Journal of Molecular Biology最新文献_第10页

J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70 j结构域蛋白与Hsp90形成二元配合物，与Hsp90和Hsp70形成三元配合物

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168184

Anushka C. Wickramaratne , Jui-Yun Liao , Shannon M. Doyle , Joel R. Hoskins , Gabrielle Puller , Madison L. Scott , John Paul Alao , Ikponwmosa Obaseki , Jerry C. Dinan , Tapan K. Maity , Lisa M. Jenkins , Andrea N. Kravats , Sue Wickner

{"title":"J-domain Proteins form Binary Complexes with Hsp90 and Ternary Complexes with Hsp90 and Hsp70","authors":"Anushka C. Wickramaratne , Jui-Yun Liao , Shannon M. Doyle , Joel R. Hoskins , Gabrielle Puller , Madison L. Scott , John Paul Alao , Ikponwmosa Obaseki , Jerry C. Dinan , Tapan K. Maity , Lisa M. Jenkins , Andrea N. Kravats , Sue Wickner","doi":"10.1016/j.jmb.2023.168184","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168184","url":null,"abstract":"<div><p>Hsp90 and Hsp70 are highly conserved molecular chaperones that help maintain proteostasis by participating in protein folding, unfolding, remodeling and activation of proteins. Both chaperones are also important for cellular recovery following environmental stresses. Hsp90 and Hsp70 function collaboratively for the remodeling and activation of some client proteins. Previous studies using <em>E. coli</em> and <em>S. cerevisiae</em> showed that residues in the Hsp90 middle domain directly interact with a region in the Hsp70 nucleotide binding domain, in the same region known to bind J-domain proteins. Importantly, J-domain proteins facilitate and stabilize the interaction between Hsp90 and Hsp70 both in <em>E. coli</em> and <em>S. cerevisiae</em>. To further explore the role of J-domain proteins in protein reactivation, we tested the hypothesis that J-domain proteins participate in the collaboration between Hsp90 and Hsp70 by simultaneously interacting with Hsp90 and Hsp70. Using <em>E. coli</em> Hsp90, Hsp70 (DnaK), and a J-domain protein (CbpA), we detected a ternary complex containing all three proteins. The interaction involved the J-domain of CbpA, the DnaK binding region of <em>E. coli</em> Hsp90, and the J-domain protein binding region of DnaK where Hsp90 also binds. Additionally, results show that <em>E. coli</em> Hsp90 interacts with <em>E. coli</em> J-domain proteins, DnaJ and CbpA, and that yeast Hsp90, Hsp82, interacts with a yeast J-domain protein, Ydj1. Together these results suggest that the complexes may be transient intermediates in the pathway of collaborative protein remodeling by Hsp90 and Hsp70.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168184"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1761472","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

Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway 迷你病毒碱基切除修复途径的生化重构

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168188

Shailesh B. Lad , Monica Upadhyay , Pracheta Thorat , Divya Nair , Gregory W. Moseley , Sanjeeva Srivastava , Pradeepkumar P.I. , Kiran Kondabagil

{"title":"Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway","authors":"Shailesh B. Lad , Monica Upadhyay , Pracheta Thorat , Divya Nair , Gregory W. Moseley , Sanjeeva Srivastava , Pradeepkumar P.I. , Kiran Kondabagil","doi":"10.1016/j.jmb.2023.168188","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168188","url":null,"abstract":"<div><p>Viruses are believed to be the obligate intracellular parasites that only carry genes essential for infecting and hijacking the host cell machinery. However, a recently discovered group of viruses belonging to the phylum nucleocytovirocota, also known as the nucleo-cytoplasmic large DNA viruses (NCLDVs), possess a number of genes that code for proteins predicted to be involved in metabolism, and DNA replication, and repair. In the present study, first, using proteomics of viral particles, we show that several proteins required for the completion of the DNA base excision repair (BER) pathway are packaged within the virions of Mimivirus as well as related viruses while they are absent from the virions of Marseillevirus and Kurlavirus that are NCLDVs with smaller genomes. We have thoroughly characterized three putative base excision repair enzymes from Mimivirus, a prototype NCLDV and successfully reconstituted the BER pathway using the purified recombinant proteins. The mimiviral uracil-DNA glycosylase (mvUDG) excises uracil from both ssDNA and dsDNA, a novel finding contrary to earlier studies. The putative AP-endonuclease (mvAPE) specifically cleaves at the abasic site created by the glycosylase while also exhibiting the 3′-5′ exonuclease activity. The Mimivirus polymerase X protein (mvPolX) can bind to gapped DNA substrates and perform single nucleotide gap-filling followed by downstream strand displacement. Furthermore, we show that when reconstituted <em>in vitro</em>, mvUDG, mvAPE, and mvPolX function cohesively to repair a uracil-containing DNA predominantly by long patch BER and together, may participate in the BER pathway during the early phase of Mimivirus life-cycle.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168188"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1827158","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

Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA 构象特异性合成抗体鉴别离子通道CorA的多种功能状态

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168192

Satchal K. Erramilli , Pawel K. Dominik , Dawid Deneka , Piotr Tokarz , Sangwoo S. Kim , Bharat G. Reddy , Blazej M. Skrobek , Olivier Dalmas , Eduardo Perozo , Anthony A. Kossiakoff

{"title":"Conformation-specific Synthetic Antibodies Discriminate Multiple Functional States of the Ion Channel CorA","authors":"Satchal K. Erramilli , Pawel K. Dominik , Dawid Deneka , Piotr Tokarz , Sangwoo S. Kim , Bharat G. Reddy , Blazej M. Skrobek , Olivier Dalmas , Eduardo Perozo , Anthony A. Kossiakoff","doi":"10.1016/j.jmb.2023.168192","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168192","url":null,"abstract":"<div><p>CorA, the primary magnesium ion channel in prokaryotes and archaea, is a prototypical homopentameric ion channel that undergoes ion-dependent conformational transitions. CorA adopts five-fold symmetric non-conductive states in the presence of high concentrations of Mg<sup>2+</sup>, and highly asymmetric flexible states in its complete absence. However, the latter were of insufficient resolution to be thoroughly characterized. In order to gain additional insights into the relationship between asymmetry and channel activation, we exploited phage display selection strategies to generate conformation-specific synthetic antibodies (sABs) against CorA in the absence of Mg<sup>2+</sup>. Two sABs from these selections, C12 and C18, showed different degrees of Mg<sup>2+</sup>-sensitivity. Through structural, biochemical, and biophysical characterization, we found the sABs are both conformation-specific but probe different features of the channel under open-like conditions. C18 is highly specific to the Mg<sup>2+</sup>-depleted state of CorA and through negative-stain electron microscopy (ns-EM), we show sAB binding reflects the asymmetric arrangement of CorA protomers in Mg<sup>2+</sup>-depleted conditions. We used X-ray crystallography to determine a structure at 2.0 Å resolution of sAB C12 bound to the soluble N-terminal regulatory domain of CorA. The structure shows C12 is a competitive inhibitor of regulatory magnesium binding through its interaction with the divalent cation sensing site. We subsequently exploited this relationship to capture and visualize asymmetric CorA states in different [Mg<sup>2+</sup>] using ns-EM. We additionally utilized these sABs to provide insights into the energy landscape that governs the ion-dependent conformational transitions of CorA.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168192"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3399838","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: 1

Stable Mammalian Serum Albumins Designed for Bacterial Expression 设计用于细菌表达的稳定哺乳动物血清白蛋白

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168191

Olga Khersonsky , Moshe Goldsmith , Irina Zaretsky , Shelly Hamer-Rogotner , Orly Dym , Tamar Unger , Meital Yona , Yael Fridmann-Sirkis , Sarel J. Fleishman

