Biochimica et biophysica acta. Proteins and proteomics最新文献

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Co-chaperonin GroES subunit exchange as dependent on time, pH, protein concentration, and urea 共合子蛋白 GroES 亚基交换与时间、pH 值、蛋白质浓度和尿素有关。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-07-14 DOI: 10.1016/j.bbapap.2024.141032
Victor Marchenkov , Alexey Surin , Victor Ugarov , Nina Kotova , Natalia Marchenko , Alexey Fedorov , Alexei Finkelstein , Vladimir Filimonov , Gennady Semisotnov
{"title":"Co-chaperonin GroES subunit exchange as dependent on time, pH, protein concentration, and urea","authors":"Victor Marchenkov ,&nbsp;Alexey Surin ,&nbsp;Victor Ugarov ,&nbsp;Nina Kotova ,&nbsp;Natalia Marchenko ,&nbsp;Alexey Fedorov ,&nbsp;Alexei Finkelstein ,&nbsp;Vladimir Filimonov ,&nbsp;Gennady Semisotnov","doi":"10.1016/j.bbapap.2024.141032","DOIUrl":"10.1016/j.bbapap.2024.141032","url":null,"abstract":"<div><p>The discovery of a subunit exchange in some oligomeric proteins, implying short-term dissociation of their oligomeric structure, requires new insights into the role of the quaternary structure in oligomeric protein stability and function. Here we demonstrate the effect of pH, protein concentration, and urea on the efficiency of GroES heptamer (GroES<sub>7</sub>) subunit exchange. A mixture of equimolar amounts of wild-type (WT) GroES<sub>7</sub> and its Ala97Cys mutant modified with iodoacetic acid (97-carboxymethyl cysteine or CMC-GroES<sub>7</sub>) was incubated in various conditions and subjected to isoelectric focusing (IEF) in polyacrylamide gel. For each sample, there are eight Coomassie-stained electrophoretic bands showing different charges that result from a different number of included mutant subunits, each carrying an additional negative charge. The intensities of these bands serve to analyze the protein subunit exchange. The protein stability is evaluated using the transverse urea gradient gel electrophoresis (TUGGE). At pH 8.0, the intensities of the initial bands corresponding to WT-GroES<sub>7</sub> and CMC-GroES<sub>7</sub> are decreased with a half-time of (23 ± 2) min. The exchange decreases with decreasing pH and seems to be strongly hindered at pH 5.2 due to the protonation of groups with pK ∼ 6.3, which stabilizes the protein quaternary structure. The destabilization of the protein quaternary structure caused by increased pH, decreased protein concentration, or urea accelerates the GroES subunit exchange. This study allows visualizing the subunit exchange in oligomeric proteins and confirms its direct connection with the stability of the protein quaternary structure.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141032"},"PeriodicalIF":2.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 regulation of the thermal stability and affinity of the HSPA5 (Grp78/BiP) by clients and nucleotides is modulated by domains coupling HSPA5 (Grp78/BiP)的热稳定性和亲和性受客户和核苷酸的调节,并受结构域耦合的调控。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-07-14 DOI: 10.1016/j.bbapap.2024.141034
Noeli S.M. Silva , Bruna Siebeneichler , Carlos S. Oliveira , Paulo R. Dores-Silva , Júlio C. Borges
{"title":"The regulation of the thermal stability and affinity of the HSPA5 (Grp78/BiP) by clients and nucleotides is modulated by domains coupling","authors":"Noeli S.M. Silva ,&nbsp;Bruna Siebeneichler ,&nbsp;Carlos S. Oliveira ,&nbsp;Paulo R. Dores-Silva ,&nbsp;Júlio C. Borges","doi":"10.1016/j.bbapap.2024.141034","DOIUrl":"10.1016/j.bbapap.2024.141034","url":null,"abstract":"<div><p>The HSPA5 protein (BiP/Grp78) serves as a pivotal chaperone in maintaining cellular protein quality control. As a member of the human HSP70 family, HSPA5 comprises two distinct domains: a nucleotide-binding domain (NBD) and a peptide-binding domain (PBD). In this study, we investigated the interdomain interactions of HSPA5, aiming to elucidate how these domains regulate its function as a chaperone. Our findings revealed that HSPA5-FL, HSPA5-T, and HSPA5-N exhibit varying affinities for ATP and ADP, with a noticeable dependency on Mg<sup>2+</sup> for optimal interactions. Interestingly, in ADP assays, the presence of the metal ion seems to enhance NBD binding only for HSPA5-FL and HSPA5-T. Moreover, while the truncation of the C-terminus does not significantly impact the thermal stability of HSPA5, experiments involving MgATP underscore its essential role in mediating interactions and nucleotide hydrolysis. Thermal stability assays further suggested that the NBD-PBD interface