Protein Science最新文献

Preferential binding of ADP-bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2. ADP 结合的线粒体 HSP70 与核苷酸交换因子 GRPEL1 的结合优于 GRPEL2。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5190

Pooja Manjunath, Gorazd Stojkovič, Liliya Euro, Svetlana Konovalova, Sjoerd Wanrooij, Kristian Koski, Henna Tyynismaa

{"title":"Preferential binding of ADP-bound mitochondrial HSP70 to the nucleotide exchange factor GRPEL1 over GRPEL2.","authors":"Pooja Manjunath, Gorazd Stojkovič, Liliya Euro, Svetlana Konovalova, Sjoerd Wanrooij, Kristian Koski, Henna Tyynismaa","doi":"10.1002/pro.5190","DOIUrl":"10.1002/pro.5190","url":null,"abstract":"Human nucleotide exchange factors GRPEL1 and GRPEL2 play pivotal roles in the ADP-ATP exchange within the protein folding cycle of mitochondrial HSP70 (mtHSP70), a crucial chaperone facilitating protein import into the mitochondrial matrix. Studies in human cells and mice have indicated that while GRPEL1 serves as an essential co-chaperone for mtHSP70, GRPEL2 has a role regulated by stress. However, the precise structural and biochemical mechanisms underlying the distinct functions of the GRPEL proteins have remained elusive. In our study, we present evidence revealing that ADP-bound mtHSP70 exhibits remarkably higher affinity for GRPEL1 compared to GRPEL2, with the latter experiencing a notable decrease in affinity upon ADP binding. Additionally, Pi assay showed that GRPEL1, but not GRPEL2, enhanced the ATPase activity of mtHSP70. Utilizing Alphafold modeling, we propose that the interaction between GRPEL1 and mtHSP70 can induce the opening of the nucleotide binding cleft of the chaperone, thereby facilitating the release of ADP, whereas GRPEL2 lacks this capability. Additionally, our findings suggest that the redox-regulated Cys87 residue in GRPEL2 does not play a role in dimerization but rather reduces its affinity for mtHSP70. Our findings on the structural and functional disparities between GRPEL1 and GRPEL2 may have implications for mitochondrial protein folding and import processes under varying cellular conditions.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506691","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

Unraveling the molecular determinants of a rare human mitochondrial disorder caused by the P144L mutation of FDX2. 揭示由 FDX2 的 P144L 突变引起的罕见人类线粒体疾病的分子决定因素。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5197

Deborah Grifagni, Davide Doni, Bianca Susini, Bruno M Fonseca, Ricardo O Louro, Paola Costantini, Simone Ciofi-Baffoni

{"title":"Unraveling the molecular determinants of a rare human mitochondrial disorder caused by the P144L mutation of FDX2.","authors":"Deborah Grifagni, Davide Doni, Bianca Susini, Bruno M Fonseca, Ricardo O Louro, Paola Costantini, Simone Ciofi-Baffoni","doi":"10.1002/pro.5197","DOIUrl":"10.1002/pro.5197","url":null,"abstract":"Episodic mitochondrial myopathy with or without optic atrophy and reversible leukoencephalopathy (MEOAL) is a rare, orphan autosomal recessive disorder caused by mutations in ferredoxin-2 (FDX2), which is a [2Fe-2S] cluster-binding protein participating in the formation of iron-sulfur clusters in mitochondria. In this biosynthetic pathway, FDX2 works as electron donor to promote the assembly of both [2Fe-2S] and [4Fe-4S] clusters. A recently identified missense mutation of MEOAL is the homozygous mutation c.431C>T (p.P144L) described in six patients from two unrelated families. This mutation alters a highly conserved proline residue located in a loop of FDX2 that is distant from the [2Fe-2S] cluster. How this Pro to Leu substitution damages iron-sulfur cluster biosynthesis is unknown. In this work, we have first compared the structural, dynamic, cluster binding and redox properties of WT and P144L [2Fe-2S] FDX2 to have clues on how the pathogenic P144L mutation can perturb the FDX2 function. Then, we have investigated the interaction of both WT and P144L [2Fe-2S] FDX2 with its physiological electron donor, ferredoxin reductase FDXR, comparing their electron transfer efficiency and protein-protein recognition patterns. Overall, the data indicate that the pathogenic P144L mutation negatively affects the FDXR-dependent electron transfer pathway from NADPH to FDX2, thereby reducing the capacity of FDX2 in assembling both [2Fe-2S] and [4Fe-4S] clusters. Our study also provided solid molecular evidences on the functional role of the C-terminal tail of FDX2 in the electron transfer between FDX2 and FDXR.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522795","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

