Mutant Proteins Research Articles

Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice.

Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.

Characterization of YdgH: a mediator of beta-lactam susceptibility in Enterobacterales.

Beta-lactam antibiotics are often the treatment of choice for serious bacterial infections. In a previous screen for novel genetic mediators affecting beta-lactam susceptibility, we discovered that deletion of ydgH, a conserved gene of unknown function, leads to increased resistance to beta-lactams, as well as increased susceptibility to detergent compounds. Here, we further characterize YdgH in Serratia marcescens, Enterobacter cloacae, and Escherichia coli using a combination of biochemical and cell biological approaches. We find that YdgH fractionates with periplasmic proteins, and this periplasmic localization is necessary for its function. Using purified recombinant protein, we demonstrate that YdgH is a relatively compact, globular monomer. The YdgH polypeptide contains three tandem DUF1471 domains. In a ΔydgH background, overexpression of polypeptides containing both the second and the third, but not the first DUF1471 domain, is necessary to rescue the deletion phenotype. To determine how YdgH function influences beta-lactam and detergent susceptibility, we tested several targeted hypotheses. We found that deletion of ydgH neither affects ompC or ompF transcript levels, nor does it alter the processing of lipopolysaccharide, nor does it activate the sigma E regulon alone or in combination with mutations in other periplasmic proteins. Finally, we delineate the results of a genetic screen for spontaneous mutants that complement the detergent susceptibility phenotype, the results of which may fuel the further studies that are necessary to determine the precise role YdgH plays in bacterial physiology.IMPORTANCEBeta-lactams such as penicillins and cephalosporins are the most commonly prescribed antibiotics for serious bacterial infections. Increasing antibiotic resistance threatens their effectiveness. We previously identified the uncharacterized gene ydgH as a modifier of beta-lactam susceptibility in Gram-negative bacteria. To begin to understand the specific role of YdgH, in this study, we perform initial characterizations of this protein. We also test hypotheses as to how the function of YdgH contributes to beta-lactam physiology.

Abstract A022: Discovery of conformationally constrained ALK2 inhibitors for the treatment of Diffuse Intrinsic Pontine Glioma (DIPG)

Abstract Despite considerable research on new therapeutics to treat DIPG, a universally fatal grade IV pediatric CNS tumor located in the pons region of the brainstem, there has been minimal progress. Somatic missense mutations in the bone morphogenetic protein (BMP) type I receptor ACVR1 gene encoding activin receptor-like kinase-2 (ALK2) are present in approximately 33% of children with DIPG, prompting our initial efforts towards the development of M4K2009, a 3,5-diphenylpyridine ALK2 inhibitor. Looking to improve potency, selectivity, and brain penetration, we subsequently designed, synthesized, and evaluated a first-in-class set of 5- to 7-member ether-linked and 7-member amine-linked conformationally constrained ALK2 inhibitors including M4K2308, M4K2281, M4K2304 and M4K2306. Overall, these new compounds are highly potent (ALK2 IC50 < 10 nM, nanoBRET ALK2 IC50 < 20 nM), selective (>100-fold over ALK5), brain-penetrant (Cbrain,4h/Cplasma,4h > 3, 10 mg/kg, NOD-SCID male mice) and show in vivo exposure (Cplasma,6h = 1−2 µM, 25 mg/kg, NOD-SCID male mice). In particular, M4K2308 displayed a good balance of potency and DMPK properties and is currently undergoing preclinical evaluation by M4K Pharma. Citation Format: David Smil, Héctor González-Álvarez, Deeba Ensan, Jong Fu Wong, Julien Cros, Laurent Hoffer, Taira Kiyota, Brian J. Wilson, Carlos A. Zepeda-Velázquez, Ahmed Aman, Methvin B. Isaac, Tao Xin, Alex N. Bullock, Peter B. Sampson, Rima Al-awar. Discovery of conformationally constrained ALK2 inhibitors for the treatment of Diffuse Intrinsic Pontine Glioma (DIPG) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Optimizing Therapeutic Efficacy and Tolerability through Cancer Chemistry; 2024 Dec 9-11; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(12_Suppl):Abstract nr A022.