enhances the stability of the NBD, more pronounced for HSPA5 than for the orthologous HSPA1A, and prevents self-aggregation through interdomain coupling. Enzymatic analyses indicated that the presence of PBD enhances NBD ATPase activity and augments its nucleotide affinity. Notably, the intrinsic chaperone activity of the PBD is dependent on the presence of the NBD, potentially due to the propensity of the PBD for self-oligomerization. Collectively, our data highlight the pivotal role of allosteric mechanisms in modulating thermal stability, nucleotide interaction, and ATPase activity of HSPA5, underscoring its significance in protein quality control within cellular environments.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141034"},"PeriodicalIF":2.5,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Mapping the Periostin splice isoforms in atopic dermatitis and an in vitro asthma model – A multi-platform analysis using mass spectrometry and RT-qPCR 绘制特应性皮炎和体外哮喘模型中的Periostin剪接同工酶--利用质谱法和RT-qPCR进行的多平台分析。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-07-06 DOI: 10.1016/j.bbapap.2024.141031
Christian E. Rusbjerg-Weberskov , Anne Kruse Hollensen , Christian Kroun Damgaard , Marianne Bengtson Løvendorf , Lone Skov , Jan J. Enghild , Nadia Sukusu Nielsen
{"title":"Mapping the Periostin splice isoforms in atopic dermatitis and an in vitro asthma model – A multi-platform analysis using mass spectrometry and RT-qPCR","authors":"Christian E. Rusbjerg-Weberskov ,&nbsp;Anne Kruse Hollensen ,&nbsp;Christian Kroun Damgaard ,&nbsp;Marianne Bengtson Løvendorf ,&nbsp;Lone Skov ,&nbsp;Jan J. Enghild ,&nbsp;Nadia Sukusu Nielsen","doi":"10.1016/j.bbapap.2024.141031","DOIUrl":"10.1016/j.bbapap.2024.141031","url":null,"abstract":"<div><p>Periostin is a matricellular protein known to be alternatively spliced to produce ten isoforms with a molecular weight of 78–91 kDa. Within the extracellular matrix, periostin attaches to cell surfaces to induce signaling <em>via</em> integrin-binding and actively participates in fibrillogenesis, orchestrating the arrangement of collagen in the extracellular environment. In atopic diseases such as atopic dermatitis (AD) and asthma, periostin is known to participate in driving the disease-causing type 2 inflammation. The periostin isoforms expressed in these diseases and the implication of the alternative splicing events are unknown. Here, we present two universal assays to map the expression of periostin isoforms at the mRNA (RT-qPCR) and protein (PRM-based mass spectrometry) levels. We use these assays to study the splicing profile of periostin in AD lesions as well as in <em>in vitro</em> models of AD and asthma. In these conditions, periostin displayed overexpression with isoforms 3 and 5 standing out as highly overexpressed. Notably, isoforms 9 and 10 exhibited a divergent pattern relative to the remaining isoforms. Isoforms 9 and 10 are often overlooked in periostin research and this paper presents the first evidence of their expression at the protein level. This underlines the necessity to include isoforms 9 and 10 in future research addressing periostin splice isoforms. The assays presented in this paper hold the potential to improve our insight into the splicing profile of periostin in tissues and diseases of interest. The application of these assays to AD lesions and <em>in vitro</em> models demonstrated their potential for identifying isoforms of particular significance, warranting a further in-depth investigation.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141031"},"PeriodicalIF":2.5,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1570963924000384/pdfft?md5=c12be11dda803cdf95887f728e83f8b0&pid=1-s2.0-S1570963924000384-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141557898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Robust assessment of sample preparation protocols for proteomics of cells and tissues 对细胞和组织蛋白质组学的样品制备方案进行可靠评估。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-06-27 DOI: 10.1016/j.bbapap.2024.141030
Francielle Aguiar Gomes, Douglas Ricardo Souza Junior, Mariana Pereira Massafera, Graziella Eliza Ronsein
