Current Research in Structural Biology最新文献

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FOXO transcription factors differ in their dynamics and intra/intermolecular interactions FOXO转录因子在动力学和分子内/分子间相互作用方面有所不同
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.04.001
Emil Spreitzer , T. Reid Alderson , Benjamin Bourgeois , Loretta Eggenreich , Hermann Habacher , Greta Bramerdorfer , Iva Pritišanac , Pedro A. Sánchez-Murcia , Tobias Madl
{"title":"FOXO transcription factors differ in their dynamics and intra/intermolecular interactions","authors":"Emil Spreitzer ,&nbsp;T. Reid Alderson ,&nbsp;Benjamin Bourgeois ,&nbsp;Loretta Eggenreich ,&nbsp;Hermann Habacher ,&nbsp;Greta Bramerdorfer ,&nbsp;Iva Pritišanac ,&nbsp;Pedro A. Sánchez-Murcia ,&nbsp;Tobias Madl","doi":"10.1016/j.crstbi.2022.04.001","DOIUrl":"10.1016/j.crstbi.2022.04.001","url":null,"abstract":"<div><p>Transcription factors play key roles in orchestrating a plethora of cellular mechanisms and controlling cellular homeostasis. Transcription factors share distinct DNA binding domains, which allows to group them into protein families. Among them, the Forkhead box O (FOXO) family contains transcription factors crucial for cellular homeostasis, longevity and response to stress. The dysregulation of FOXO signaling is linked to drug resistance in cancer therapy or cellular senescence, however, selective drugs targeting FOXOs are limited, thus knowledge about structure and dynamics of FOXO proteins is essential. Here, we provide an extensive study of structure and dynamics of all FOXO family members. We identify residues accounting for different dynamic and structural features. Furthermore, we show that the auto-inhibition of FOXO proteins by their C-terminal trans-activation domain is conserved throughout the family and that these interactions are not only possible intra-, but also inter-molecularly. This indicates a model in which FOXO transcription factors would modulate their activities by interacting mutually.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 118-133"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000095/pdfft?md5=2c2ec2f297b19f624c1eda55d104f5c9&pid=1-s2.0-S2665928X22000095-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47295491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids 巯基喹啉甘油结合蛋白SmoF结合并调节植物的巯基脂肪酸
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.03.001
Alexander J.D. Snow , Mahima Sharma , James P. Lingford , Yunyang Zhang , Janice W.-Y. Mui , Ruwan Epa , Ethan D. Goddard-Borger , Spencer J. Williams , Gideon J. Davies
{"title":"The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids","authors":"Alexander J.D. Snow ,&nbsp;Mahima Sharma ,&nbsp;James P. Lingford ,&nbsp;Yunyang Zhang ,&nbsp;Janice W.-Y. Mui ,&nbsp;Ruwan Epa ,&nbsp;Ethan D. Goddard-Borger ,&nbsp;Spencer J. Williams ,&nbsp;Gideon J. Davies","doi":"10.1016/j.crstbi.2022.03.001","DOIUrl":"10.1016/j.crstbi.2022.03.001","url":null,"abstract":"<div><p>Sulfoquinovose (SQ) is the anionic headgroup of the ubiquitous plant sulfolipid, sulfoquinovosyl diacylglycerol (SQDG). SQDG can undergo delipidation to give sulfoquinovosyl glycerol (SQGro) and further glycoside cleavage to give SQ, which can be metabolized through microbial sulfoglycolytic pathways. Exogenous SQDG metabolites are imported into bacteria through membrane spanning transporter proteins. The recently discovered sulfoglycolytic sulfoquinovose monooxygenase (sulfo-SMO) pathway in <em>Agrobacterium tumefaciens</em> features a periplasmic sulfoquinovosyl glycerol binding protein, SmoF, and an ATP-binding cassette (ABC) transporter. Here, we use X-ray crystallography, differential scanning fluorimetry and isothermal titration calorimetry to study SQ glycoside recognition by SmoF. This work reveals that in addition to SQGro, SmoF can also bind SQ, a simple methyl glycoside and even a short-chain SQDG analogue. Molecular recognition of these substrates is achieved through conserved interactions with the SQ-headgroup together with more plastic interactions with the aglycones. This suggests that the solute binding protein of <em>A. tumefaciens,</em> and related SQ-binding proteins from other sulfoglycolytic pathways, can provide their host organisms direct access to most of the SQ metabolites known to be produced by phototrophs.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 51-58"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000058/pdfft?md5=92ea91c60cc0a0fabd078c308ccda613&pid=1-s2.0-S2665928X22000058-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44773542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation 腺病毒早期1A区(E1A)的转激活结构域:研究折叠动力学和聚集
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.01.001
Nitin Sharma , Kundlik Gadhave , Prateek Kumar , Rajanish Giri
