Journal of Molecular Biology最新文献_第5页

iACP-DFSRA: Identification of Anticancer Peptides Based on a Dual-channel Fusion Strategy of ResCNN and Attention iACP-DFSRA：基于 ResCNN 和 Attention 双通道融合策略的抗癌肽鉴定。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-10-01 DOI: 10.1016/j.jmb.2024.168810

Xin Wang, Zimeng Zhang, Chang Liu

{"title":"iACP-DFSRA: Identification of Anticancer Peptides Based on a Dual-channel Fusion Strategy of ResCNN and Attention","authors":"Xin Wang, Zimeng Zhang, Chang Liu","doi":"10.1016/j.jmb.2024.168810","DOIUrl":"10.1016/j.jmb.2024.168810","url":null,"abstract":"<div><div>Anticancer peptides (ACPs) have been widely applied in the treatment of cancer owing to good safety, rational side effects, and high selectivity. However, the number of ACPs that have been experimentally validated is limited as identification of ACPs is extremely expensive. Hence, accurate and cost-effective identification methods for ACPs are urgently needed. In this work, we proposed a deep learning-based model, named iACP-DFSRA, for ACPs identification. Specifically, we adopted two kinds of sequence embedding technologies, ProtBert_BFD pre-training language model and handcrafted features to encode protein sequences. Then, the LightGBM was used for feature selection, and the selected features were input into ResCNN and Attention mechanism, respectively, to extract local and global features. Finally, the concatenate features were deeply fused by using the Attention mechanism to allow key features to be paid more attention to by the model and make predictions by fully connected layer. The results of 10-fold cross-validation demonstrated that the iACP-DFSRA model delivered improved results in most metrics with <em>Sp</em> of 94.15%, <em>Sn</em> of 95.32%, <em>Acc</em> of 94.74% and <em>MCC</em> of 89.48% compared to the latest AACFlow model. Indeed, the iACP-DFSRA model is the only model with <em>Acc</em> > 90% and <em>MCC</em> > 80% on this independent test dataset. Furthermore, we have further demonstrated the superiority of our model on additional datasets. In addition, t-SNE and SHAP interpretation analysis demonstrated that it is crucial to use two channels for feature extraction and use the Attention mechanism for deep fusion, which helps the iACP-DFSRA to predict ACPs more effectively.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168810"},"PeriodicalIF":4.7,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Potential vs Challenges of Expanding the Protein Universe With Genetic Code Expansion in Eukaryotic Cells 真核细胞中遗传密码扩展蛋白质宇宙的潜力与挑战。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-30 DOI: 10.1016/j.jmb.2024.168807

Rajanya Bhattacharjee , Edward A. Lemke

引用次数: 0

Sen1: The Varied Virtues of a Multifaceted Helicase. Sen1：多面螺旋酶的各种优点。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-30 DOI: 10.1016/j.jmb.2024.168808

Umberto Aiello, Odil Porrua, Domenico Libri

引用次数: 0

Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2 低温电子显微镜揭示了分枝杆菌 Dps2 的 DNA 压实机制。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-28 DOI: 10.1016/j.jmb.2024.168806

Priyanka Garg , Thejas Satheesh , Mahipal Ganji , Somnath Dutta

{"title":"Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2","authors":"Priyanka Garg , Thejas Satheesh , Mahipal Ganji , Somnath Dutta","doi":"10.1016/j.jmb.2024.168806","DOIUrl":"10.1016/j.jmb.2024.168806","url":null,"abstract":"<div><div>DNA binding protein from starved cells (Dps) is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation to maintain the integrity of bacteria under hostile conditions. Several approaches, including cryo-electron tomography, have been previously implemented by other research groups to decipher the structure of the Dps protein bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to identify the DNA binding residues. Like other bacteria, <em>Mycobacterium smegmatis also</em> expresses Dps2 (called MsDps2), which binds DNA to protect it under oxidative stress conditions. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps2 protein from <em>Mycobacterium smegmatis</em>. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA complexes and identified that the region close to the N-terminus confers the DNA binding property. Based on cryo-EM data, we also pinpointed several arginine residues, proximal to the DNA binding region, responsible for DNA binding. We also performed mutations of these residues, which dramatically reduced the MsDps2-DNA interaction. In addition, we proposed a model that elucidates the mechanism of DNA compaction, which adapts a lattice-like structure. We performed single-molecule imaging of MsDps2-DNA interactions that corroborate well with our structural studies. Taken together, our results delineate the specific MsDps2 residues that play an important role in DNA binding and compaction, providing new insights into <em>Mycobacterial</em> DNA compaction mechanisms under stress conditions.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 21","pages":"Article 168806"},"PeriodicalIF":4.7,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature 细胞色素 c 过氧化物酶的核心、活性位点和外围区域对极端压力和温度的不同反应。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-26 DOI: 10.1016/j.jmb.2024.168799

