Protein Science最新文献_第2页

BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase. BEAN和HABAS：DNA定向RNA聚合酶中的多态插入。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5194

Claudia Alvarez-Carreño, Angela T Huynh, Anton S Petrov, Christine Orengo, Loren Dean Williams

{"title":"BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.","authors":"Claudia Alvarez-Carreño, Angela T Huynh, Anton S Petrov, Christine Orengo, Loren Dean Williams","doi":"10.1002/pro.5194","DOIUrl":"10.1002/pro.5194","url":null,"abstract":"The β and β' subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the domain organizations of RNAP-β and RNAP-β' using sequence, experimentally determined structures and AlphaFold structure predictions. We observe that lineage-specific insertional domains in bacterial RNAP-β belong to a group that we call BEAN (broadly embedded annex). We observe that lineage-specific insertional domains in bacterial RNAP-β' belong to a group that we call HABAS (hammerhead/barrel-sandwich hybrid). The BEAN domain has a characteristic three-dimensional structure composed of two square bracket-like elements that are antiparallel relative to each other. The HABAS domain contains a four-stranded open β-sheet with a GD-box-like motif in one of the β-strands and the adjoining loop. The BEAN domain is inserted not only in the bacterial RNAP-β', but also in the archaeal version of universal ribosomal protein L10. The HABAS domain is inserted in several metabolic proteins. The phylogenetic distributions of bacterial lineage-specific insertional domains of β and β' subunits of RNAP follow the Tree of Life. The presence of insertional domains can help establish a relative timeline of events in the evolution of a protein because insertion is inferred to post-date the base domain. We discuss mechanisms that might account for the discovery of homologous insertional domains in non-equivalent locations in bacteria and archaea.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 11","pages":"e5194"},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Tethered heme domains in a triheme cytochrome allow for increased electron transport distances. 三heme 细胞色素中的系链血红素域可增加电子传输距离。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5200

Benjamin W Nash, Tomás M Fernandes, Joshua A J Burton, Leonor Morgado, Jessica H van Wonderen, Dimitri A Svistunenko, Marcus J Edwards, Carlos A Salgueiro, Julea N Butt, Thomas A Clarke

{"title":"Tethered heme domains in a triheme cytochrome allow for increased electron transport distances.","authors":"Benjamin W Nash, Tomás M Fernandes, Joshua A J Burton, Leonor Morgado, Jessica H van Wonderen, Dimitri A Svistunenko, Marcus J Edwards, Carlos A Salgueiro, Julea N Butt, Thomas A Clarke","doi":"10.1002/pro.5200","DOIUrl":"10.1002/pro.5200","url":null,"abstract":"Decades of research describe myriad redox enzymes that contain cofactors arranged in tightly packed chains facilitating rapid and controlled intra-protein electron transfer. Many such enzymes participate in extracellular electron transfer (EET), a process which allows microorganisms to conserve energy in anoxic environments by exploiting mineral oxides and other extracellular substrates as terminal electron acceptors. In this work, we describe the properties of the triheme cytochrome PgcA from Geobacter sulfurreducens. PgcA has been shown to play an important role in EET but is unusual in containing three CXXCH heme binding motifs that are separated by repeated (PT)x motifs, suggested to enhance binding to mineral surfaces. Using a combination of structural, electrochemical, and biophysical techniques, we experimentally demonstrate that PgcA adopts numerous conformations stretching as far as 180 Å between the ends of domains I and III, without a tightly packed cofactor chain. Furthermore, we demonstrate a distinct role for its domain III as a mineral reductase that is recharged by domains I and II. These findings show PgcA to be the first of a new class of electron transfer proteins, with redox centers separated by some nanometers but tethered together by flexible linkers, facilitating electron transfer through a tethered diffusion mechanism rather than a fixed, closely packed electron transfer chain.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 11","pages":"e5200"},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Expression and characterization of pantothenate energy-coupling factor transporters as an anti-infective drug target. 作为抗感染药物靶点的泛酸能量偶联因子转运体的表达和特征。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5195

