Journal of structural biology最新文献

{"title":"Multimodal analysis and comparison of stoichiometric and structural characteristics of parosteal and conventional osteosarcoma with massive sclerosis in human bone","authors":"Benjamin Zanghellini ,&nbsp;Nicole Zechmann ,&nbsp;Dieter Baurecht ,&nbsp;Tilman A. Grünewald ,&nbsp;Manfred Burghammer ,&nbsp;Bernadette Liegl-Atzwanger ,&nbsp;Andreas Leithner ,&nbsp;Anton Davydok ,&nbsp;Helga Lichtenegger","doi":"10.1016/j.jsb.2024.108106","DOIUrl":"10.1016/j.jsb.2024.108106","url":null,"abstract":"<div><p>Osteosarcoma (OS) is the most common malignant primary bone tumor in humans and occurs in various subtypes. Tumor formation happens through malignant osteoblasts producing immature bone. In the present paper we studied two different subtypes of osteosarcoma, from one individual with conventional OS with massive sclerosis and one individual with parosteal OS, based on a multimodal approach including small angle x-ray scattering (SAXS), wide angle x-ray diffraction (WAXS), backscattered electron imaging (BEI) and Raman spectroscopy. It was found that both tumors showed reduced mineral particle sizes and degree of orientation of the collagen-mineral composite in the affected areas, alongside with a decreased crystallinity. Distinct differences between the tumor material from the two individuals were found in the degree of mineralization. Further differences were observed in the carbonate to phosphate ratio, which is related to the degree of carbonate substitution in bone mineral and indicative of the turnover rate. The contraction of the c-axis of the bone mineral crystals proved to be a further, very sensitive parameter, potentially indicative of malignancy.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108106"},"PeriodicalIF":3.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000467/pdfft?md5=9ed1e569d95f001da854c6690b71c1fe&pid=1-s2.0-S1047847724000467-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317638","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}

{"title":"The CryoEM structure of human serum albumin in complex with ligands","authors":"Claudio Catalano,&nbsp;Kyle W. Lucier,&nbsp;Dennis To ,&nbsp;Skerdi Senko,&nbsp;Nhi L. Tran,&nbsp;Ashlyn C. Farwell,&nbsp;Sabrina M. Silva,&nbsp;Phat V. Dip,&nbsp;Nicole Poweleit,&nbsp;Giovanna Scapin","doi":"10.1016/j.jsb.2024.108105","DOIUrl":"10.1016/j.jsb.2024.108105","url":null,"abstract":"<div><p>Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108105"},"PeriodicalIF":3.0,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000455/pdfft?md5=a8ac3ab74049b019ec266934fd28d96a&pid=1-s2.0-S1047847724000455-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141296291","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}

{"title":"Honeycomb gold specimen supports enabling orthogonal focussed ion beam-milling of elongated cells for cryo-ET","authors":"Victoria L. Hale,&nbsp;James Hooker,&nbsp;Christopher J. Russo,&nbsp;Jan Löwe","doi":"10.1016/j.jsb.2024.108097","DOIUrl":"10.1016/j.jsb.2024.108097","url":null,"abstract":"<div><p>Cryo-focussed ion beam (FIB)-milling is a powerful technique that opens up thick, cellular specimens to high-resolution structural analysis by electron cryotomography (cryo-ET). FIB-milled lamellae can be produced from cells on grids, or cut from thicker, high-pressure frozen specimens. However, these approaches can put geometrical constraints on the specimen that may be unhelpful, particularly when imaging structures within the cell that have a very defined orientation. For example, plunge frozen rod-shaped bacteria orient parallel to the plane of the grid, yet the Z-ring, a filamentous structure of the tubulin-like protein FtsZ and the key organiser of bacterial division, runs around the circumference of the cell such that it is perpendicular to the imaging plane. It is therefore difficult or impractical to image many complete rings with current technologies. To circumvent this problem, we have fabricated monolithic gold specimen supports with a regular array of cylindrical wells in a honeycomb geometry, which trap bacteria in a vertical orientation. These supports, which we call “honeycomb gold discs”, replace standard EM grids and when combined with FIB-milling enable the production of lamellae containing cross-sections through cells. The resulting lamellae are more stable and resistant to breakage and charging than conventional lamellae. The design of the honeycomb discs can be modified according to need and so will also enable cryo-ET and cryo-EM imaging of other specimens in otherwise difficult to obtain orientations.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108097"},"PeriodicalIF":3.0,"publicationDate":"2024-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000376/pdfft?md5=e359a194a50eb4de33526eb62b457aa2&pid=1-s2.0-S1047847724000376-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074934","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}