Self-association and multimer formation in AtLEA4-5, a desiccation-induced intrinsically disordered protein from plants. AtLEA4-5（一种来自植物的干燥诱导型本征无序蛋白）的自结合和多聚体形成。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5192

Paulette Sofía Romero-Pérez, Laura V Martínez-Castro, Alejandro Linares, Inti Arroyo-Mosso, Nuria Sánchez-Puig, Cesar L Cuevas-Velazquez, Shahar Sukenik, Adán Guerrero, Alejandra A Covarrubias

{"title":"Self-association and multimer formation in AtLEA4-5, a desiccation-induced intrinsically disordered protein from plants.","authors":"Paulette Sofía Romero-Pérez, Laura V Martínez-Castro, Alejandro Linares, Inti Arroyo-Mosso, Nuria Sánchez-Puig, Cesar L Cuevas-Velazquez, Shahar Sukenik, Adán Guerrero, Alejandra A Covarrubias","doi":"10.1002/pro.5192","DOIUrl":"10.1002/pro.5192","url":null,"abstract":"During seed maturation, plants may experience severe desiccation, leading to the accumulation of late embryogenesis abundant (LEA) proteins. These intrinsically disordered proteins also accumulate in plant tissues under water deficit. Functional roles of LEA proteins have been proposed based on in vitro studies, where monomers are considered as the functional units. However, the potential formation of homo-oligomers has been little explored. In this work, we investigated the potential self-association of Arabidopsis thaliana group 4 LEA proteins (AtLEA4) using in vitro and in vivo approaches. LEA4 proteins represent a compelling case of study due to their high conservation throughout the plant kingdom. This protein family is characterized by a conserved N-terminal region, with a high alpha-helix propensity and invitro protective activity, as compared to the highly disordered and low-conserved C-terminal region. Our findings revealed that full-length AtLEA4 proteins oligomerize and that both terminal regions are sufficient for self-association in vitro. However, the ability of both amino and carboxy regions of AtLEA4-5 to self-associate invivo is significantly lower than that of the entire protein. Using high-resolution and quantitative fluorescence microscopy, we were able to disclose the unreported ability of LEA proteins to form high-order oligomers in planta. Additionally, we found that high-order complexes require the simultaneous engagement of both terminal regions, indicating that the entire protein is needed to attain such structural organization. This research provides valuable insights into the self-association of LEA proteins in plants and emphasizes the role of protein oligomer formation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11516066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522792","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

Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly. 细菌 ESCRT-III 超家族成员的单体折叠与寡聚体解体相关联。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5187

Ndjali Quarta, Tika Ram Bhandari, Martin Girard, Nadja Hellmann, Dirk Schneider

{"title":"Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly.","authors":"Ndjali Quarta, Tika Ram Bhandari, Martin Girard, Nadja Hellmann, Dirk Schneider","doi":"10.1002/pro.5187","DOIUrl":"10.1002/pro.5187","url":null,"abstract":"The inner membrane associated protein of 30 kDa (IM30), a member of the endosomal sorting complex required for transport (ESCRT-III) superfamily, is crucially involved in the biogenesis and maintenance of thylakoid membranes in cyanobacteria and chloroplasts. In solution, IM30 assembles into various large oligomeric barrel- or tube-like structures, whereas upon membrane binding it forms large, flat carpet structures. Dynamic localization of the protein in solution, to membranes and changes of the oligomeric states are crucial for its in vivo function. ESCRT-III proteins are known to form oligomeric structures that are dynamically assembled from monomeric/smaller oligomeric proteins, and thus these smaller building blocks must be assembled sequentially in a highly orchestrated manner, a still poorly understood process. The impact of IM30 oligomerization on function remains difficult to study due to its high intrinsic tendency to homo-oligomerize. Here, we used molecular dynamics simulations to investigate the stability of individual helices in IM30 and identified unstable regions that may provide structural flexibility. Urea-mediated disassembly of the IM30 barrel structures was spectroscopically monitored, as well as changes in the protein's tertiary and secondary structure. The experimental data were finally compared to a three-state model that describes oligomer disassembly and monomer unfolding. In this study, we identified a highly stable conserved structural core of ESCRT-III proteins and discuss the advantages of having flexible intermediate structures and their putative relevance for ESCRT-III proteins.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522791","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