{"title":"Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation","authors":"Nitin Sharma ,&nbsp;Kundlik Gadhave ,&nbsp;Prateek Kumar ,&nbsp;Rajanish Giri","doi":"10.1016/j.crstbi.2022.01.001","DOIUrl":"10.1016/j.crstbi.2022.01.001","url":null,"abstract":"<div><p>Transactivation domain of Adenovirus Early region 1A (E1A) oncoprotein is an intrinsically disordered molecular hub protein. It is involved in binding to different domains of human cell transcriptional co-activators such as retinoblastoma (pRb), CREB-binding protein (CBP), and its paralogue p300. The conserved region 1 (TAD) of E1A is known to undergo structural transitions and folds upon interaction with transcriptional adaptor zinc finger 2 (TAZ2). Previous reports on Taz2-E1A studies have suggested the formation of helical conformations of E1A-TAD. However, the folding behavior of the TAD region in isolation has not been studied in detail. Here, we have elucidated the folding behavior of E1A peptide at varied temperatures and solution conditions. Further, we have studied the effects of macromolecular crowding on E1A-TAD peptide. Additionally, we have also predicted the molecular recognition features of E1A using MoRF predictors. The predicted MoRFs are consistent with its structural transitions observed during TAZ2 interactions for transcriptional regulation in literature. Also, as a general rule of MoRFs, E1A undergoes helical transitions in alcohol and osmolyte solution. Finally, we studied the aggregation behavior of E1A, where we observed that the E1A could form amyloid-like aggregates that are cytotoxic to mammalian cells.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 29-40"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/da/77/main.PMC8801969.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39908538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase HGDiscovery:一个在线工具,提供均质1,2-二氧合酶新变异的功能和表型信息
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.08.001
Malancha Karmakar , Vittoria Cicaloni , Carlos H.M. Rodrigues , Ottavia Spiga , Annalisa Santucci , David B. Ascher
{"title":"HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase","authors":"Malancha Karmakar ,&nbsp;Vittoria Cicaloni ,&nbsp;Carlos H.M. Rodrigues ,&nbsp;Ottavia Spiga ,&nbsp;Annalisa Santucci ,&nbsp;David B. Ascher","doi":"10.1016/j.crstbi.2022.08.001","DOIUrl":"10.1016/j.crstbi.2022.08.001","url":null,"abstract":"<div><p>Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack functional levels of an enzyme required to breakdown HGA. Mutations in the homogentisate 1,2-dioxygenase (HGD) gene cause AKU and they are responsible for deficient levels of functional HGD, which, in turn, leads to excess levels of HGA. Although HGA is rapidly cleared from the body by the kidneys, in the long term it starts accumulating in various tissues, especially cartilage. Over time (rarely before adulthood), it eventually changes the color of affected tissue to slate blue or black. Here we report a comprehensive mutation analysis of 111 pathogenic and 190 non-pathogenic HGD missense mutations using protein structural information. Using our comprehensive suite of graph-based signature methods, mCSM complemented with sequence-based tools, we studied the functional and molecular consequences of each mutation on protein stability, interaction and evolutionary conservation. The scores generated from the structure and sequence-based tools were used to train a supervised machine learning algorithm with 89% accuracy. The empirical classifier was used to generate the variant phenotype for novel HGD missense mutations. All this information is deployed as a user friendly freely available web server called HGDiscovery (<span>https://biosig.lab.uq.edu.au/hgdiscovery/</span><svg><path></path></svg>).</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 271-277"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9471331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40367389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022) SARS-CoV-2刺突蛋白在融合过程中的整合结构研究(2022)
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.06.004
Jacob C. Miner , Paul W. Fenimore , William M. Fischer , Benjamin H. McMahon , Karissa Y. Sanbonmatsu , Chang-Shung Tung
{"title":"Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022)","authors":"Jacob C. Miner ,&nbsp;Paul W. Fenimore ,&nbsp;William M. Fischer ,&nbsp;Benjamin H. McMahon ,&nbsp;Karissa Y. Sanbonmatsu ,&nbsp;Chang-Shung Tung","doi":"10.1016/j.crstbi.2022.06.004","DOIUrl":"10.1016/j.crstbi.2022.06.004","url":null,"abstract":"<div><p>SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and catastrophic, worldwide health and economic impacts. The spike protein on the viral surface is responsible for viral entry into the host cell<del>.