Enhancing Drug Discovery through Iterative Screening and Advanced Computational Analysis of Notch3 R90C Mutations

Being the leading cause of death and disability in China, stroke encompasses a number of risk factors, one of them being genetic mutations. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is the most prevalent genetically induced stroke. This study investigates the feasibility of utilizing iterative screening rounds to identify potential drug candidates that effectively target the Notch3 R90C mutant protein associated with CADASIL. Through multiple rounds of molecular docking using AutoDock Vina and structural predictions by AlphaFold, we systematically narrowed down a large set of small molecules from the DrugBank database to identify those with the highest binding affinities. The research highlights the effectiveness of leveraging structural data and hierarchical clustering in refining the selection process, ultimately enhancing the precision in identifying promising therapeutic agents.

The measles virus matrix F50S mutation from a lethal case of subacute sclerosing panencephalitis promotes receptor-independent neuronal spread.

Subacute sclerosing panencephalitis (SSPE) is a lethal neurological disorder occurring several years after measles. Reconstruction of the evolution of the measles virus (MeV) genome in an SSPE case suggested that the matrix (M) protein mutation M-F50S, when added to other mutations, drove neuropathogenesis. However, whether and how M-F50S would promote spread independently from other mutations was in question. We investigated here the cell specificity of MeV spread in this brain and documented that both neurons and astrocytes were heavily infected. We then generated recombinant MeV with individual mutations in the three proteins of the viral membrane fusion apparatus, M, fusion (F), and hemagglutinin (H). These viruses reached similar titers as the parental wild-type virus, kept the respective mutations upon passage, and infected cells expressing the tissue-specific MeV receptors SLAM and nectin-4 with similar efficiencies. However, after inoculation of receptor-negative neurons and astrocytes differentiated from human induced pluripotent stem cells, only MeV M-F50S spread with moderate efficiency; the parental virus and its derivatives coding for a hyperfusogenic F protein, or for a cytoplasmic tail-mutated H protein, did not spread. When delivered to primary mouse neurons by cell-mediated neurite overlay, MeV M-F50S frequently reached the cell bodies and occasionally formed small infectious centers, while the other MeV reached the cell bodies only sporadically. These results demonstrate that, in neuronal cell cultures, M-F50S can enable receptor-independent spread in the absence of other mutations, and validate the inference that this single amino acid change initiated ubiquitous MeV brain spread.IMPORTANCEMeasles virus (MeV), a non-integrating negative-strand RNA virus, rarely causes subacute sclerosing panencephalitis (SSPE) several years after acute infection. During brain adaptation, the MeV genome acquires multiple mutations reducing the dependence of its membrane fusion apparatus (MFA) from an activating receptor. It was proposed that one of these mutations, matrix protein F50S, drove neuropathogenesis in an SSPE case. We report here that, in two types of neuronal cultures, a recombinant MeV with only this mutation gained receptor-independent spread, whereas viruses expressing MFA proteins with other mutations acquired during brain adaptation did not. Our results validate the inference that M-F50S initiated ubiquitous MeV brain spread resulting in lethal disease. They also prompt studies of the impact of analogous amino acid changes of the M proteins of other nonsegmented negative-strand RNA viruses on their interactions with membrane lipids and cytoskeletal components.

Novel low-frequency maternal mosaicism mutation of <i>CHRDL1</i> gene resulted in the X-linked megalocornea in the offspring

X-linked megalocornea (MGC1) is an inherited disorder resulting from mutations of the CHRDL1 gene. Common symptoms of megalocornea include oversized cornea, deeper fluid-filled space between the cornea and iris, blurred or distorted vision at every distance, leading to mild vision issues. In this report, we present the first cases of megalocornea caused by the maternal low-frequency somatic mosaicism of the novel CHRDL1 mutation. Two Vietnamese siblings, 5 years old (MG001) and 13 years old (MG002) visited the hospital for regular check-ups with manifestations such as myopic, exophthalmia, and enlarged cornea. They were suspected of having inherited megalocornea disorder without glaucoma symptoms. The DNA genome of the proband (MG001) was applied for whole exome sequencing (WES) analysis, and the result revealed a hemizygous pathogenic variant c.943dupA in the CHRDL1 gene, which results in a frameshift mutation (p.Ile315fs) in protein. This mutation was also identified in the proband (MG002) by Sanger sequencing. Notably, the CHRDL1 c.943dupA mutation was recognized at a very low fraction in the maternal DNA after triplicate Sanger sequencing, indicating that the mother has a mosaicism mutation of CHRDL1 c.943dupA. This study reported a rare case of X-linked megalocornea in a family and provides a novel genetic factor relating to an eye disorder in Vietnam.

PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery

Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.

The co-chaperone DNAJA2 buffers proteasomal degradation of cytosolic proteins with missense mutations

Mutations can disrupt a protein's native function by causing misfolding, which is generally handled by an intricate protein quality control network. To better understand the triaging mechanisms of misfolded cytosolic proteins, we screened a human mutation library to identify a panel of unstable mutations. The degradation of these mutated cytosolic proteins is largely dependent on the ubiquitin proteasome system. Using BioID proximity labelling, we found that the co-chaperones DNAJA1 and DNAJA2 are key interactors with one of the mutated proteins. Notably, the absence of DNAJA2 increases the turnover of the mutant but not the wild-type protein. Our work indicates that specific missense mutations in cytosolic proteins can promote enhanced interactions with molecular chaperones. Assessment of the broader panel of cytosolic mutant proteins shows that the co-chaperone DNAJA2 exhibits two distinct behaviours: acting to stabilize a wide array of cytosolic proteins including wild type variants, and specifically “buffer” some mutant proteins to reduce their turnover. Our work illustrates how distinct elements of the protein homeostasis network are utilized in the presence of a cytosolic misfolded protein.

Differential Impact of Spike Protein Mutations on SARS-CoV-2 Infectivity and Immune Evasion: Insights from Delta and Kappa Variants.

SARS-CoV-2 continues to pose a global health challenge due to its high transmissibility and mutability, with new variants emerging that potentially undermine vaccination and therapeutic efforts. Mutations in the spike protein, particularly in the receptor-binding domain (RBD), significantly influence viral transmissibility and immune escape. However, the complex interplay of these mutations and their combined effects on viral fitness remain to be analyzed. In this study, we investigated the functional impact of key mutations found in the Delta and Kappa variants of SARS CoV-2. Using pseudovirus assays, we demonstrated that the T478K and L452R mutations characteristic of the Delta variant primarily enhance viral infectivity, with minimal effect on antibody-mediated neutralization. Conversely, the E484Q mutation of the Kappa variant, alone or in combination with L452R, significantly improved evasion of antibody-mediated neutralization but appeared to compromise viral fitness and infectivity. Notably, contrary to previous reports, we found that the P681R mutation contributed neither to increased infectivity nor immune evasion at least in the assay system employed in this study. Our findings suggest that the Delta variant's global dominance over the Kappa variant may be attributed to its superior infectivity and transmissibility rather than enhanced immune evasion capabilities. These results provide valuable insights into the functional consequences of spike protein mutations and may aid in predicting the emergence and spread of future SARS-CoV-2 variants. Such understanding is crucial for enhancing public health preparedness and informing the development of next-generation vaccines and therapeutics.

Genetic Mutations in Cell Junction Proteins Associated with Brain Calcification

AbstractIntracerebral calcium deposition, classified into primary familial brain calcification (PFBC) and secondary brain calcification, occurs within the brain parenchyma and vasculature. PFBC manifests with progressive motor decline, dysarthria, and cognitive impairment, with limited treatment options available. Recent research has suggested a link between dysfunction of the blood–brain barrier (BBB) and PFBC, with certain genetic variants potentially affecting neurovascular unit (NVU) function, thereby contributing to BBB integrity disruption and brain calcification. Cell junctions play an indispensable role in maintaining the function of NVUs. The pathogenic mechanisms of PFBC‐causative genes, such as PDGFRB, PDGFB, MYORG, and JAM2, involve NVU disruption. Cell junctions, such as tight junctions, gap junctions, adherens junctions, desmosomes, hemidesmosomes, and focal adhesions, are vital for cell–cell and cell–extracellular matrix connections, maintaining barrier function, cell adhesion, and facilitating ion and metabolite exchange. Several recent studies have highlighted the role of mutations in genes encoding cell junction proteins in the onset and progression of brain calcification and its related phenotypes. This emerging body of research offers a unique perspective for investigating the underlying mechanisms driving brain calcification. In this review, we conducted an examination of the literature reporting on genetic variants in cell junction proteins associated with brain calcification to delineate potential molecular pathways and investigate genotype–phenotype correlations. This approach not only reinforces the rationale for molecular subtyping of brain calcification but also lays the groundwork for the discovery of novel causative genes involved in pathogenesis. © 2024 International Parkinson and Movement Disorder Society.