Atanaz Shams, Spyridon Bousis, Eleonora Diamanti, Walid A M Elgaher, Lucie Zeimetz, Jörg Haupenthal, Dirk J Slotboom, Anna K H Hirsch

{"title":"Expression and characterization of pantothenate energy-coupling factor transporters as an anti-infective drug target.","authors":"Atanaz Shams, Spyridon Bousis, Eleonora Diamanti, Walid A M Elgaher, Lucie Zeimetz, Jörg Haupenthal, Dirk J Slotboom, Anna K H Hirsch","doi":"10.1002/pro.5195","DOIUrl":"10.1002/pro.5195","url":null,"abstract":"This study investigates the potential of energy-coupling factor (ECF) transporters as promising anti-infective targets to combat antimicrobial resistance (AMR). ECF transporters, a subclass of ATP-binding cassette (ABC) transporters, facilitate the uptake of B-vitamins across bacterial membranes by utilizing ATP as an energy source. Vitamins are essential cofactors for bacterial metabolism and growth, and they can either be synthesized de novo or absorbed from the environment. These transporters are considered promising drug targets, underscoring the need for further research to harness their medicinal potential and develop selective inhibitors that block vitamin uptake in bacteria. Herein, we focused on the ECF transporter for pantothenate (vitamin B5) from Streptococcus pneumoniae and the ECF transporter for folate (vitamin B9) from Lactobacillus delbrueckii as a reference protein. We also included the energizing module for pantothenate along with both full transporter complexes. Initially, we transformed and purified the transporters, followed by an assessment of their thermal stability under various buffer composition, pH, and salt concentrations. Additionally, we monitored the melting temperature over six days to confirm their stability for further assays. We then measured the binding affinities of six ECF inhibitors using surface plasmon resonance (SPR) and evaluated their inhibitory effects through in vitro assays, including bacterial growth assay, whole-cell uptake, and transport-activity assays. After determining cytotoxicity in two human cell lines, we established an in vivo infection model using Galleria mellonella larvae to further validate our findings.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 11","pages":"e5195"},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity. Aggrescan4D：根据 pH 值分析和设计蛋白质聚集倾向的综合工具。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-10-01 DOI: 10.1002/pro.5180

Mateusz Zalewski, Valentin Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik

{"title":"Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.","authors":"Mateusz Zalewski, Valentin Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik","doi":"10.1002/pro.5180","DOIUrl":"10.1002/pro.5180","url":null,"abstract":"Aggrescan4D (A4D) is an advanced computational tool designed for predicting protein aggregation, leveraging structural information and the influence of pH. Building upon its predecessor, Aggrescan3D (A3D), A4D has undergone numerous enhancements aimed at assisting the improvement of protein solubility. This manuscript reviews A4D's updated functionalities and explains the fundamental principles behind its pH-dependent calculations. Additionally, it presents an antibody case study to evaluate its performance in comparison with other structure-based predictors. Notably, A4D integrates advanced protein engineering protocols with pH-dependent calculations, enhancing its utility in advising solubility-enhancing mutations. A4D considers the impact of structural flexibility on aggregation propensities, and includes a large set of precalculated predictions. These capabilities should help to open new avenues for both understanding and managing protein aggregation. A4D is accessible through a dedicated web server at https://biocomp.chem.uw.edu.pl/a4d/.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 10","pages":"e5180"},"PeriodicalIF":4.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11425640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142352674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Evaluating the potential of non-immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies. 评估非免疫抑制性环孢素类似物靶向弓形虫嗜环蛋白的潜力：结构研究的启示。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-10-01 DOI: 10.1002/pro.5157

Filippo Favretto, Eva Jiménez-Faraco, Gianluca Catucci, Adele Di Matteo, Carlo Travaglini-Allocatelli, Sheila J Sadeghi, Paola Dominici, Juan A Hermoso, Alessandra Astegno

