Journal of structural biology最新文献_第7页

Ensemble-function relationships: From qualitative to quantitative relationships between protein structure and function 集合-功能关系：蛋白质结构与功能之间从定性到定量的关系。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-11-21 DOI: 10.1016/j.jsb.2024.108152

Filip Yabukarski

{"title":"Ensemble-function relationships: From qualitative to quantitative relationships between protein structure and function","authors":"Filip Yabukarski","doi":"10.1016/j.jsb.2024.108152","DOIUrl":"10.1016/j.jsb.2024.108152","url":null,"abstract":"<div><div>Structure-function relationships are deeply rooted in modern biochemistry and structural biology and have provided the basis for our understanding of how protein structure defines function. While structure–function relationships continue to provide invaluable <em>qualitative</em> information, they cannot, in principle, provide the <em>quantitative</em> information ultimately needed to fully understand how proteins function and to make quantitative predictions about changes in activity from changes in sequence and structure. These limitations appear to arise from fundamental principles of physics, which dictate that proteins exist as interchanging ensembles of conformations, rather than as static structures that underly conventional structure–function relationships. This perspective discusses the concept of ensemble-function relationships as quantitative relationships that build on and extend traditional structure–function relationships. The concepts of free energy landscapes and conformational ensembles and their application to proteins are reviewed. The perspective summarizes a range of approaches that can provide conformational ensemble information and focuses on X-ray crystallography methods for obtaining experimental protein conformational ensembles. Focusing on enzymes as archetypes of protein function, recent literature examples are reviewed that used ensemble-function relationships to understand how protein residues contribute to function and how changes in protein sequence and structure impact activity, leading to new models and providing previously inaccessible mechanistic insights. Potential applications of conformational ensembles and ensemble-function relationships to protein design are examined. The perspective concludes with current limitations of the ensemble-function relationships and potential paths forward toward the next generation of quantitative ensemble-function models.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108152"},"PeriodicalIF":3.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693247","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

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA MgcRacGAP 的 Ser387 磷酸化对其 CDC42 和 RHOA 的 GTPase 激活活性的影响的结构基础。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-11-09 DOI: 10.1016/j.jsb.2024.108151

Kazutaka Murayama , Miyuki Kato-Murayama , Toshiaki Hosaka , Toshio Kitamura , Shigeyuki Yokoyama , Mikako Shirouzu

{"title":"Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA","authors":"Kazutaka Murayama , Miyuki Kato-Murayama , Toshiaki Hosaka , Toshio Kitamura , Shigeyuki Yokoyama , Mikako Shirouzu","doi":"10.1016/j.jsb.2024.108151","DOIUrl":"10.1016/j.jsb.2024.108151","url":null,"abstract":"<div><div>MgcRacGAP is a GTPase-activating protein (GAP) for the Rho family GTPases. During cytokinesis, MgcRacGAP localizes to the midbody, where it activates the GTPase activity of Rho family GTPases to facilitate cytokinesis. In the midbody, Aurora B phosphorylates Ser387 within the GAP domain of human MgcRacGAP, a modification that is suggested to influence GTPase preference. However, there are conflicting reports, with some studies indicating that Ser387 phosphorylation does not alter the GTPase preference of MgcRacGAP. This controversy highlights the need for a deeper understanding of the molecular interactions involved, which can be clarified through structural analyses. In the present study, we determined the crystal structures of the wild-type MgcRacGAP GAP domain complexed with CDC42•GDP•AlF<sub>4</sub><sup>−</sup> and the S378D phosphomimetic mutant GAP domain fused with RHOA•GDP•AlF<sub>4</sub><sup>−</sup>. Additionally, crystal structures of the GAP domains were determined for the S387D and S387A mutants. Our analysis revealed that neither GTPase binding nor S387D mutation affected the overall structure of the GAP domain. However, comparison of the CDC42•MgcRacGAP (wild-type) complex with the RHOA-MgcRacGAP(S378D) fusion protein structure indicated that the S387D mutation caused positional shifts in both CDC42 and RHOA relative to MgcRacGAP. These shifts reduced interactions with CDC42 more severely than those with RHOA. In fact, the S387D mutation decreased the GTPase-activating activity of MgcRacGAP toward CDC42, while its impact on RHOA was only moderate. This difference in the rate of activity reduction may play an important role in GTPase preference.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108151"},"PeriodicalIF":3.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622763","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

Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance 对 HLTF ATPase 重塑结构域的计算研究表明了它在 dsDNA 上的活性以及对损伤耐受性的影响。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-11-02 DOI: 10.1016/j.jsb.2024.108149

Martin Ljubic , Claudia D’Ercole , Yossma Waheed , Ario de Marco , Jure Borišek , Matteo De March

{"title":"Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance","authors":"Martin Ljubic , Claudia D’Ercole , Yossma Waheed , Ario de Marco , Jure Borišek , Matteo De March","doi":"10.1016/j.jsb.2024.108149","DOIUrl":"10.1016/j.jsb.2024.108149","url":null,"abstract":"<div><div>The Helicase-Like Transcription Factor (HLTF) is member of the SWI/SNF-family of ATP dependent chromatin remodellers known primarily for maintaining genome stability. Biochemical and cellular assays support its multiple roles in DNA Damage Tolerance. However, the lack of sufficient structural data limits the comprehension of the molecular basis of its modes of action.</div><div>In this work we have modelled and characterized the HLTF ATPase remodeling domain by using bioinformatic tools and all-atoms molecular dynamics simulations.</div><div><em>In-silico</em> results suggested that its binding to dsDNA is mainly mediated by the positively charged residues Arg563 and Lys913, found conserved in HLTF homologs, and Arg620 and Lys999, found only in HLTF. Interestingly, these residues are mutated in cancer cells. During translocation on dsDNA, HLTF remains persistently bound through the N-terminal ATPase subunit. However, DNA advancement occurs only in the presence of the synergic-anticorrelated action of both motor lobes. In contrast, the C-terminal facilitates substrate remodeling through DNA deformation and generation of bulges according to a wave-model. Finally, the large conformational change suggested between the two motor-remodeling subunits might be activated upon the release of PARP1 on stalled fork and be responsible for the intervention of HLTF-HIRAN in the formation of D-loop and 4-way junction DNA structures.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108149"},"PeriodicalIF":3.0,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568819","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

Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles 囊泡拾取器：有效识别囊泡中膜蛋白复合物的工具。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-30 DOI: 10.1016/j.jsb.2024.108148

Ryan Karimi , Claire E. Coupland , John L. Rubinstein

{"title":"Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles","authors":"Ryan Karimi , Claire E. Coupland , John L. Rubinstein","doi":"10.1016/j.jsb.2024.108148","DOIUrl":"10.1016/j.jsb.2024.108148","url":null,"abstract":"<div><div>Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of these vesicles can be challenging due to the strong signal contributed from the lipid bilayer. This challenge often requires iterative and laborious particle selection workflows to generate a dataset of high-quality particle images for subsequent analysis. Here we present Vesicle Picker, an open-source program built on the Segment Anything model. Vesicle Picker enables automatic identification of vesicles in cryo-EM micrographs with high recall and precision. It then exhaustively selects all potential particle locations, either at the perimeter or uniformly over the surface of the projection of the vesicle. The program is designed to interface with cryoSPARC, which performs both upstream micrograph processing and downstream single particle image analysis. We demonstrate Vesicle Picker’s utility by determining a high-resolution map of the vacuolar-type ATPase from micrographs of native synaptic vesicles (SVs) and identifying an additional protein or protein complex in the SV membrane.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108148"},"PeriodicalIF":3.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558096","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

An inducible model for medial calcification based on matrix Gla protein deficiency 基于基质 Gla 蛋白缺乏症的内侧钙化诱导模型。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-24 DOI: 10.1016/j.jsb.2024.108144

Kyoungmi Bak , Abhinav Parashar , Raphaela Allgayer , Juliana Marulanda , Ophélie Gourgas , Marta Cerruti , Monzur Murshed