Protein degradation of antizyme depends on the N-terminal degrons. 抗酶的蛋白质降解取决于 N 端脱胶子。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5199

Ju-Yi Hsieh, Pui-Ying Leong, Yi-Fang Yang, Yi-Liang Liu, Guang-Yaw Liu, Hui-Chih Hung

{"title":"Protein degradation of antizyme depends on the N-terminal degrons.","authors":"Ju-Yi Hsieh, Pui-Ying Leong, Yi-Fang Yang, Yi-Liang Liu, Guang-Yaw Liu, Hui-Chih Hung","doi":"10.1002/pro.5199","DOIUrl":"10.1002/pro.5199","url":null,"abstract":"Antizyme (AZ) is a regulatory protein that plays a crucial role in modulating the activity of ornithine decarboxylase (ODC), which is the initial and rate-limiting enzyme in the complex pathway of polyamine biosynthesis. AZ facilitates the swift degradation of ODC, thereby modulating the levels of cellular polyamines. This study unveils a new ubiquitin-independent mechanism for AZ degradation, emphasizing the essential role of N-terminal degrons. Contrary to traditional ubiquitin-dependent degradation, our findings reveal that AZ degradation is significantly influenced by its N-terminal region. By conducting a series of experiments, including in vitro degradation assays, cycloheximide chase experiments, differential scanning calorimetry, and measurement of cellular concentrations of polyamines, we demonstrate that N-terminal truncation significantly enhances AZ's stability and facilitates the reduction of polyamine levels by accelerating ODC degradation. The removal of the N-terminal portion of AZ results in a reduced degradation rate and enhanced thermal stability of the protein, leading to a more efficient inhibition of polyamine synthesis. These findings are corroborated by the analysis of AZ isoforms, AZ1, AZ2, and AZ3, which display differential degradation patterns based on the specific N-terminal segments. This substantiates a degradation mechanism driven by an intrinsically disordered N-terminal region acting as a degron, independent of lysine ubiquitination. These results underscore the significant regulatory function of the N-terminal domain in the activity of AZ and the maintenance of polyamine homeostasis.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547017","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

Unique Fn3-like biosensor in σ^I/anti-σ^I factors for regulatory expression of major cellulosomal scaffoldins in Pseudobacteroides cellulosolvens. σI/抗σI因子中独特的Fn3类生物传感器，用于调控假杆菌（Pseudobacteroides cellulosolvens）中主要纤维素体支架蛋白的表达。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5193

Sheng Dong, Chao Chen, Jie Li, Ya-Jun Liu, Edward A Bayer, Raphael Lamed, Itzhak Mizrahi, Qiu Cui, Yingang Feng

{"title":"Unique Fn3-like biosensor in σI/anti-σI factors for regulatory expression of major cellulosomal scaffoldins in Pseudobacteroides cellulosolvens.","authors":"Sheng Dong, Chao Chen, Jie Li, Ya-Jun Liu, Edward A Bayer, Raphael Lamed, Itzhak Mizrahi, Qiu Cui, Yingang Feng","doi":"10.1002/pro.5193","DOIUrl":"10.1002/pro.5193","url":null,"abstract":"Lignocellulolytic clostridia employ multiple pairs of alternative σ/anti-σ (SigI/RsgI) factors to regulate cellulosomal components for substrate-specific degradation of cellulosic biomass. The current model has proposed that RsgIs use a sensor domain to bind specific extracellular lignocellulosic components and activate cognate SigIs to initiate expression of corresponding cellulosomal enzyme genes, while expression of scaffoldins can be initiated by several different SigIs. Pseudobacteroides cellulosolvens contains the most complex known cellulosome system and the highest number of SigI-RsgI regulons yet discovered. However, the function of many RsgI sensor domains and their relationship with the various enzyme types are not fully understood. Here, we report that RsgI4 from P. cellulosolvens employs a C-terminal module that bears distant similarity to the fibronectin type III (Fn3) domain and serves as the sensor domain. Substrate-binding analysis revealed that the Fn3-like domain of RsgI4 represents a novel carbohydrate-binding module (CBM) that binds to a wide range of polysaccharide types. Structure determination further revealed that the Fn3-like domain belongs to the type B group of CBMs with a predicted concave face for substrate binding. Promoter sequence analysis of cellulosomal genes revealed that SigI4 is responsible for cellulosomal regulation of major scaffoldins rather than enzymes, consistent with the broad substrate specificity of the RsgI4 sensor domain. Notably, scaffoldins are invariably required as cellulosome components regardless of the substrate type. These findings suggest that the intricate cellulosome system of P. cellulosolvens comprises a more elaborate regulation mechanism than other bacteria and thus expands the paradigm of cellulosome regulation.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522794","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

Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors. BET/BRPF1 双重抑制剂可增强肝癌和乳腺癌细胞的细胞死亡。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5191

Giulia Cazzanelli, Andrea Dalle Vedove, Nicolò Sbardellati, Luca Valer, Amedeo Caflisch, Graziano Lolli

{"title":"Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors.","authors":"Giulia Cazzanelli, Andrea Dalle Vedove, Nicolò Sbardellati, Luca Valer, Amedeo Caflisch, Graziano Lolli","doi":"10.1002/pro.5191","DOIUrl":"10.1002/pro.5191","url":null,"abstract":"The acetylpyrrole scaffold is an acetylated lysine mimic that has been previously explored to develop bromodomain inhibitors. When tested on the hepatoma cell line Huh7 and the breast cancer cell line MDA-MB-231, a few compounds in our acetylpyrrole-thiazole library induced peculiar morphological changes, progressively causing cell death at increasing concentrations. Their evaluation on a panel of human bromodomains revealed concurrent inhibition of BRPF1 and BET bromodomains. To dissect the observed cellular effects, the acetylpyrrole derivatives were compared to JQ1 and GSK6853, chemical probes for the bromodomains of BET and BRPF1, respectively. The appearance of neurite-like extrusions, accompanied by βIII-tubulin overexpression, is caused by BET inhibition, with limited effect on cellular viability. Conversely, interference with BRPF1 induces cellular death but not phenotypic alterations. Combined treatment with JQ1 and GSK6853 showed additivity in reducing cellular viability, comparably to the acetylpyrrole-thiazole-based BET/BRPF1 inhibitors. In addition, we determined the crystallographic structures of the BRD4 and BRPF1 bromodomains in complex with the acetylpyrrole-thiazole compounds. The binding modes in the two bromodomains show similar interactions for the acetylpyrrole and different orientations of the moiety that point to the rim of the acetyl-lysine pocket.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547014","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

Diversity and structural-functional insights of alpha-solenoid proteins. α-类烯醇蛋白的多样性和结构功能见解。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5189

Paula Nazarena Arrías, Zarifa Osmanli, Estefanía Peralta, Patricio Manuel Chinestrad, Alexander Miguel Monzon, Silvio C E Tosatto

{"title":"Diversity and structural-functional insights of alpha-solenoid proteins.","authors":"Paula Nazarena Arrías, Zarifa Osmanli, Estefanía Peralta, Patricio Manuel Chinestrad, Alexander Miguel Monzon, Silvio C E Tosatto","doi":"10.1002/pro.5189","DOIUrl":"10.1002/pro.5189","url":null,"abstract":"Alpha-solenoids are a significant and diverse subset of structured tandem repeat proteins (STRPs) that are important in various domains of life. This review examines their structural and functional diversity and highlights their role in critical cellular processes such as signaling, apoptosis, and transcriptional regulation. Alpha-solenoids can be classified into three geometric folds: low curvature, high curvature, and corkscrew, as well as eight subfolds: ankyrin repeats; Huntingtin, elongation factor 3, protein phosphatase 2A, and target of rapamycin; armadillo repeats; tetratricopeptide repeats; pentatricopeptide repeats; Pumilio repeats; transcription activator-like; and Sel-1 and Sel-1-like repeats. These subfolds represent distinct protein families with unique structural properties and functions, highlighting the versatility of alpha-solenoids. The review also discusses their association with disease, highlighting their potential as therapeutic targets and their role in protein design. Advances in state-of-the-art structure prediction methods provide new opportunities and challenges in the functional characterization and classification of this kind of fold, emphasizing the need for continued development of methods for their identification and proper data curation and deposition in the main databases.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506688","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