{"title":"Structure and conformational variability of the HER2-trastuzumab-pertuzumab complex","authors":"Rémi Ruedas ,&nbsp;Rémi Vuillemot ,&nbsp;Thibault Tubiana ,&nbsp;Jean-Marie Winter ,&nbsp;Laura Pieri ,&nbsp;Ana-Andreea Arteni ,&nbsp;Camille Samson ,&nbsp;Slavica Jonic ,&nbsp;Magali Mathieu ,&nbsp;Stéphane Bressanelli","doi":"10.1016/j.jsb.2024.108095","DOIUrl":"10.1016/j.jsb.2024.108095","url":null,"abstract":"<div><p>Single particle analysis from cryogenic transmission electron microscopy (cryo-EM) is particularly attractive for complexes for which structure prediction remains intractable, such as antibody-antigen complexes. Here we obtain the detailed structure of a particularly difficult complex between human epidermal growth factor receptor 2 (HER2) and the antigen-binding fragments from two distinct therapeutic antibodies binding to distant parts of the flexible HER2, pertuzumab and trastuzumab (HTP). We highlight the strengths and limitations of current data processing software in dealing with various kinds of heterogeneities, particularly continuous conformational heterogeneity, and in describing the motions that can be extracted from our dataset. Our HTP structure provides a more detailed view than the one previously available for this ternary complex. This allowed us to pinpoint a previously overlooked loop in domain IV that may be involved both in binding of trastuzumab and in HER2 dimerization. This finding may contribute to explain the synergistic anticancer effect of the two antibodies. We further propose that the flexibility of the HTP complex, beyond the difficulties it causes for cryo-EM analysis, actually reflects regulation of HER2 signaling and its inhibition by therapeutic antibodies. Notably we obtain our best data with ultra-thin continuous carbon grids, showing that with current cameras their use to alleviate particle misdistribution is compatible with a protein complex of only 162 kDa. Perhaps most importantly, we provide here a dataset for such a smallish protein complex for further development of software accounting for continuous conformational heterogeneity in cryo-EM images.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108095"},"PeriodicalIF":3.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898518","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}

{"title":"Cell-induced collagen alignment in a 3D in vitro culture during extracellular matrix production","authors":"Judith M. Schaart ,&nbsp;Mariska Kea-te Lindert ,&nbsp;Rona Roverts ,&nbsp;Wouter H. Nijhuis ,&nbsp;Nico Sommerdijk ,&nbsp;Anat Akiva","doi":"10.1016/j.jsb.2024.108096","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108096","url":null,"abstract":"<div><p>The bone extracellular matrix consists of a highly organized collagen matrix that is mineralized with carbonated hydroxyapatite. Even though the structure and composition of bone have been studied extensively, the mechanisms underlying collagen matrix organization remain elusive. In this study, we used a 3D cell culture system in which osteogenic cells deposit and orient the collagen matrix that is subsequently mineralized. Using live fluorescence imaging combined with volume electron microscopy, we visualize the organization of the cells and collagen in the cell culture. We show that the osteogenically induced cells are organizing the collagen matrix during development. Based on the observation of tunnel-like structures surrounded by aligned collagen in the center of the culture, we propose that osteoblasts organize the deposited collagen during migration through the culture. Overall, we show that cell-matrix interactions are involved in collagen alignment during early-stage osteogenic differentiation and that the matrix is organized by the osteoblasts in the absence of osteoclast activity.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108096"},"PeriodicalIF":3.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000364/pdfft?md5=1dcb6f2b251d72a852d9c2932682efa1&pid=1-s2.0-S1047847724000364-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140843828","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}

{"title":"Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives","authors":"Nigam Jyoti Maiti ,&nbsp;Swastika Ganguly ,&nbsp;Kiattawee Choowongkomon ,&nbsp;Supaphorn Seetaha ,&nbsp;Siriwan Saehlee ,&nbsp;Thitinan Aiebchun","doi":"10.1016/j.jsb.2024.108094","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108094","url":null,"abstract":"<div><p>This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound <strong>3 h</strong>, followed closely by <strong>6 h</strong>, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. <em>In vivo</em> oral toxicity studies were conducted for the most active compound <strong>3 h</strong>, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of <strong>3 h</strong>, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108094"},"PeriodicalIF":3.0,"publicationDate":"2024-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140650029","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}