Missense mutant p53 transactivates Wnt/β-catenin signaling in neighboring p53-destablized cells through the COX-2/PGE2 pathway.

Missense-type p53 mutations have shown to acquire novel oncogenic roles through gain-of-function mechanism. However, there is an intratumor heterogeneity in stabilization of mutant p53 protein, and it has not been well understood about interaction of p53-stabilized and p53-destabilized cells in the same tumors. We established mouse intestinal tumor-derived organoids carrying Apcδ716, KrasG12D, and Tgfbr2-/- mutations with Trp53R270H or Trp53Null mutation (AKTPR270H and AKTPNull, respectively). Using these organoids, we found that the activation level of Wnt/β-catenin signaling is significantly higher in AKTPR270H cells compared to AKTPNull cells. Notably, Wnt activation in the AKTPNull cells was significantly increased when cocultured with AKTPR270H cells. Expression analysis revealed that cyclooxygenase (COX)-2 is significantly upregulated in AKTPR270H but not in AKTPNull cells, suggesting that mutant p53 induces COX-2/prostaglandin E2 (PGE2) pathway. Importantly, Wnt activation in cocultured AKTPNull cells with AKTPR270H was significantly suppressed when treated with COX-2 inhibitor or PGE2 receptor EP2/EP4 inhibitor. Furthermore, stimulation with PGE2 increased Wnt signaling activity in AKTPNull cells. These results indicate that COX-2/PGE2 pathway is activated in the p53-stabilized cells in the missense-type p53 mutant cancer, and secreted PGE2 may transactivate Wnt/β-catenin signaling in neighboring p53-destabilized tumor cells in the intratumor microenvironment. Therefore, targeting stabilized mutant p53 or COX-2/PGE2 pathway may suppress Wnt/β-catenin signaling of both mutant p53-stabilized and destabilized cells, thus can be a possible preventive or therapeutic strategy.

De novo variants in LRRC8C resulting in constitutive channel activation cause a human multisystem disorder

AbstractVolume-regulated anion channels (VRACs) are multimeric proteins composed of different paralogs of the LRRC8 family. They are activated in response to hypotonic swelling, but little is known about their specific functions. We studied two human individuals with the same congenital syndrome affecting blood vessels, brain, eyes, and bones. The LRRC8C gene harbored de novo variants in both patients, located in a region of the gene encoding the boundary between the pore and a cytoplasmic domain, which is depleted of sequence variations in control subjects. When studied by cryo-EM, both LRRC8C mutant proteins assembled as their wild-type counterparts, but showed increased flexibility, suggesting a destabilization of subunit interactions. When co-expressed with the obligatory LRRC8A subunit, the mutants exhibited enhanced activation, resulting in channel activity even at isotonic conditions in which wild-type channels are closed. We conclude that structural perturbations of LRRC8C impair channel gating and constitute the mechanistic basis of the dominant gain-of-function effect of these pathogenic variants. The pleiotropic phenotype of this novel clinical entity associated with monoallelic LRRC8C variants indicates the fundamental roles of VRACs in different tissues and organs.