Rebecca K. Zawistowski, Brian R. Crane

{"title":"Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature","authors":"Rebecca K. Zawistowski, Brian R. Crane","doi":"10.1016/j.jmb.2024.168799","DOIUrl":"10.1016/j.jmb.2024.168799","url":null,"abstract":"<div><div>In consideration of life in extreme environments, the effects of hydrostatic pressure on proteins at the atomic level have drawn substantial interest. Large deviations of temperature and pressure from ambient conditions can shift the free energy landscape of proteins to reveal otherwise lowly populated structural states and even promote unfolding. We report the crystal structure of the heme-containing peroxidase, cytochrome <em>c</em> peroxidase (CcP) at 1.5 and 3.0 kbar and make comparisons to structures determined at 1.0 bar and cryo-temperatures (100 K). Pressure produces anisotropic changes in CcP, but compressibility plateaus after 1.5 kbar. CcP responds to pressure with volume declines at the periphery of the protein where B-factors are relatively high but maintains nearly intransient core structure, hydrogen bonding interactions and active site channels. Changes in active-site solvation and heme ligation reveal pressure sensitivity to protein–ligand interactions and a potential docking site for the substrate peroxide. Compression at the surface affects neither alternate side-chain conformers nor B-factors. Thus, packing in the core, which resembles a crystalline solid, limits motion and protects the active site, whereas looser packing at the surface preserves side-chain dynamics. These data demonstrate that conformational dynamics and packing densities are not fully correlated in proteins and that encapsulation of cofactors by the polypeptide can provide a precisely structured environment resistant to change across a wide range of physical conditions.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168799"},"PeriodicalIF":4.7,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nuclear Receptor Interdomain Communication is Mediated by the Hinge with Ligand Specificity 核受体域间通讯由具有配体特异性的铰链介导。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-25 DOI: 10.1016/j.jmb.2024.168805

Saurov Hazarika , Tracy Yu , Arumay Biswas , Namita Dube , Priscilla Villalona , C. Denise Okafor

{"title":"Nuclear Receptor Interdomain Communication is Mediated by the Hinge with Ligand Specificity","authors":"Saurov Hazarika , Tracy Yu , Arumay Biswas , Namita Dube , Priscilla Villalona , C. Denise Okafor","doi":"10.1016/j.jmb.2024.168805","DOIUrl":"10.1016/j.jmb.2024.168805","url":null,"abstract":"<div><div>Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full-length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (>10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein–protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full-length nuclear receptors.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168805"},"PeriodicalIF":4.7,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rational Design of Untranslated Regions to Enhance Gene Expression 合理设计非翻译区，提高基因表达。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-24 DOI: 10.1016/j.jmb.2024.168804

Mingchun Liu , Zhuoer Jin , Qing Xiang , Huawei He , Yuhan Huang , Mengfei Long , Jicheng Wu , Cheng Zhi Huang , Chengde Mao , Hua Zuo

{"title":"Rational Design of Untranslated Regions to Enhance Gene Expression","authors":"Mingchun Liu , Zhuoer Jin , Qing Xiang , Huawei He , Yuhan Huang , Mengfei Long , Jicheng Wu , Cheng Zhi Huang , Chengde Mao , Hua Zuo","doi":"10.1016/j.jmb.2024.168804","DOIUrl":"10.1016/j.jmb.2024.168804","url":null,"abstract":"<div><div>How to improve gene expression by optimizing mRNA structures is a crucial question for various medical and biotechnological applications. Previous efforts focus largely on investigation of the 5′ UTR hairpin structures. In this study, we present a rational strategy that enhances mRNA stability and translation by engineering both the 5′ and 3′ UTR sequences. We have successfully demonstrated this strategy using green fluorescent protein (GFP) as a model in <em>Escherichia coli</em> and across different expression vectors. We further validated it with luciferase and <em>Plasmodium falciparum</em> lactate dehydrogenase (PfLDH). To elucidate the underlying mechanism, we have quantitatively analyzed both protein, mRNA levels and half-life time. We have identified several key aspects of UTRs that significantly influence mRNA stability and protein expression in our system: (1) The optimal length of the single-stranded spacer between the stabilizer hairpin and ribosome binding site (RBS) in the 5′ UTR is 25–30 nucleotide (nt) long. An optimal 32% GC content in the spacer yielded the highest levels of GFP protein production. (2) The insertion of a homodimerdizable, G-quadruplex structure containing RNA aptamer, “Corn”, in the 3′ UTR markedly increased the protein expression. Our findings indicated that the carefully engineered 5′ UTRs and 3′ UTRs significantly boosted gene expression. Specifically, the inclusion of 5 × Corn in the 3′ UTR appeared to facilitate the local aggregation of mRNA, leading to the formation of mRNA condensates. Aside from shedding light on the regulation of mRNA stability and expression, this study is expected to substantially increase biological protein production.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168804"},"PeriodicalIF":4.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