Molecular and energetic analysis of the interaction and specificity of Maximin 3 with lipid membranes: In vitro and in silico assessments. Maximin 3 与脂质膜相互作用和特异性的分子和能量分析：体外和硅学评估。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5188

Pablo Luis Hernández-Adame, Brandt Bertrand, Martha Itzel Escamilla-Ruiz, Jaime Ruiz-García, Carlos Munoz-Garay

{"title":"Molecular and energetic analysis of the interaction and specificity of Maximin 3 with lipid membranes: In vitro and in silico assessments.","authors":"Pablo Luis Hernández-Adame, Brandt Bertrand, Martha Itzel Escamilla-Ruiz, Jaime Ruiz-García, Carlos Munoz-Garay","doi":"10.1002/pro.5188","DOIUrl":"https://doi.org/10.1002/pro.5188","url":null,"abstract":"In this study, the interaction of antimicrobial peptide Maximin 3 (Max3) with three different lipid bilayer models was investigated to gain insight into its mechanism of action and membrane specificity. Bilayer perturbation assays using liposome calcein leakage dose-response curves revealed that Max3 is a selective membrane-active peptide. Dynamic light scattering recordings suggest that the peptide incorporates into the liposomal structure without producing a detergent effect. Langmuir monolayer compression assays confirmed the membrane inserting capacity of the peptide. Attenuated total reflection-Fourier transform infrared spectroscopy showed that the fingerprint signals of lipid phospholipid hydrophilic head groups and hydrophobic acyl chains are altered due to Max3-membrane interaction. On the other hand, all-atom molecular dynamics simulations (MDS) of the initial interaction with the membrane surface corroborated peptide-membrane selectivity. Peptide transmembrane MDS shed light on how the peptide differentially modifies lipid bilayer properties. Molecular mechanics Poisson-Boltzmann surface area calculations revealed a specific electrostatic interaction fingerprint of the peptide for each membrane model with which they were tested. The data generated from the in silico approach could account for some of the differences observed experimentally in the activity and selectivity of Max3.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547016","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

Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B. 门控残基控制着配体从 HIF-2α PAS-B 的埋藏腔中解除结合的动力学。

IF 4.5 3区生物学

Protein Science Pub Date : 2024-11-01 DOI: 10.1002/pro.5198

Marion L Silvestrini, Riccardo Solazzo, Soumendu Boral, Melanie J Cocco, Joseph D Closson, Matteo Masetti, Kevin H Gardner, Lillian T Chong

{"title":"Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.","authors":"Marion L Silvestrini, Riccardo Solazzo, Soumendu Boral, Melanie J Cocco, Joseph D Closson, Matteo Masetti, Kevin H Gardner, Lillian T Chong","doi":"10.1002/pro.5198","DOIUrl":"10.1002/pro.5198","url":null,"abstract":"While transcription factors have been generally perceived as \"undruggable,\" an exception is the HIF-2 hypoxia-inducible transcription factor, which contains an internal cavity that is sufficiently large to accommodate a range of small-molecules, including the therapeutically used inhibitor belzutifan. Given the relatively long ligand residence times of these small molecules and the lack of any experimentally observed pathway connecting the cavity to solvent, there has been great interest in understanding how these drug ligands exit the buried receptor cavity. Here, we focus on the relevant PAS-B domain of hypoxia-inducible factor 2α (HIF-2α) and examine how one such small molecule (THS-017) exits from the buried cavity within this domain on the seconds-timescale using atomistic simulations and ZZ-exchange NMR. To enable the simulations, we applied the weighted ensemble path sampling strategy, which generates continuous pathways for a rare-event process [e.g., ligand (un)binding] with rigorous kinetics in orders of magnitude less computing time compared to conventional simulations. Results reveal the formation of an encounter complex intermediate and two distinct classes of pathways for ligand exit. Based on these pathways, we identified two pairs of conformational gating residues in the receptor: one for the major class (N288 and S304) and another for the minor class (L272 and M309). ZZ-exchange NMR validated the kinetic importance of N288 for ligand unbinding. Our results provide an ideal simulation dataset for rational manipulation of ligand unbinding kinetics.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11516114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522790","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