Genomic analysis and overexpressing the acetyl-CoA carboxylase of oleaginous Saccharomyces cerevisiae CU-TPD4 for enhanced lipid production from agricultural residues

Single-cell oil produced using oleaginous yeasts is emerging as a promising source for biofuels and oleochemicals. Saccharomyces cerevisiae is the model yeast and is widely utilized in several industrial applications. This study presents a genome analysis of the oleaginous S. cerevisiae strain CU-TPD4, which has been reported to accumulate a high amount of lipids. The analysis revealed a genome size of 17.5 million bases and 7,619 predicted genes were identified. To understand the differences between oleaginous and non-oleaginous S. cerevisiae, a comparative analysis was conducted. The results identified 5,169 shared gene clusters, 36 unique clusters in S. cerevisiae S288C and 22 unique clusters in S. cerevisiae CU-TPD4. Notably, mutations in proteins associated in lipid biosynthesis that affect phosphorylation, such as ACC1, ALE1, and FAA4, were observed, influencing lipid accumulation. Additionally, overexpression of the ACC1 gene under different promoters revealed an approximately 16% improved lipid production under the ENO2 promoter compared to the wild-type strain. Subsequently, lipid production process using rice straw hydrolysate was evaluated. The strain produced a highest total lipid of 1.60 g/L, corresponding to a lipid content of 34.12%. Interestingly, the FA composition of the lipids obtained from the rice straw hydrolysate was comprised of more than 75% monounsaturated FAs. This study provides the first draft genome of oleaginous S. cerevisiae CU-TPD4 and insights into genetic improvements to facilitate lipid production.

Genetic Variability in Neisseria meningitidis Strains Isolated in A Japanese Hospital

Neisseria meningitidis is a significant pathogen causing invasive meningococcal disease, posing clinical and public health concerns worldwide. This study aimed to investigate the genetic characteristics of N. meningitidis clinical isolates at Okayama University Hospital in Japan. Between 2018 and 2023, five clinical strains were isolated, of which three were subjected to the antimicrobial susceptibility testing and whole genetic analysis using MiSeq platform (Illumina, San Diego, CA, USA). One non-groupable isolate, belonging to sequence types (STs)-11026 (ST-32 complex), exhibited non-susceptibility to penicillin G, with a five-mutation pattern (F504L, A510V, I515V, H541N, I566V) in the penA amino acid sequence and additional mutations (XXXIV, N513Y) characteristic of a mosaic penA gene. The other two isolates, ST-1655 (ST-23 complex) with serogroup Y and ST-2057 with serogroup B, were susceptible to penicillin G, neither of which contained the five-mutation pattern. Levofloxacin resistance was observed in two isolates carrying T91I mutation in the gyrA protein. Our findings suggest the presence of antimicrobial-resistant N. meningitidis in Japan, underscoring the necessity for continuous local surveillance. Additional research is crucial for clarifying the ongoing spread of resistance mechanisms and for establishing effective countermeasures to reduce the clinical burden of invasive meningococcal disease.

Two NPC1 homologous proteins are involved in asexual reproduction, pathogenicity, and lipid trafficking in Phytophthora sojae

Niemann-Pick type C (NPC) disease is characterized by lysosomal lipid storage disorders and defects in lipid trafficking, primarily due to mutations in the NPC1 protein. Two NPC1 homologous proteins are present in the genome of Phytophthora sojae, named as PsNPC1-1 and PsNPC1-2. Both proteins exhibit high sequence identity, consistent conserved functional domains, similar gene expression patterns, and comparable subcellular localization. Deletion of a single PsNPC1 gene did not result in significant phenotypic changes. However, simultaneous deletion of both PsNPC1 genes led to reduced mycelial growth, decreased sporangial production, impaired pathogenicity, and an inability to release normal zoospores in P. sojae. Furthermore, dysfunction of PsNPC1s did not completely block the absorption and utilization of exogenous sterols by P. sojae. While lipidome analysis revealed that the relative contents of fatty acyls, sphingolipids and saccharolipids were significantly elevated in the double-gene deletion mutant, alongside obvious alterations in glycerophospholipid and glycerolipid metabolism. Additionally, we observed a significant down-regulation of PsCDP-AP protein along with its interactions with both PsNPC1s. Deletion of PsCDP-AP also impaired asexual reproduction and virulence of P. sojae. These findings demonstrate that both PsNPC1 proteins may collaborate with other key regulators to modulate asexual reproduction, pathogenicity and lipid trafficking in P. sojae.