π-π Interactions Drive the Homotypic Phase Separation of the Prion-like Diatom Pyrenoid Scaffold PYCO1 π-π相互作用驱动朊病毒样硅藻火绒素支架PYCO1的同型相分离。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-24 DOI: 10.1016/j.jmb.2024.168800

Cheng Wei Poh, Oliver Mueller-Cajar

{"title":"π-π Interactions Drive the Homotypic Phase Separation of the Prion-like Diatom Pyrenoid Scaffold PYCO1","authors":"Cheng Wei Poh, Oliver Mueller-Cajar","doi":"10.1016/j.jmb.2024.168800","DOIUrl":"10.1016/j.jmb.2024.168800","url":null,"abstract":"<div><div>CO<sub>2</sub> fixation in most unicellular algae relies on the pyrenoid, a biomolecular condensate, which sequesters the cell’s carboxylase Rubisco. In the marine diatom <em>Phaeodactylum tricornutum</em>, the pyrenoid tandem repeat protein Pyrenoid Component 1 (PYCO1) multivalently binds Rubisco to form a heterotypic Rubisco condensate. PYCO1 contains prion-like domains and can phase-separate homotypically in a salt-dependent manner. Here we dissect PYCO1 homotypic liquid–liquid phase separation (LLPS) by evaluating protein fragments and the effect of site-directed mutagenesis. Two of PYCO1′s six repeats are required for homotypic LLPS. Mutagenesis of a minimal phase-separating fragment reveals tremendous sensitivity to the substitution of aromatic residues. Removing positively charged lysines and arginines instead enhances the propensity of the fragment to condense. We conclude that PYCO1 homotypic LLPS is mostly driven by π-π interactions mediated by tyrosine and tryptophan stickers. In contrast π-cation interactions involving arginine or lysine are not significant drivers of LLPS in this system.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168800"},"PeriodicalIF":4.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination. 决定在何处切断转录线的致命决定：与 3'末端异常处理和转录终止有关的病理学。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-24 DOI: 10.1016/j.jmb.2024.168802

Pawel Grzechnik, Hannah E Mischo

引用次数: 0

Structural Analysis of Mammalian Sialic Acid Esterase 哺乳动物丝胶酸酯酶的结构分析。

IF 4.7 2区生物学

Journal of Molecular Biology Pub Date : 2024-09-24 DOI: 10.1016/j.jmb.2024.168801

Danilo Ide, Alexei Gorelik, Katalin Illes, Bhushan Nagar

{"title":"Structural Analysis of Mammalian Sialic Acid Esterase","authors":"Danilo Ide, Alexei Gorelik, Katalin Illes, Bhushan Nagar","doi":"10.1016/j.jmb.2024.168801","DOIUrl":"10.1016/j.jmb.2024.168801","url":null,"abstract":"<div><div>Sialic acid esterase (SIAE) catalyzes the removal of <em>O</em>-acetyl groups from sialic acids found on cell surface glycoproteins to regulate cellular processes such as B cell receptor signalling and apoptosis. Loss-of-function mutations in SIAE are associated with several common autoimmune diseases including Crohn’s, ulcerative colitis, and arthritis. To gain a better understanding of the function and regulation of this protein, we determined crystal structures of SIAE from three mammalian homologs, including an acetate bound structure. The structures reveal that the catalytic domain adopts the fold of the SGNH hydrolase superfamily. The active site is composed of a catalytic dyad, as opposed to the previously reported catalytic triad. Attempts to determine a substrate-bound structure yielded only the hydrolyzed product acetate in the active site. Rigid docking of complete substrates followed by molecular dynamics simulations revealed that the active site does not form specific interactions with substrates, rather it appears to be broadly specific to accept sialoglycans with diverse modifications. Based on the acetate bound structure, a catalytic mechanism is proposed. Structural mapping of disease mutations reveals that most are located on the surface of the enzyme and would only cause minor disruptions to the protein fold, suggesting that these mutations likely affect binding to other factors. These results improve our understanding of SIAE biology and may aid in the development of therapies for autoimmune diseases and cancer.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"436 22","pages":"Article 168801"},"PeriodicalIF":4.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0