{"title":"An inducible model for medial calcification based on matrix Gla protein deficiency","authors":"Kyoungmi Bak , Abhinav Parashar , Raphaela Allgayer , Juliana Marulanda , Ophélie Gourgas , Marta Cerruti , Monzur Murshed","doi":"10.1016/j.jsb.2024.108144","DOIUrl":"10.1016/j.jsb.2024.108144","url":null,"abstract":"<div><div>Calcific deposits in the arterial media have been associated with a number of metabolic and genetic disorders including diabetes, chronic kidney disease and generalized arterial calcification of infancy. The loss of matrix Gla protein (MGP) leads to medial elastic lamina calcification (elastocalcinosis) in both humans and animal models. While MGP-deficient (<em>Mgp<sup>-/-</sup></em>) mice have been used as a reliable model to study medial elastocalcinosis, these mice are difficult to maintain because of their fragility. Also, these mice are unsuitable for long-term calcification studies in relation to age and sex as most often they die prematurely. In order to circumvent these problems we generated <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice, which in addition to the ablation of <em>Mgp</em> alleles, carries a transgene expressing the phosphaturic hormone FGF23. Increased FGF23 levels in the circulation and ensuing hypophosphatemia in these mice lead to a complete prevention of medial calcification until late adulthood. Interestingly, upon feeding a high phosphorus diet for 10 days, we were able to induce medial calcification in 3-week-old <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice. Our mineral analyses showed that the Ca/P% in the calcific deposits in these mice were comparable to that of 5-week-old <em>Mgp<sup>-/-</sup></em> mice although the level of crystallinity differed. The aorta explants from <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice resulted in elastocalcinosis in the presence of 2 mM phosphate in the culture medium which was completely prevented by pyrophosphate analogue alendronate. <em>Mgp<sup>-/-</sup>;ApoE-FGF23</em> mice will be suitable for future in vivo or ex vivo studies examining the effects of age, sex and mineralization inhibitors on medial elastocalcinosis.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108144"},"PeriodicalIF":3.0,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502744","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

NMR residual dipolar couplings investigation in the topology of house dust mite Group V allergens 屋尘螨 V 组过敏原拓扑结构中的核磁共振残余偶极耦合研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108138

Mandar T. Naik , Nandita Naik , Camy C.-H. Kung , Tai-Huang Huang

引用次数: 0

Correlative Raman spectroscopy and electron microscopy identifies glycogen rich deposits correlated with local structural defects in long bones of type IV osteogenesis imperfecta patients 拉曼光谱和电子显微镜的相关研究发现，富含糖原的沉积物与 IV 型成骨不全症患者长骨的局部结构缺陷有关。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108142

R.H.M. Van der Meijden , M.H. Scholten , W.H. Nijhuis , R.J.B. Sakkers , N. Sommerdijk , A. Akiva

{"title":"Correlative Raman spectroscopy and electron microscopy identifies glycogen rich deposits correlated with local structural defects in long bones of type IV osteogenesis imperfecta patients","authors":"R.H.M. Van der Meijden , M.H. Scholten , W.H. Nijhuis , R.J.B. Sakkers , N. Sommerdijk , A. Akiva","doi":"10.1016/j.jsb.2024.108142","DOIUrl":"10.1016/j.jsb.2024.108142","url":null,"abstract":"<div><div>Osteogenesis imperfecta (OI) is a genetic bone disease occurring in approximately 1 in 10,000 births, usually as a result of genetic mutation. OI patients suffer from increased fracture risk and – depending on the severity of the disease – deformation of the limbs, which can even lead to perinatal death.</div><div>Despite extensive studies, the way in which the genetic mutation is translated into structural and compositional anomalies of the tissue is still an open question. Different observations have been reported, ranging from no structural (or chemical) differences to completely chaotic bone structure and composition.</div><div>Here, we investigated bone samples from two adolescent OI-IV patients, focusing on the bone structure and chemistry in naturally occurring fractures. The exposed fracture plane allows the investigation of the structure and composition of the weakest bone plane. We do so by combining scanning electron microscopy (SEM) imaging with chemical information from Raman microscopy.</div><div>The exposed fracture planes show different regions within the same tissue, displaying normal osteonal structures next to disorganized osteons and totally disordered structures, while the collagen mineralization in all cases is similar to that of a healthy bone.</div><div>In addition, we also detected significant amounts of depositions of glycogen-rich, organic, globules of 250–1000 nm in size. These depositions point to a role of cellular disfunction in the disorganization of the collagen in qualitative OI.</div><div>Overall, our results unite multiple, sometimes contradicting views from the literature on qualitative OI.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108142"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502746","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

Bone strength and residual compressive stress in apatite crystals 骨强度和磷灰石晶体中的残余压应力

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108141

Victoria Schemenz , Ernesto Scoppola , Paul Zaslansky , Peter Fratzl

引用次数: 0

Deletion within ameloblastin multitargeting domain reduces its interaction with artificial cell membrane 缺失母细胞蛋白多靶向结构域会降低其与人工细胞膜的相互作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108143