A single-base deletion in exon 2 of Hd1 delineates monogenic recessive photoperiod insensitivity in aromatic Joha rice: a novel allele for seasonal adaptability

BackgroundAssam's aromatic Joha rice is a unique rice class famous for its aroma, taste, and nutritional benefits, which fetch high market prices in domestic and international markets. Joha landraces are inherently poor yielders due to their strong aroma and predominantly photoperiod sensitivity. Hybridization involving non-aromatic HYVs improves yield with concomitant loss of quality. In this context, mutation breeding, a sustainable approach where genetic mutations are induced to create desirable traits, often provides useful allelic variation in specific morpho-agronomic traits. The present study delves into the genetic characterization of a photoperiod-insensitive mutant. As part of our mutation breeding programme, this mutant was isolated from a gamma ray-induced M2 population of a Joha rice landrace, Kon Joha.ResultsThe mutant was unique, and a single recessive gene conditions the induced photoperiod insensitivity. Mutant gene tagging involved 402 SSR and InDel markers, and later polymorphic markers were used for bulk segregant analysis (BSA) in the F2 population of ‘mutant × Kalijeera (distant parent)’. BSA revealed an association between the SSR marker RM527 and this mutant trait. This marker is present on chromosome 6 of the rice genome. Using chromosome 6-specific SSR markers in polymorphic screening and BSA revealed another associated marker, RM19725, for the mutant trait. The genomic interval between RM527 and RM19725 harbors a photoperiod-insensitive gene, Hd1, on chromosome 6. Cloning and sequencing of Hd1 genomic fragments from the parents and mutants revealed a single-base deletion in exon 2, leading to a frameshift mutation in the Hd1 protein. This mutation in exon 2 leads to severe structural abnormalities in the CCT domain of the Hd1 protein that is critical for the interaction of the repressing complex with conserved response elements in the florigen gene under long-day conditions, thereby causing photoperiod insensitivity.ConclusionsThe mutant's pleasant aroma and other quality characteristics, comparable to those of the parent cultivar, hold significant promise. They expand its potential use in a structured breeding programme aimed at developing high-value aromatic Joha rice. This rice, resilient to winter- and summer-growing environments and with broad seasonal adaptability, could revolutionize the rice market. The practical value of our research is underscored by this exciting possibility.

A general temperature-guided language model to design proteins of enhanced stability and activity.

Designing protein mutants with both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants with improved stability and activity without any prior experimental mutagenesis data for the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive ability compared to current state-of-the-art models on the public mutagenesis dataset across 283 protein assays. Furthermore, we validated PRIME's predictions on five proteins, examining the impact of the top 30 to 45 single-site mutations on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize nonnatural nucleic acid or resilience to extreme alkaline conditions. More than 30% of PRIME-recommended mutants exhibited superior performance compared to their premutation counterparts across all proteins and desired properties. We developed an efficient and effective method based on PRIME to rapidly obtain multisite mutants with enhanced activity and stability. Hence, PRIME demonstrates broad applicability in protein engineering.

A closer look at pathogenic amyloid-β in Alzheimer’s disease using cryo-electron microscopy: a narrative review

Alzheimer’s disease is a progressive neurodegenerative disorder that affects millions of people worldwide. The identification of amyloid-β in Alzheimer’s disease brains, together with the association of mutations in the amyloid-β precursor protein with Alzheimer’s disease pathology, is the basis of the amyloid cascade hypothesis, which suggests that amyloid-β plays a central role in Alzheimer’s disease pathogenesis. Recent studies have further highlighted the role of intraneuronal amyloid-β in Alzheimer’s disease development. Moreover, the success of anti-amyloid-β immunotherapies supports the amyloid cascade hypothesis, emphasizing the importance of targeting specific amyloid-β conformations to achieve better therapeutic outcomes. In recent years, cryo-electron microscopy has become an invaluable tool for obtaining near-atomic resolution images of protein assemblies, and multiple structures of brain-derived amyloid fibrils have been elucidated. In this article, we review the role of pathogenic amyloid-β according to the amyloid cascade hypothesis and explore the relationship between intraneuronal amyloid-β accumulation and the development of key pathological features of Alzheimer’s disease—amyloid plaques and neurofibrillary tangles. We also connect cryo-electron microscopy structures of amyloid-β aggregates with amyloid-β-targeting treatment and highlight recent advances and future research directions. The application of cryo-electron microscopy can provide molecular insights into amyloid-β structure, which is expected to help uncover the underlying mechanisms of Alzheimer’s disease and provide new therapeutic strategies for the clearance of amyloid-β aggregates.