{"title":"Evaluating the potential of non-immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies.","authors":"Filippo Favretto, Eva Jiménez-Faraco, Gianluca Catucci, Adele Di Matteo, Carlo Travaglini-Allocatelli, Sheila J Sadeghi, Paola Dominici, Juan A Hermoso, Alessandra Astegno","doi":"10.1002/pro.5157","DOIUrl":"10.1002/pro.5157","url":null,"abstract":"Toxoplasmosis persists as a prevalent disease, facing challenges from parasite resistance and treatment side effects. Consequently, identifying new drugs by exploring novel protein targets is essential for effective intervention. Cyclosporin A (CsA) possesses antiparasitic activity against Toxoplasma gondii, with cyclophilins identified as possible targets. However, CsA immunosuppressive nature hinders its use as an antitoxoplasmosis agent. Here, we evaluate the potential of three CsA derivatives devoid of immunosuppressive activity, namely, NIM811, Alisporivir, and dihydrocyclosporin A to target a previously characterized cyclophilin from Toxoplasma gondii (TgCyp23). We determined the X-ray crystal structures of TgCyp23 in complex with the three analogs and elucidated their binding and inhibitory properties. The high resolution of the structures revealed the precise positioning of ligands within the TgCyp23 binding site and the details of protein-ligand interactions. A comparison with the established ternary structure involving calcineurin indicates that substitutions at position 4 in CsA derivatives prevent calcineurin binding. This finding provides a molecular explanation for why CsA analogs can target Toxoplasma cyclophilins without compromising the human immune response.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 10","pages":"e5157"},"PeriodicalIF":4.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch. 基于接触的局部能量挫折动力学分析确定了实现 RfaH 折叠转换的关键残基。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-10-01 DOI: 10.1002/pro.5182

Jorge González-Higueras, María Inés Freiberger, Pablo Galaz-Davison, R Gonzalo Parra, César A Ramírez-Sarmiento

{"title":"A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch.","authors":"Jorge González-Higueras, María Inés Freiberger, Pablo Galaz-Davison, R Gonzalo Parra, César A Ramírez-Sarmiento","doi":"10.1002/pro.5182","DOIUrl":"https://doi.org/10.1002/pro.5182","url":null,"abstract":"Fold-switching enables metamorphic proteins to reversibly interconvert between two highly dissimilar native states to regulate their protein functions. While about 100 proteins have been identified to undergo fold-switching, unveiling the key residues behind this mechanism for each protein remains challenging. Reasoning that fold-switching in proteins is driven by dynamic changes in local energetic frustration, we combined fold-switching simulations generated using simplified structure-based models with frustration analysis to identify key residues involved in this process based on the change in the density of minimally frustrated contacts during refolding. Using this approach to analyze the fold-switch of the bacterial transcription factor RfaH, we identified 20 residues that significantly change their frustration during its fold-switch, some of which have been experimentally and computationally reported in previous works. Our approach, which we developed as an additional module for the FrustratometeR package, highlights the role of local frustration dynamics in protein fold-switching and offers a robust tool to enhance our understanding of other proteins with significant conformational shifts.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 10","pages":"e5182"},"PeriodicalIF":4.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11425668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142352673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

An in vitro set-up to study Pdr5-mediated substrate translocation. 研究 Pdr5 介导的底物转运的体外装置。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-10-01 DOI: 10.1002/pro.5181

Stefanie L Gala Marti, Manuel Wagner, Lea-Marie Nentwig, Sander H J Smits, Lutz Schmitt