</del> The binding of spike protein to the host cell receptor ACE2 is the first step leading to fusion of the host and viral membranes. Despite the vast amount of structure data that has been generated for the spike protein of SARS-CoV-2, many of the detailed structures of the spike protein in different stages of the fusion pathway are unknown, leaving a wealth of potential drug-target space unexplored. The atomic-scale structure of the complete S2 segment, as well as the complete fusion intermediate are also unknown and represent major gaps in our knowledge of the infectious pathway of SAR-CoV-2. The conformational changes of the spike protein during this process are similarly not well understood. Here we present structures of the spike protein at different stages of the fusion process. With the transitions being a necessary step before the receptor binding, we propose sites along the transition pathways as potential targets for drug development.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 220-230"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/50/main.PMC9221923.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40407521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fragment-based exploration of the 14-3-3/Amot-p130 interface 基于片段的14-3-3/Amot-p130接口探索
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2021.12.003
Federica Centorrino, Blaž Andlovic, Peter Cossar, Luc Brunsveld, Christian Ottmann
{"title":"Fragment-based exploration of the 14-3-3/Amot-p130 interface","authors":"Federica Centorrino,&nbsp;Blaž Andlovic,&nbsp;Peter Cossar,&nbsp;Luc Brunsveld,&nbsp;Christian Ottmann","doi":"10.1016/j.crstbi.2021.12.003","DOIUrl":"10.1016/j.crstbi.2021.12.003","url":null,"abstract":"<div><p>The modulation of protein-protein interactions (PPIs) has developed into a well-established field of drug discovery. Despite the advances achieved in the field, many PPIs are still deemed as ‘<em>undruggable’</em> targets and the design of PPIs stabilizers remains a significant challenge. The application of fragment-based methods for the identification of drug leads and to evaluate the ‘<em>tractability’</em> of the desired protein target has seen a remarkable development in recent years. In this study, we explore the molecular characteristics of the 14-3-3/Amot-p130 PPI and the conceptual possibility of targeting this interface using X-ray crystallography fragment-based screening. We report the first structural elucidation of the 14-3-3 binding motif of Amot-p130 and the characterization of the binding mode and affinities involved. We made use of fragments to probe the ‘<em>ligandability’</em> of the 14-3-3/Amot-p130 composite binding pocket. Here we disclose initial hits with promising stabilizing activity and an early-stage selectivity toward the Amot-p130 motifs over other representatives 14-3-3 partners. Our findings highlight the potential of using fragments to characterize and explore proteins' surfaces and might provide a starting point toward the development of small molecules capable of acting as <em>molecular glues</em>.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 21-28"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5e/bc/main.PMC8743172.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39826584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Nonexponential kinetics captured in sequential unfolding of polyproteins over a range of loads 在负载范围内多蛋白的顺序展开中捕获的非指数动力学
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.04.003
Einat Chetrit , Sabita Sharma , Uri Maayan , Maya Georgia Pelah , Ziv Klausner , Ionel Popa , Ronen Berkovich
{"title":"Nonexponential kinetics captured in sequential unfolding of polyproteins over a range of loads","authors":"Einat Chetrit ,&nbsp;Sabita Sharma ,&nbsp;Uri Maayan ,&nbsp;Maya Georgia Pelah ,&nbsp;Ziv Klausner ,&nbsp;Ionel Popa ,&nbsp;Ronen Berkovich","doi":"10.1016/j.crstbi.2022.04.003","DOIUrl":"10.1016/j.crstbi.2022.04.003","url":null,"abstract":"<div><p>While performing under mechanical loads <em>in vivo</em>, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L<sub>8</sub> under varying loads, specifically high (150, 100 ​pN) and moderate-low (45, 30, 20 ​pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 106-117"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000113/pdfft?md5=34c74cdfdd79fbd9202a5be67013bd05&pid=1-s2.0-S2665928X22000113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45431399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Insights into the structural properties of SARS-CoV-2 main protease SARS-CoV-2主蛋白酶结构特性研究
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.11.001
Ibrahim Yagiz Akbayrak , Sule Irem Caglayan , Lukasz Kurgan , Vladimir N. Uversky , Orkid Coskuner-Weber