{"title":"Robust assessment of sample preparation protocols for proteomics of cells and tissues","authors":"Francielle Aguiar Gomes,&nbsp;Douglas Ricardo Souza Junior,&nbsp;Mariana Pereira Massafera,&nbsp;Graziella Eliza Ronsein","doi":"10.1016/j.bbapap.2024.141030","DOIUrl":"10.1016/j.bbapap.2024.141030","url":null,"abstract":"<div><p>In proteomic studies, the reliability and reproducibility of results hinge on well-executed protein extraction and digestion protocols. Here, we systematically compared three established digestion methods for macrophages, namely filter-assisted sample preparation (FASP), in-solution, and in-gel digestion protocols. We also compared lyophilization and manual lysis for liver tissue protein extraction, each of them tested using either sodium deoxycholate (SDC)- or RIPA-based lysis buffer. For the macrophage cell line, FASP using passivated filter units outperformed the other tested methods regarding the number of identified peptides and proteins. However, a careful standardization has shown that all three methods can yield robust results across a wide range of starting material (even starting with 1 μg of proteins). Importantly, inter and intra-day coefficients of variance (CVs) were determined for all sample preparation protocols. Thus, the median inter-day CVs for in-solution, in-gel and FASP protocols were respectively 10, 8 and 9%, very similar to the median CVs obtained for the intra-day analysis (9, 8 and 8%, respectively). Moreover, FASP digestion presented 80% of proteins with a CV lower than 25%, followed closely by in-gel digestion (78%) and in-solution sample preparation (72%) protocols. For tissue proteomics, both manual lysis and lyophilization presented similar proteome coverage and reproducibility, but the efficiency of protein extraction depended on the lysis buffer used, with RIPA buffer showing better results. In conclusion, although each sample preparation method has its own particularity, they are all suited for successful proteomic experiments if a careful standardization of the sample preparation workflow is carried out.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141030"},"PeriodicalIF":2.5,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Exploring liquid-liquid phase separation in the organisation of Golgi matrix proteins 探索高尔基体基质蛋白组织中的液-液相分离。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-06-23 DOI: 10.1016/j.bbapap.2024.141029
Luis Felipe S. Mendes , Carolina G. Oliveira , Kevin F. Simões , Emanuel Kava , Antonio J. Costa-Filho
{"title":"Exploring liquid-liquid phase separation in the organisation of Golgi matrix proteins","authors":"Luis Felipe S. Mendes ,&nbsp;Carolina G. Oliveira ,&nbsp;Kevin F. Simões ,&nbsp;Emanuel Kava ,&nbsp;Antonio J. Costa-Filho","doi":"10.1016/j.bbapap.2024.141029","DOIUrl":"10.1016/j.bbapap.2024.141029","url":null,"abstract":"<div><p>The Golgi apparatus is a critical organelle in protein sorting and lipid metabolism. Characterized by its stacked, flattened cisternal structure, the Golgi exhibits distinct polarity with its <em>cis</em>- and <em>trans</em>-faces orchestrating various protein maturation and transport processes. At the heart of its structural integrity and organisation are the Golgi Matrix Proteins (GMPs), predominantly comprising Golgins and GRASPs. These proteins contribute to this organelle's unique stacked and polarized structure and ensure the precise localization of Golgi-resident enzymes, which is crucial for accurate protein processing. Despite over a century of research since its discovery, the Golgi architecture's intricate mechanisms still need to be fully understood. Here, we discuss that GMPs across different Eukaryotic lineages present a significant tendency to form biomolecular condensates. Moreover, we validated experimentally that members of the GRASP family also exhibit a strong tendency. Our findings offer a new perspective on the possible roles of protein disorder and condensation of GMPs in the Golgi organisation.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141029"},"PeriodicalIF":2.5,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures Plumbagin 可加速血清白蛋白淀粉样蛋白的聚集动力学,并通过诱导非原生β片结构产生纤维多态性。
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-06-05 DOI: 10.1016/j.bbapap.2024.141028
Chanchal Chauhan , Poonam Singh , Shivani A. Muthu , Suhel Parvez , Angamuthu Selvapandiyan , Basir Ahmad
{"title":"Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures","authors":"Chanchal Chauhan ,&nbsp;Poonam Singh ,&nbsp;Shivani A. Muthu ,&nbsp;Suhel Parvez ,&nbsp;Angamuthu Selvapandiyan ,&nbsp;Basir Ahmad","doi":"10.1016/j.bbapap.2024.141028","DOIUrl":"10.1016/j.bbapap.2024.141028","url":null,"abstract":"<div><p>The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant <em>Plumbago zeylanica</em>, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant K<sub>a</sub> ∼ 10<sup>−4</sup> M<sup>−1</sup>)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141028"},"PeriodicalIF":3.2,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141287674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Identification of the interfacial regions in misfolded transthyretin oligomers 识别折叠错误的转甲状腺素寡聚体中的界面区