{"title":"An in vitro set-up to study Pdr5-mediated substrate translocation.","authors":"Stefanie L Gala Marti, Manuel Wagner, Lea-Marie Nentwig, Sander H J Smits, Lutz Schmitt","doi":"10.1002/pro.5181","DOIUrl":"10.1002/pro.5181","url":null,"abstract":"Pdr5 is the most abundant ABC transporter in Saccharomyces cerevisiae and plays a major role in the pleiotropic drug resistance (PDR) network, which actively prevents cell entry of a large number of structurally unrelated compounds. Due to a high level of asymmetry in one of its nucleotide binding sites (NBS), Pdr5 serves as a perfect model system for asymmetric ABC transporter such as its medical relevant homologue Cdr1 from Candida albicans. In the past 30 years, this ABC transporter was intensively studied in vivo and in plasma membrane vesicles. Nevertheless, these studies were limited since it was not possible to isolate and reconstitute Pdr5 in a synthetic membrane system while maintaining its activity. Here, the functional reconstitution of Pdr5 in a native-like environment in an almost unidirectional inside-out orientation is described. We demonstrate that reconstituted Pdr5 is capable of translocating short-chain fluorescent NBD lipids from the outer to the inner leaflet of the proteoliposomes. Moreover, this transporter revealed its ability to utilize other nucleotides to accomplish transport of substrates in a reconstituted system. Besides, we were also able to estimate the NTPase activity of reconstituted Pdr5 and determine the kinetic parameters for ATP, GTP, CTP, and UTP.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"33 10","pages":"e5181"},"PeriodicalIF":4.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane‐bound cytochrome P450 2B4 多分辨率分子动力学模拟揭示了膜结合细胞色素 P450 2B4 的构象变化和功能相互作用之间的相互作用

IF 8 3区生物学

Protein Science Pub Date : 2024-09-18 DOI: 10.1002/pro.5165

Sungho Bosco Han, Jonathan Teuffel, Goutam Mukherjee, Rebecca C. Wade

{"title":"Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane‐bound cytochrome P450 2B4","authors":"Sungho Bosco Han, Jonathan Teuffel, Goutam Mukherjee, Rebecca C. Wade","doi":"10.1002/pro.5165","DOIUrl":"https://doi.org/10.1002/pro.5165","url":null,"abstract":"Cytochrome P450 2B4 (CYP 2B4) is one of the best‐characterized CYPs and serves as a key model system for understanding the mechanisms of microsomal class II CYPs, which metabolize most known drugs. The highly flexible nature of CYP 2B4 is apparent from crystal structures that show the active site with either a wide open or a closed heme binding cavity. Here, we investigated the conformational ensemble of the full‐length CYP 2B4 in a phospholipid bilayer, using multiresolution molecular dynamics (MD) simulations. Coarse‐grained MD simulations revealed two predominant orientations of CYP 2B4's globular domain with respect to the bilayer. Their refinement by atomistic resolution MD showed adaptation of the enzyme's interaction with the lipid bilayer, leading to open configurations that facilitate ligand access to the heme binding cavity. CAVER analysis of enzyme tunnels, AquaDuct analysis of water routes, and Random Acceleration Molecular Dynamics simulations of ligand dissociation support the conformation‐dependent passage of molecules between the active site and the protein surroundings. Furthermore, simulation of the re‐entry of the inhibitor bifonazole into the open conformation of CYP 2B4 resulted in binding at a transient hydrophobic pocket within the active site cavity that may play a role in substrate binding or allosteric regulation. Together, these results show how the open conformation of CYP 2B4 facilitates the binding of substrates from and release of products to the membrane, whereas the closed conformation prolongs the residence time of substrates or inhibitors and selectively allows the passage of smaller reactants via the solvent and water channels.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"8 1","pages":""},"PeriodicalIF":8.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Molecular mechanisms for DNA methylation defects induced by ICF syndrome‐linked mutations in DNMT3B 与ICF综合征相关的DNMT3B突变诱发DNA甲基化缺陷的分子机制