{"title":"Dual pattern of cholesterol-induced decoupling of residue-residue interactions of Kir2.2","authors":"Katie M. Beverley ,&nbsp;Nicolas Barbera ,&nbsp;Irena Levitan","doi":"10.1016/j.jsb.2024.108091","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108091","url":null,"abstract":"<div><p>Cholesterol is a negative regulator of a variety of ion channels. We have previously shown that cholesterol suppresses Kir2.2 channels via residue-residue uncoupling on the inter-subunit interfaces within the close state of the channels (3JYC). In this study, we extend this analysis to the other known structure of Kir2.2 that is closer to the open state of Kir2.2 channels (3SPI) and provide additional analysis of the residue distances between the uncoupled residues and cholesterol binding domains in the two conformation states of the channels. We found that the general phenomenon of cholesterol binding leading to uncoupling between specific residues is conserved in both channel states but the specific pattern of the uncoupling residues is distinct between the two states and implies different mechanisms. Specifically, we found that cholesterol binding in the 3SPI state results in an uncoupling of residues in three distinct regions; the transmembrane domain, membrane-cytosolic interface, and the cytosolic domain, with the first two regions forming an envelope around PI(4,5)P2 and cholesterol binding sites and the distal region overlapping with the subunit-subunit interface characterized in our previous study of the disengaged state. We also found that this uncoupling is dependent upon the number of cholesterol molecules bound to the channel. We further generated a mutant channel Kir2.2^P187V with a single point mutation in a residue proximal to the PI(4,5)P2 binding site, which is predicted to be uncoupled from other residues in its vicinity upon cholesterol binding and found that this mutation abrogates the sensitivity of Kir2.2 to cholesterol changes in the membrane. These findings suggest that cholesterol binding to this conformation state of Kir2.2 channels may destabilize the PI(4,5)P2 interactions with the channels while in the disengaged state the destabilization occurs where the subunits interact. These findings give insight into the structural mechanistic basis for the functional effects of cholesterol binding to the Kir2.2 channel.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108091"},"PeriodicalIF":3.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140622003","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}

{"title":"An electrostatic cluster guides Aβ40 fibril formation in sporadic and Dutch-type cerebral amyloid angiopathy","authors":"Ziao Fu ,&nbsp;Elliot J. Crooks ,&nbsp;Brandon A. Irizarry ,&nbsp;Xiaoyue Zhu ,&nbsp;Saikat Chowdhury ,&nbsp;William E. Van Nostrand ,&nbsp;Steven O. Smith","doi":"10.1016/j.jsb.2024.108092","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108092","url":null,"abstract":"<div><p>Cerebral amyloid angiopathy (CAA) is associated with the accumulation of fibrillar Aβ peptides upon and within the cerebral vasculature, which leads to loss of vascular integrity and contributes to disease progression in Alzheimer’s disease (AD). We investigate the structure of human-derived Aβ40 fibrils obtained from patients diagnosed with sporadic or familial Dutch-type (E22Q) CAA. Using cryo-EM, two primary structures are identified containing elements that have not been observed in <em>in vitro</em> Aβ40 fibril structures. One population has an ordered N-terminal fold comprised of two β-strands stabilized by electrostatic interactions involving D1, E22, D23 and K28. This charged cluster is disrupted in the second population, which exhibits a disordered N-terminus and is favored in fibrils derived from the familial Dutch-type CAA patient. These results illustrate differences between human-derived CAA and AD fibrils, and how familial CAA mutations can guide fibril formation.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108092"},"PeriodicalIF":3.0,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000327/pdfft?md5=40eb245f121be7c4952bc3bc62c89872&pid=1-s2.0-S1047847724000327-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140606585","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}

{"title":"Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis","authors":"Sergio Aguirre-Sampieri ,&nbsp;Ana Casañal ,&nbsp;Paul Emsley ,&nbsp;Georgina Garza-Ramos","doi":"10.1016/j.jsb.2024.108093","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108093","url":null,"abstract":"<div><p>Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from <em>Rhodococcus</em> sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108093"},"PeriodicalIF":3.0,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000339/pdfft?md5=47ad576135cc948b9dab3bbfca52d616&pid=1-s2.0-S1047847724000339-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140606584","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}

{"title":"Corrigendum to “Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap” [J. Struct. Biol. 215 (2023) 107982]","authors":"Peter Kirchweger ,&nbsp;Debakshi Mullick ,&nbsp;Prabhu Prasad Swain ,&nbsp;Sharon G. Wolf ,&nbsp;Michael Elbaum","doi":"10.1016/j.jsb.2024.108085","DOIUrl":"https://doi.org/10.1016/j.jsb.2024.108085","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 2","pages":"Article 108085"},"PeriodicalIF":3.0,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S104784772400025X/pdfft?md5=42332a4dd8dca3ab8b5fc14f9edabd5e&pid=1-s2.0-S104784772400025X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330754","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}