Natalie C. Kegulian, Janet Moradian-Oldak

{"title":"Deletion within ameloblastin multitargeting domain reduces its interaction with artificial cell membrane","authors":"Natalie C. Kegulian, Janet Moradian-Oldak","doi":"10.1016/j.jsb.2024.108143","DOIUrl":"10.1016/j.jsb.2024.108143","url":null,"abstract":"<div><div>In human, mutations in the gene encoding the enamel matrix protein ameloblastin (Ambn) have been identified in cases of <em>amelogenesis imperfecta</em>. In mouse models, perturbations in the <em>Ambn</em> gene have caused loss of enamel and dramatic disruptions in enamel-making ameloblast cell function. Critical roles for Ambn in ameloblast cell signaling and polarization as well as adhesion to the nascent enamel matrix have been supported. Recently, we have identified a multitargeting domain (MTD) in Ambn that interacts with cell membrane, with the majority enamel matrix protein amelogenin, and with itself. This domain includes an amphipathic helix (AH) motif that directly interacts with cell membrane. In this study, we analyzed the sequence of the MTD for evolutionary conservation and found high conservation among mammals within the MTD and particularly within the AH motif. We computationally predicted that the AH motif lost its hydrophobic moment upon deleting hydrophobic but not hydrophilic residues from the motif. Furthermore, we rationally designed peptides that encompassed the Ambn MTD and contained deletions of largely hydrophobic or hydrophilic stretches of residues. To assess their AH-forming and membrane-binding abilities, we combined those peptides with synthetic phospholipid membrane vesicles and performed circular dichroism, membrane leakage, and vesicle clearance measurements. Circular dichroism showed retention of α-helix formation in all peptides except the one with the largest deletion of eleven amino acids including seven that were hydrophobic. This same peptide variant failed to cause leakage or clearance of synthetic membranes, while smaller deletions yielded intermediate membrane interaction as measured by leakage and clearance assays. Our data revealed that deletion of key hydrophobic residues from the AH leads to the most dramatic loss of Ambn–membrane interaction. Pinpointing roles of residues within the MTD has important implications for the multifunctionality of Ambn.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108143"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502747","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

On the role of the glycosylation of type I collagen in bone 关于 I 型胶原蛋白糖基化在骨骼中的作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2024-10-22 DOI: 10.1016/j.jsb.2024.108145

Luco Rutten , Elena Macías-Sánchez , Nico Sommerdijk

{"title":"On the role of the glycosylation of type I collagen in bone","authors":"Luco Rutten , Elena Macías-Sánchez , Nico Sommerdijk","doi":"10.1016/j.jsb.2024.108145","DOIUrl":"10.1016/j.jsb.2024.108145","url":null,"abstract":"<div><div>Glycan-protein interactions play a crucial role in biology, providing additional functions capable of inducing biochemical and cellular responses. In the extracellular matrix of bone, this type of interactions is ubiquitous. During the synthesis of the collagen molecule, glycans are post-translationally added to specific lysine residues through an enzymatically catalysed hydroxylation and subsequent glycosylation. During and after fibril assembly, proteoglycans are essential for maintaining tissue structure, porosity, and integrity. Glycosaminoglycans (GAGs), the carbohydrate chains attached to interstitial proteoglycans, are known to be involved in mineralization. They can attract and retain water, which is critical for the mechanical properties of bone. In addition, like other long-lived proteins, collagen is susceptible to glycation. Prolonged exposure of the amine group to glucose eventually leads to the formation of advanced glycation end-products (AGEs). Changes in the degree of glycosylation and glycation have been identified in bone pathologies such as osteogenesis imperfecta and diabetes and appear to be associated with a reduction in bone quality. However, how these changes affect mineralization is not well understood.</div><div>Based on the literature review, we hypothesize that the covalently attached carbohydrates may have a water-attracting function similar to that of GAGs, but at different lengths and timescales in the bone formation process. Glycosylation potentially increases the hydration around the collagen triple helix, leading to increased mineralization (hypermineralization) after water has been replaced by mineral. Meanwhile, glycation leads to the formation of crosslinking AGEs, which are associated with a decrease in hydration levels, reducing the mechanical properties of bone.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108145"},"PeriodicalIF":3.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502750","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