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-05-23 DOI: 10.1016/j.bbapap.2024.141027
Anvesh K.R. Dasari , Matthew F. Coats , Abdullah B. Ali , Kwang Hun Lim
{"title":"Identification of the interfacial regions in misfolded transthyretin oligomers","authors":"Anvesh K.R. Dasari ,&nbsp;Matthew F. Coats ,&nbsp;Abdullah B. Ali ,&nbsp;Kwang Hun Lim","doi":"10.1016/j.bbapap.2024.141027","DOIUrl":"https://doi.org/10.1016/j.bbapap.2024.141027","url":null,"abstract":"<div><p>Misfolding and aggregation of transthyretin (TTR) is associated with numerous ATTR amyloidosis. TTR aggregates extracted from ATTR patients consist of not only full-length TTR, but also N-terminally truncated TTR fragments that can be produced by proteolytic cleavage, suggesting the presence of multiple misfolding pathways. Here, we report mechanistic studies of an early stage of TTR aggregation to probe the oligomerization process for the full-length as well as N-terminally truncated TTR. Our kinetic analyses using size exclusion chromatography revealed that amyloidogenic monomers dissociated from wild-type (WT) as well as pathogenic variants (V30M and L55P) form misfolded dimers, which self-assemble into oligomers, precursors of fibril formation. Dimeric interfaces in the full-length misfolded oligomers were investigated by examining the effect of single-point mutations on the two β-strands (F and H). The single-point mutations on the two β-strands (E92P on strand F and T119W on strand H) inhibited the dimerization of misfolded monomers, while the TTR variants can still form native dimers through the same F and H strands. These results suggest that the two strands are involved in intermolecular associations for both native and misfolded dimers, but detailed intermolecular interactions are different in the two forms of dimers. In the presence of a proteolytic enzyme, TTR aggregation is greatly accelerated. The two mutations on the two β-strands, however, inhibited TTR aggregation even in the presence of a proteolytic enzyme, trypsin. These results suggest that the two β-strands (F and H) play a critical role in aggregation of the N-terminally truncated TTR as well.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141027"},"PeriodicalIF":3.2,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141097790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Assessing the Martini 3 protein model: A review of its path and potential 评估马丁尼 3 号蛋白质模型:回顾其发展道路和潜力
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-04-25 DOI: 10.1016/j.bbapap.2024.141014
Luís Borges-Araújo , Gilberto P. Pereira , Mariana Valério , Paulo C.T. Souza
{"title":"Assessing the Martini 3 protein model: A review of its path and potential","authors":"Luís Borges-Araújo ,&nbsp;Gilberto P. Pereira ,&nbsp;Mariana Valério ,&nbsp;Paulo C.T. Souza","doi":"10.1016/j.bbapap.2024.141014","DOIUrl":"10.1016/j.bbapap.2024.141014","url":null,"abstract":"<div><p>Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force field is one of the most widely used CG models for bio-molecular simulations, partly because of the enormous success of its protein model. With the recent release of a new and improved version of the Martini force field – Martini 3 – a new iteration of its protein model was also made available. The Martini 3 protein force field is an evolution of its Martini 2 counterpart, aimed at improving many of the shortcomings that had been previously identified. In this mini-review, we first provide a general overview of the model and then focus on the successful advances made in the short time since its release, many of which would not have been possible before. Furthermore, we discuss reported limitations, potential directions for model improvement and comment on what the likely future development and application avenues are.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 4","pages":"Article 141014"},"PeriodicalIF":3.2,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140775132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Chemical proteomics approaches for protein post-translational modification studies 用于蛋白质翻译后修饰研究的化学蛋白质组学方法
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-04-18 DOI: 10.1016/j.bbapap.2024.141017