Autism-Linked Mutations in α2δ-1 and α2δ-3 Reduce Protein Membrane Expression but Affect Neither Calcium Channels nor Trans-Synaptic Signaling

Background: α2δ proteins regulate membrane trafficking and biophysical properties of voltage-gated calcium channels. Moreover, they modulate axonal wiring, synapse formation, and trans-synaptic signaling. Several rare missense variants in CACNA2D1 (coding for α2δ-1) and CACNA2D3 (coding for α2δ-3) genes were identified in patients with autism spectrum disorder (ASD). However, the pathogenicity of these variants is not known, and the molecular mechanism by which α2δ proteins may contribute to the pathophysiology of autism is, as of today, not understood. Therefore, in this study we functionally characterized two heterozygous missense variants in α2δ-1 (p.R351T) and α2δ-3 (p.A275T), previously identified in patients with ASD. Methods: Electrophysiological recordings in transfected tsA201 cells were used to study specific channel-dependent functions of mutated α2δ proteins. Membrane expression, presynaptic targeting, and trans-synaptic signaling of mutated α2δ proteins were studied upon expression in murine cultured hippocampal neurons. Results: Homologous expression of both mutated α2δ proteins revealed a strongly reduced membrane expression and synaptic localization compared to the corresponding wild type α2δ proteins. Moreover, the A275T mutation in α2δ-3 resulted in an altered glycosylation pattern upon heterologous expression. However, neither of the mutations compromised the biophysical properties of postsynaptic L-type (CaV1.2 and CaV1.3) and presynaptic P/Q-type (CaV2.1) channels when co-expressed in tsA201 cells. Furthermore, presynaptic expression of p.R351T in the α2δ-1 splice variant lacking exon 23 did not affect trans-synaptic signaling to postsynaptic GABAA receptors. Conclusions: Our data provide evidence that the pathophysiological mechanisms of ASD-causing mutations of α2δ proteins may not involve their classical channel-dependent and trans-synaptic functions. Alternatively, these mutations may induce subtle changes in synapse formation or neuronal network function, highlighting the need for future α2δ protein-linked disease models.

GPTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in G Protein-Coupled Receptors.

Accurately predicting mutations in G protein-coupled receptors (GPCRs) is critical for advancing disease diagnosis and drug discovery. In response to this imperative, GPTrans has emerged as a highly accurate predictor of disease-related mutations in GPCRs. The core innovation of GPTrans resides in the design of a novel feature extraction network, that is capable of integrating features from both wildtype and mutant protein variant sites, utilizing multifeature connections within a transformer framework to ensure comprehensive feature extraction. A key aspect of GPTrans's effectiveness is our introduction of an innovative deep feature integration strategy, which merges embeddings and class tokens from multiple protein language models, including evolutionary scale modeling and ProtTrans, thus shedding light on the biochemical properties of proteins. Leveraging transformer components and a self-attention mechanism, GPTrans captures higher-level representations of protein features. Employing both wildtype and mutation site information for feature fusion not only enriches the predictive feature set but also avoids the common issue of overestimation associated with sequence-based predictions. This approach distinguishes GPTrans, enabling it to significantly outperform existing methods. Our evaluations across diverse GPCR data sets, including ClinVar and MutHTP, demonstrate GPTrans's superior performance, with average AUC values of 0.874 and 0.590 in 10-fold cross-validation. Notably, compared to the AlphaMissense method, GPTrans exhibited a remarkable 38.03% improvement in accuracy when predicting disease-associated mutations in the MutHTP data set. A thorough analysis of the predicted results further validates the model's effectiveness. The source code, data sets, and prediction results for GPTrans are available for academic use at https://github.com/EduardWang/GPTrans.