IF 8 3区生物学

Protein Science Pub Date : 2024-09-18 DOI: 10.1002/pro.5131

Chao‐Cheng Cho, Cheng‐Yin Fei, Bo‐Chen Jiang, Wei‐Zen Yang, Hanna S. Yuan

{"title":"Molecular mechanisms for DNA methylation defects induced by ICF syndrome‐linked mutations in DNMT3B","authors":"Chao‐Cheng Cho, Cheng‐Yin Fei, Bo‐Chen Jiang, Wei‐Zen Yang, Hanna S. Yuan","doi":"10.1002/pro.5131","DOIUrl":"https://doi.org/10.1002/pro.5131","url":null,"abstract":"DNA methyltransferase 3B (DNMT3B) plays a crucial role in DNA methylation during mammalian development. Mutations in DNMT3B are associated with human genetic diseases, particularly immunodeficiency, centromere instability, facial anomalies (ICF) syndrome. Although ICF syndrome‐related missense mutations in the DNMT3B have been identified, their precise impact on protein structure and function remains inadequately explored. Here, we delve into the impact of four ICF syndrome‐linked mutations situated in the DNMT3B dimeric interface (H814R, D817G, V818M, and R823G), revealing that each of these mutations compromises DNA‐binding and methyltransferase activities to varying degrees. We further show that H814R, D817G, and V818M mutations severely disrupt the proper assembly of DNMT3B homodimer, whereas R823G does not. We also determined the first crystal structure of the methyltransferase domain of DNMT3B‐DNMT3L tetrameric complex hosting the R823G mutation showing that the R823G mutant displays diminished hydrogen bonding interactions around T775, K777, G823, and Q827 in the protein‐DNA interface, resulting in reduced DNA‐binding affinity and a shift in sequence preference of +1 to +3 flanking positions. Altogether, our study uncovers a wide array of fundamental defects triggered by DNMT3B mutations, including the disassembly of DNMT3B dimers, reduced DNA‐binding capacity, and alterations in flanking sequence preferences, leading to aberrant DNA hypomethylation and ICF syndrome.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"10 1","pages":"e5131"},"PeriodicalIF":8.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Inhibitor binding and disruption of coupled motions in MmpL3 protein: Unraveling the mechanism of trehalose monomycolate transport MmpL3 蛋白中的抑制剂结合和耦合运动破坏：揭示三卤糖单霉素转运机制

IF 8 3区生物学

Protein Science Pub Date : 2024-09-18 DOI: 10.1002/pro.5166

Likun Zhao, Bo Liu, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Qianqian Zhang

{"title":"Inhibitor binding and disruption of coupled motions in MmpL3 protein: Unraveling the mechanism of trehalose monomycolate transport","authors":"Likun Zhao, Bo Liu, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Qianqian Zhang","doi":"10.1002/pro.5166","DOIUrl":"https://doi.org/10.1002/pro.5166","url":null,"abstract":"Mycobacterial membrane protein Large 3 (MmpL3) of Mycobacterium tuberculosis (Mtb) is crucial for the translocation of trehalose monomycolate (TMM) across the inner bacterial cell membrane, making it a promising target for anti‐tuberculosis (TB) drug development. While several structural, microbiological, and in vitro studies have provided significant insights, the precise mechanisms underlying TMM transport by MmpL3 and its inhibition remain incompletely understood at the atomic level. In this study, molecular dynamic (MD) simulations for the apo form and seven inhibitor‐bound forms of Mtb MmpL3 were carried out to obtain a thorough comprehension of the protein's dynamics and function. MD simulations revealed that the seven inhibitors in this work stably bind to the central channel of the transmembrane domain and primarily forming hydrogen bonds with ASP251, ASP640, or both residues. Through dynamical cross‐correlation matrix and principal component analysis analyses, several types of coupled motions between different domains were observed in the apo state, and distinct conformational states were identified using Markov state model analysis. These coupled motions and varied conformational states likely contribute to the transport of TMM. However, simulations of inhibitor‐bound MmpL3 showed an enlargement of the proton channel, potentially disrupting coupled motions. This indicates that inhibitors may impair MmpL3's transport function by directly blocking the proton channel, thereby hindering coordinated domain movements and indirectly affecting TMM translocation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"8 1","pages":"e5166"},"PeriodicalIF":8.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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