRNA array demonstrates a promising avenue for efficient citrus genome editing, equipping us with potent tools in the ongoing battle against HLB. Statements and DeclarationsO_ST_ABSCompeting interestsC_ST_ABSThe authors declare that they have no competing interests. Supplementary InformationSupplementary File 1

plant biology↗

How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot

NINJ1 is a recently identified active executioner of plasma membrane rupture (PMR), a process previously thought to be a passive osmotic lysis event in lytic cell death. NINJ2 is a close paralog of NINJ1 but it failed to mediate PMR. By cryoEM, we found that both NINJ1 and NINJ2 were able to assemble into linear filament that binds strongly to lipids on one side but is water-soluble on the other side. The more-or-less straight NINJ1 filament was able to wrap around a membrane bleb and solubilize it from the plasma membrane to induce PMR; however, the intrinsically curved NINJ2 filament failed to do so, explaining its incapability of mediating PMR. We further demonstrated that binding to cholesterol at the inner leaflet of the lipid bilayer was responsible for the curving of the NINJ2 filament, while strong lipid binding at the outer leaflet was contributing to NINJ1s capability of mediating PMR.

immunology↗

High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike

Designing prefusion-stabilized SARS-CoV-2 spike is critical for the effectiveness of COVID-19 vaccines. All COVID-19 vaccines in the US encode spike with K986P/V987P mutations to stabilize its prefusion conformation. However, contemporary methods on engineering prefusion-stabilized spike immunogens involve tedious experimental work and heavily rely on structural information. Here, we established a systematic and unbiased method of identifying mutations that concomitantly improve expression and stabilize the prefusion conformation of the SARS-CoV-2 spike. Our method integrated a fluorescence-based fusion assay, mammalian cell display technology, and deep mutational scanning. As a proof-of-concept, this method was applied to a region in the S2 domain that includes the first heptad repeat and central helix. Our results revealed that besides K986P and V987P, several mutations simultaneously improved expression and significantly lowered the fusogenicity of the spike. As prefusion stabilization is a common challenge for viral immunogen design, this work will help accelerate vaccine development against different viruses.

biochemistry↗

Protection of mice against experimental cryptococcosis by synthesized peptides delivered in glucan particles

The high global burden of cryptococcosis has made development of a protective vaccine a public health priority. We previously demonstrated that a vaccine composed of recombinant Cryptococcus neoformans chitin deacetylase 2 (Cda2) delivered in glucan particles (GPs) protects BALB/c and C57BL/6 mice from an otherwise lethal challenge with a highly virulent C. neoformans strain. An immunoinformatic analysis of Cda2 revealed a peptide sequence predicted to have strong binding to the MHC Class II (MHC II) H2-IAd allele found in BALB/c mice. BALB/c mice vaccinated with GPs containing a 32 amino acid peptide (Cda2-Pep1) that included this strong binding region were protected from cryptococcosis. Protection was lost with GP-based vaccines containing versions of recombinant Cda2 protein and Cda2-Pep1 with mutations predicted to greatly diminish MHC II binding. Cda2 has homology to the three other C. neoformans chitin deacetylases, Cda1, Cda3 and Fpd1, in the high MHC II binding region. GPs loaded with homologous peptides of Cda1, Cda3 and Fpd1 protected BALB/c mice from experimental cryptococcosis, albeit not as robustly as the Cda2-Pep1 vaccine. Finally, seven other peptides were synthesized based on regions in Cda2 predicted to contain promising CD4+ T cell epitopes in BALB/c or C57BL/6 mice. While five peptide vaccines significantly protected BALB/c mice, only one protected C57BL/6 mice. Thus, GP-based vaccines containing a single peptide can protect mice against cryptococcosis. However, given the diversity of human MHC II alleles, a peptide-based Cryptococcus vaccine for use in humans would be challenging and likely need to contain multiple peptide sequences. ImportanceCryptococcosis, due to infection by fungi of the Cryptococcus neoformans species complex, is responsible for substantial morbidity and mortality in immunocompromised persons, particularly those with AIDS. Cryptococcal vaccines are a public health priority yet are not available for human use. We previously demonstrated mice could be protected from experimental cryptococcosis with vaccines composed of recombinant cryptococcal proteins encased in hollow highly purified yeast cell walls (glucan particles). Here, we examined one such protective protein, Cda2, and using bioinformatics, identified a region predicted to stimulate strong T cell responses. A peptide containing this region formulated in glucan particle-based vaccines protected mice as well as the recombinant protein. Other peptide vaccines also protected, including peptides containing sequences from proteins homologous to Cda2. These preclinical mouse studies provide a proof of principle that peptides can be effective as vaccines to protect against cryptococcosis and that bioinformatic approaches can guide peptide selection.

immunology↗

Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning

Both SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor. Based on high-resolution structures, the two viruses bind in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Here we have used molecular dynamics (MD) simulations, machine learning (ML), and free energy perturbation (FEP) calculations to elucidate the differences in RBD binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

biophysics↗