Nan Zhang , Jinghua Wu , Qingfei Zheng
{"title":"Chemical proteomics approaches for protein post-translational modification studies","authors":"Nan Zhang ,&nbsp;Jinghua Wu ,&nbsp;Qingfei Zheng","doi":"10.1016/j.bbapap.2024.141017","DOIUrl":"https://doi.org/10.1016/j.bbapap.2024.141017","url":null,"abstract":"<div><p>The diversity and dynamics of proteins play essential roles in maintaining the basic constructions and functions of cells. The abundance of functional proteins is regulated by the transcription and translation processes, while the alternative splicing enables the same gene to generate distinct protein isoforms of different lengths. Beyond the transcriptional and translational regulations, post-translational modifications (PTMs) are able to further expand the diversity and functional scope of proteins. PTMs have been shown to make significant changes in the surface charges, structures, activation states, and interactome of proteins. Due to the functional complexity, highly dynamic nature, and low presence percentage, the study of protein PTMs remains challenging. Here we summarize and discuss the major chemical biology tools and chemical proteomics approaches to enrich and investigate the protein PTM of interest.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 4","pages":"Article 141017"},"PeriodicalIF":3.2,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1570963924000244/pdfft?md5=074377f1e99350ee49a95930dfa4ebb8&pid=1-s2.0-S1570963924000244-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140631771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Conformational and dynamic properties of the KH1 domain of FMRP and its fragile X syndrome linked G266E variant FMRP的KH1结构域及其与脆性X综合征相关的G266E变体的构象和动态特性
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-04-17 DOI: 10.1016/j.bbapap.2024.141019
Flavia Catalano , Daniele Santorelli , Alessandra Astegno , Filippo Favretto , Marco D'Abramo , Alessandra Del Giudice , Maria Laura De Sciscio , Francesca Troilo , Giorgio Giardina , Adele Di Matteo , Carlo Travaglini-Allocatelli
{"title":"Conformational and dynamic properties of the KH1 domain of FMRP and its fragile X syndrome linked G266E variant","authors":"Flavia Catalano ,&nbsp;Daniele Santorelli ,&nbsp;Alessandra Astegno ,&nbsp;Filippo Favretto ,&nbsp;Marco D'Abramo ,&nbsp;Alessandra Del Giudice ,&nbsp;Maria Laura De Sciscio ,&nbsp;Francesca Troilo ,&nbsp;Giorgio Giardina ,&nbsp;Adele Di Matteo ,&nbsp;Carlo Travaglini-Allocatelli","doi":"10.1016/j.bbapap.2024.141019","DOIUrl":"https://doi.org/10.1016/j.bbapap.2024.141019","url":null,"abstract":"<div><p>The Fragile X messenger ribonucleoprotein (FMRP) is a multi-domain protein involved in interactions with various macromolecules, including proteins and coding/non-coding RNAs. The three KH domains (KH0, KH1 and KH2) within FMRP are recognized for their roles in mRNA binding. In the context of Fragile X syndrome (FXS), over-and-above CGG triplet repeats expansion, three specific point mutations have been identified, each affecting one of the three KH domains (<sup>R138Q</sup>KH0, <sup>G266E</sup>KH1, and <sup>I304N</sup>KH2) resulting in the expression of non-functional FMRP. This study aims to elucidate the molecular mechanism underlying the loss of function associated with the <sup>G266E</sup>KH1 pathological variant. We investigate the conformational and dynamic properties of the isolated KH1 domain and the two KH1 site-directed mutants <sup>G266E</sup>KH1 and <sup>G266A</sup>KH1. Employing a combined <em>in vitro</em> and <em>in silico</em> approach, we reveal that the <sup>G266E</sup>KH1 variant lacks the characteristic features of a folded domain. This observation provides an explanation for functional impairment observed in FMRP carrying the G266E mutation within the KH1 domain, as it renders the domain unable to fold properly. Molecular Dynamics simulations suggest a pivotal role for residue 266 in regulating the structural stability of the KH domains, primarily through stabilizing the α-helices of the domain. Overall, these findings enhance our comprehension of the molecular basis for the dysfunction associated with the <sup>G266E</sup>KH1 variant in FMRP.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 4","pages":"Article 141019"},"PeriodicalIF":3.2,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140645123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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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