{"title":"Insights into the structural properties of SARS-CoV-2 main protease","authors":"Ibrahim Yagiz Akbayrak ,&nbsp;Sule Irem Caglayan ,&nbsp;Lukasz Kurgan ,&nbsp;Vladimir N. Uversky ,&nbsp;Orkid Coskuner-Weber","doi":"10.1016/j.crstbi.2022.11.001","DOIUrl":"10.1016/j.crstbi.2022.11.001","url":null,"abstract":"<div><p>SARS-CoV-2 is the infectious agent responsible for the coronavirus disease since 2019, which is the viral pneumonia pandemic worldwide. The structural knowledge on SARS-CoV-2 is rather limited. These limitations are also applicable to one of the most attractive drug targets of SARS-CoV-2 proteins – namely, main protease M<sup>pro</sup>, also known as 3C-like protease (3CL<sup>pro</sup>). This protein is crucial for the processing of the viral polyproteins and plays crucial roles in interfering viral replication and transcription. In fact, although the crystal structure of this protein with an inhibitor was solved, M<sup>pro</sup> conformational dynamics in aqueous solution is usually studied by molecular dynamics simulations without special sampling techniques. We conducted replica exchange molecular dynamics simulations on M<sup>pro</sup> in water and report the dynamic structures of M<sup>pro</sup> in an aqueous environment including root mean square fluctuations, secondary structure properties, radius of gyration, and end-to-end distances, chemical shift values, intrinsic disorder characteristics of M<sup>pro</sup> and its active sites with a set of computational tools. The active sites we found coincide with the currently known sites and include a new interface for interaction with a protein partner.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 349-355"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/56/cc/main.PMC9700396.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35257030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein conformation and biomolecular condensates 蛋白质构象和生物分子凝聚物
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.09.004
Diego S. Vazquez, Pamela L. Toledo, Alejo R. Gianotti, Mario R. Ermácora
{"title":"Protein conformation and biomolecular condensates","authors":"Diego S. Vazquez,&nbsp;Pamela L. Toledo,&nbsp;Alejo R. Gianotti,&nbsp;Mario R. Ermácora","doi":"10.1016/j.crstbi.2022.09.004","DOIUrl":"10.1016/j.crstbi.2022.09.004","url":null,"abstract":"<div><p>Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 285-307"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1b/ed/main.PMC9508354.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40377924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase 抗结核药物贝达喹啉和TBAJ-876与分枝杆菌F-ATP合酶的结合特性
IF 2.8
Current Research in Structural Biology Pub Date : 2022-01-01 DOI: 10.1016/j.crstbi.2022.09.001
Alexander Krah , Gerhard Grüber , Peter J. Bond
{"title":"Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase","authors":"Alexander Krah ,&nbsp;Gerhard Grüber ,&nbsp;Peter J. Bond","doi":"10.1016/j.crstbi.2022.09.001","DOIUrl":"10.1016/j.crstbi.2022.09.001","url":null,"abstract":"<div><p>Tuberculosis (TB), the deadly disease caused by <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>), kills more people worldwide than any other bacterial infectious disease. There has been a recent resurgence of TB drug discovery activities, resulting in the identification of a number of novel enzyme inhibitors. Many of these inhibitors target the electron transport chain complexes and the F<sub>1</sub>F<sub>O</sub>-ATP synthase; these enzymes represent new target spaces for drug discovery, since the generation of ATP is essential for the bacterial pathogen's physiology, persistence, and pathogenicity. The anti-TB drug bedaquiline (BDQ) targets the <em>Mtb</em> F-ATP synthase and is used as salvage therapy against this disease. Medicinal chemistry efforts to improve the physio-chemical properties of BDQ resulted in the discovery of 3,5-dialkoxypyridine (DARQ) analogs to which TBAJ-876 belongs. TBAJ-876, a clinical development candidate, shows attractive <em>in vitro</em> and <em>in vivo</em> antitubercular activity. Both BDQ and TBAJ-876 inhibit the mycobacterial F<sub>1</sub>F<sub>O</sub>-ATP synthase by stopping rotation of the <em>c</em>-ring turbine within the F<sub>O</sub> domain, thereby preventing proton translocation and ATP synthesis to occur. While structural data for the BDQ bound state are available, no structural information about TBAJ-876 binding have been described. In this study, we show how TBAJ-876 binds to the F<sub>O</sub> domain of the <em>M. smegmatis</em> F<sub>1</sub>F<sub>O</sub>-ATP synthase. We further calculate the binding free energy of both drugs bound to their target and predict an increased affinity of TBAJ-876 for the F<sub>O</sub> domain. This approach will be useful in future efforts to design new and highly potent DARQ analogs targeting F-ATP synthases of <em>Mtb</em>, nontuberculosis mycobacteria (NTM) as well as the <em>M. leprosis</em> complex.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 278-284"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9516385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40388872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
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