{"title":"Stable Mammalian Serum Albumins Designed for Bacterial Expression","authors":"Olga Khersonsky , Moshe Goldsmith , Irina Zaretsky , Shelly Hamer-Rogotner , Orly Dym , Tamar Unger , Meital Yona , Yael Fridmann-Sirkis , Sarel J. Fleishman","doi":"10.1016/j.jmb.2023.168191","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168191","url":null,"abstract":"<div><p>Albumin is the most abundant protein in the blood serum of mammals and has essential carrier and physiological roles. Albumins are also used in a wide variety of molecular and cellular experiments and in the cultivated meat industry. Despite their importance, however, albumins are challenging for heterologous expression in microbial hosts, likely due to 17 conserved intramolecular disulfide bonds. Therefore, albumins used in research and biotechnological applications either derive from animal serum, despite severe ethical and reproducibility concerns, or from recombinant expression in yeast or rice. We use the PROSS algorithm to stabilize human and bovine serum albumins, finding that all are highly expressed in <em>E. coli</em>. Design accuracy is verified by crystallographic analysis of a human albumin variant with 16 mutations. This albumin variant exhibits ligand binding properties similar to those of the wild type. Remarkably, a design with 73 mutations relative to human albumin exhibits over 40 °C improved stability and is stable beyond the boiling point of water. Our results suggest that proteins with many disulfide bridges have the potential to exhibit extreme stability when subjected to design. The designed albumins may be used to make economical, reproducible, and animal-free reagents for molecular and cell biology. They also open the way to high-throughput screening to study and enhance albumin carrier properties.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168191"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"3204666","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

Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing 揭示APOBEC3A介导的RNA编辑的酶底物性质。

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168198

Kyumin Kim , Alan B. Shi , Kori Kelley , Xiaojiang S. Chen

{"title":"Unraveling the Enzyme-Substrate Properties for APOBEC3A-Mediated RNA Editing","authors":"Kyumin Kim , Alan B. Shi , Kori Kelley , Xiaojiang S. Chen","doi":"10.1016/j.jmb.2023.168198","DOIUrl":"10.1016/j.jmb.2023.168198","url":null,"abstract":"<div><p>The APOBEC3 family of human cytidine deaminases is involved in various cellular processes, including the innate and acquired immune system, mostly through inducing C-to-U in single-stranded DNA and/or RNA mutations. Although recent studies have examined RNA editing by APOBEC3A (A3A), its intracellular target specificity are not fully characterized. To address this gap, we performed in-depth analysis of cellular RNA editing using our recently developed sensitive cell-based fluorescence assay. Our findings demonstrate that A3A and an A3A-loop1-containing APOBEC3B (A3B) chimera are capable of RNA editing. We observed that A3A prefers to edit specific RNA substrates which are not efficiently deaminated by other APOBEC members. The editing efficiency of A3A is influenced by the RNA sequence contexts and distinct stem-loop secondary structures. Based on the identified RNA specificity features, we predicted potential A3A-editing targets in the encoding region of cellular mRNAs and discovered novel RNA transcripts that are extensively edited by A3A. Furthermore, we found a trend of increased synonymous mutations at the sites for more efficient A3A-editing, indicating evolutionary adaptation to the higher editing rate by A3A. Our results shed light on the intracellular RNA editing properties of A3A and provide insights into new RNA targets and potential impact of A3A-mediated RNA editing.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168198"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9988006","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: 1

Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola 热梭菌热稳定性CRISPR-Cas13a核糖核酸酶活性的结构基础

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168197

Feng Wang , Chendi Zhang , Haijiang Xu, Wanting Zeng, Lixin Ma, Zhuang Li

{"title":"Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola","authors":"Feng Wang , Chendi Zhang , Haijiang Xu, Wanting Zeng, Lixin Ma, Zhuang Li","doi":"10.1016/j.jmb.2023.168197","DOIUrl":"10.1016/j.jmb.2023.168197","url":null,"abstract":"<div><p>The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria <em>Thermoclostridium caenicola</em> (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 Å, and TccCas13a at 3.5 Å. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5′-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5′-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2′-OH of crRNA 5′-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168197"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10029440","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

Tau Fibrillation Induced by Heparin or a Lysophospholipid Show Different Initial Oligomer Formation 肝素或溶血磷脂诱导的Tau纤颤显示不同的初始低聚物形成

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168194

Helena Østergaard Rasmussen , Janni Nielsen , Angela de Poli , Daniel E. Otzen , Jan Skov Pedersen

{"title":"Tau Fibrillation Induced by Heparin or a Lysophospholipid Show Different Initial Oligomer Formation","authors":"Helena Østergaard Rasmussen , Janni Nielsen , Angela de Poli , Daniel E. Otzen , Jan Skov Pedersen","doi":"10.1016/j.jmb.2023.168194","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168194","url":null,"abstract":"<div><p>The protein tau is involved in several neurogenerative diseases such as Alzheimer’s Disease, where tau content and fibrillation have been linked to disease progression. Tau colocalizes with phospholipids and glycosaminoglycans <em>in vivo</em>. We investigated if and how tau fibrillation can be induced by two lysophospholipids, namely the zwitterionic 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (LPC) and the anionic 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1′-rac-glycerol) (LPG) as well as the glycosaminoglycan heparin. We used a range of biophysical techniques including small-angle X-ray scattering, Thioflavin T fluorescence, and SDS-PAGE, collecting data at various time points to obtain structural information on each phase of the fibrillation. We find that LPC does not induce fibrillation or interact with tau. Low concentrations of LPG induce fibrillation by formation of small hydrophobic clusters with monomeric tau. At higher LPG concentrations, a core–shell complex is formed where tau wraps around LPG micelles with regions extending away from the micelles. For heparin, loosely associated oligomers are formed rapidly with around ten tau molecules. Fibrils formed with either LPG or heparin show similar final cross-section dimensions. Furthermore, SDS-resistant oligomers are observed for both LPG and heparin. Our study demonstrates that tau fibrillation can be induced by two different biologically relevant cofactors leading to structurally different initial states but similar cross-sectional dimensions for the fibrils. Structural information about initial states prior to fibril formation is important both to gain a better understanding of the onset of fibrillation <em>in vivo</em>, and for the development of targeted drugs that can reduce or abolish tau fibrillation.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168194"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1827159","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

The Dysferlin C2A Domain Binds PI(4,5)P2 and Penetrates Membranes Dysferlin C2A结构域结合PI(4,5)P2并穿透膜

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168193

Ethiene Kwok , Shauna C. Otto , Patricia Khuu , Andrew P. Carpenter , Sara J. Codding , Patrick N. Reardon , Juan Vanegas , Tanushri M. Kumar , Chapman J. Kuykendall , Ryan A. Mehl , Joe Baio , Colin P. Johnson

{"title":"The Dysferlin C2A Domain Binds PI(4,5)P2 and Penetrates Membranes","authors":"Ethiene Kwok , Shauna C. Otto , Patricia Khuu , Andrew P. Carpenter , Sara J. Codding , Patrick N. Reardon , Juan Vanegas , Tanushri M. Kumar , Chapman J. Kuykendall , Ryan A. Mehl , Joe Baio , Colin P. Johnson","doi":"10.1016/j.jmb.2023.168193","DOIUrl":"https://doi.org/10.1016/j.jmb.2023.168193","url":null,"abstract":"<div><p>Dysferlin is a large membrane protein found most prominently in striated muscle. Loss of dysferlin activity is associated with reduced exocytosis, abnormal intracellular Ca2+ and the muscle diseases limb-girdle muscular dystrophy and Miyoshi myopathy. The cytosolic region of dysferlin consists of seven C2 domains with mutations in the C2A domain at the N-terminus resulting in pathology. Despite the importance of Ca2+ and membrane binding activities of the C2A domain for dysferlin function, the mechanism of the domain remains poorly characterized. In this study we find that the C2A domain preferentially binds membranes containing PI(4,5)P2 through an interaction mediated by residues Y23, K32, K33, and R77 on the concave face of the domain. We also found that subsequent to membrane binding, the C2A domain inserts residues on the Ca2+ binding loops into the membrane. Analysis of solution NMR measurements indicate that the domain inhabits two distinct structural states, with Ca2+ shifting the population between states towards a more rigid structure with greater affinity for PI(4,5)P2. Based on our results, we propose a mechanism where Ca<sup>2+</sup><span> converts C2A from a structurally dynamic, low PI(4,5)P2 affinity state to a high affinity state that targets dysferlin to PI(4,5)P2 enriched membranes through interaction with Tyr23, K32, K33, and R77. Binding also involves changes in lipid packing and insertion by the third Ca2+ binding loop of the C2 domain into the membrane, which would contribute to dysferlin function in exocytosis and Ca2+ regulation.</span></p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168193"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"1606199","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

Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction 不仅仅是扩张:脯氨酸的含量和密度也会导致无序的蛋白质构象压实

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168196

Milan Kumar Hazra, Yishai Gilron, Yaakov Levy

{"title":"Not Only Expansion: Proline Content and Density Also Induce Disordered Protein Conformation Compaction","authors":"Milan Kumar Hazra, Yishai Gilron, Yaakov Levy","doi":"10.1016/j.jmb.2023.168196","DOIUrl":"10.1016/j.jmb.2023.168196","url":null,"abstract":"<div><p>Intrinsically disordered proteins (IDPs) adopt a wide array of different conformations that can be constrained by the presence of proline residues, which are frequently found in IDPs. To assess the effects of proline, we designed a series of peptides that differ with respect to the number of prolines in the sequence and their organization. Using high-resolution atomistic molecular dynamics simulations, we found that accounting for whether the proline residues are clustered or isolated contributed significantly to explaining deviations in the experimentally-determined gyration radii of IDPs from the values expected based on the Flory scaling-law. By contrast, total proline content makes smaller contribution to explaining the effect of prolines on IDP conformation. Proline residues exhibit opposing effects depending on their organizational pattern in the IDP sequence. Clustered prolines (<em>i.e</em>., prolines with ≤2 intervening non-proline residues) result in expanded peptide conformations whereas isolated prolines (<em>i.e</em>., prolines with >2 intervening non-proline residues) impose compacted conformations. Clustered prolines were estimated to induce an expansion of ∼20% in IDP dimension (via formation of PPII structural elements) whereas isolated prolines were estimated to induce a compaction of ∼10% in IDP dimension (via the formation of backbone turns). This dual role of prolines provides a mechanism for conformational switching that does not rely on the kinetically much slower isomerization of <em>cis</em> proline to the <em>trans</em> form. Bioinformatic analysis demonstrates high populations of both isolated and clustered prolines and implementing them in coarse-grained molecular dynamics models illustrates that they improve the characterization of the conformational ensembles of IDPs.</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168196"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10029437","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

Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates 脊椎动物toll样受体病原体核酸特异性分析与预测

IF 5.6 2区生物学

Journal of Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.jmb.2023.168208

Anuja Jain, Tina Begum, Shandar Ahmad

{"title":"Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates","authors":"Anuja Jain, Tina Begum, Shandar Ahmad","doi":"10.1016/j.jmb.2023.168208","DOIUrl":"10.1016/j.jmb.2023.168208","url":null,"abstract":"<div><p><span>Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism. Interestingly, our findings reveal that such host-specific features are directly related to the strand (single or double) specificity of nucleic acid from pathogens. However, during host-pathogen interactions, such features were unable to explain the pathogenic PAMP (</span><em>i.e.</em>, DNA, RNA or other) selectivity, suggesting a more complex mechanism. Using these features, we developed a number of machine learning models, of which Random Forest achieved a high performance (94.57% accuracy) to predict strand specificity of TLRs from protein-derived features. We applied the trained model to propose strand specificity of some previously uncharacterized distinct fish-specific novel TLRs (TLR18, TLR23, TLR24, TLR25, TLR27).</p></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"435 17","pages":"Article 168208"},"PeriodicalIF":5.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10030748","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}

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