Journal of Structural Biology: X最新文献

{"title":"Nucleic acid–protein interfaces studied by MAS solid-state NMR spectroscopy","authors":"Philipp Innig Aguion ,&nbsp;Alexander Marchanka ,&nbsp;Teresa Carlomagno","doi":"10.1016/j.yjsbx.2022.100072","DOIUrl":"10.1016/j.yjsbx.2022.100072","url":null,"abstract":"<div><p>Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid–protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid–protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid–protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA–protein complex that has been determined from ssNMR-derived intermolecular restraints.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100072"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a2/10/main.PMC9449856.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33459847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hierarchical organization of bone in three dimensions: A twist of twists","authors":"Daniel J. Buss ,&nbsp;Roland Kröger ,&nbsp;Marc D. McKee ,&nbsp;Natalie Reznikov","doi":"10.1016/j.yjsbx.2021.100057","DOIUrl":"10.1016/j.yjsbx.2021.100057","url":null,"abstract":"<div><p>Structural hierarchy of bone – observed across multiple scales and in three dimensions (3D) – is essential to its mechanical performance. While the mineralized extracellular matrix of bone consists predominantly of carbonate-substituted hydroxyapatite, type I collagen fibrils, water, and noncollagenous organic constituents (mainly proteins and small proteoglycans), it is largely the 3D arrangement of these inorganic and organic constituents at each length scale that endow bone with its exceptional mechanical properties. Focusing on recent volumetric imaging studies of bone at each of these scales – from the level of individual mineralized collagen fibrils to that of whole bones – this graphical review builds upon and re-emphasizes the original work of James Bell Pettigrew and D’Arcy Thompson who first described the ubiquity of spiral structure in Nature. Here we illustrate and discuss the omnipresence of twisted, curved, sinusoidal, coiled, spiraling, and braided motifs in bone in at least nine of its twelve hierarchical levels – a visualization undertaking that has not been possible until recently with advances in 3D imaging technologies (previous 2D imaging does not provide this information). From this perspective, we hypothesize that the twisting motif occurring across each hierarchical level of bone is directly linked to enhancement of function, rather than being simply an energetically favorable way to assemble mineralized matrix components. We propose that attentive consideration of twists in bone and the skeleton at different scales will likely develop, and will enhance our understanding of structure–function relationships in bone.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100057"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2d/5c/main.PMC8762463.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39716021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conformational switches that control the TEC kinase – PLCγ signaling axis","authors":"Jacques Lowe,&nbsp;Raji E. Joseph,&nbsp;Amy H. Andreotti","doi":"10.1016/j.yjsbx.2022.100061","DOIUrl":"10.1016/j.yjsbx.2022.100061","url":null,"abstract":"<div><p>Cell surface receptors such as the T-cell receptor (TCR) and B-cell receptor (BCR) engage with external stimuli to transmit information into the cell and initiate a cascade of signaling events that lead to gene expression that drives the immune response. At the heart of controlling T- and B-cell cell signaling, phospholipase Cγ hydrolyzes membrane associated PIP₂, leading to generation of the second messengers IP₃ and DAG. These small molecules trigger mobilization of intracellular Ca²⁺ and promote transcription factor transport into the nucleus launching the adaptive immune response. The TEC family kinases are responsible for phosphorylating and activating PLCγ, and our group aims to understand mechanisms that regulate immune cell signal transduction by focusing on this kinase/phospholipase axis in T-cells and B-cells. Here, we review the current molecular level understanding of how the TEC kinases (ITK and BTK) and PLCγ1/2 are autoinhibited prior to activation of cell surface receptors, how TEC kinases are activated to specifically recognize the PLCγ substrate, and how conformational changes induced by phosphorylation trigger PLCγ activation.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100061"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8803661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39772131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural plasticity in the loop region of engineered lipocalins with novel ligand specificities, so-called Anticalins","authors":"S. Achatz,&nbsp;A. Jarasch,&nbsp;A. Skerra","doi":"10.1016/j.yjsbx.2021.100054","DOIUrl":"10.1016/j.yjsbx.2021.100054","url":null,"abstract":"<div><p>Anticalins are generated via combinatorial protein design on the basis of the lipocalin protein scaffold and constitute a novel class of small and robust engineered binding proteins that offer prospects for applications in medical therapy as well as <em>in vivo</em> diagnostics as an alternative to antibodies. The lipocalins are natural binding proteins with diverse ligand specificities which share a simple architecture with a central eight-stranded antiparallel β-barrel and an α-helix attached to its side. At the open end of the β-barrel, four structurally variable loops connect the β-strands in a pair-wise manner and, together, shape the ligand pocket. Using targeted random mutagenesis in combination with molecular selection techniques, this loop region can be reshaped to generate pockets for the tight binding of various ligands ranging from small molecules over peptides to proteins. While such Anticalin proteins can be derived from different natural lipocalins, the human lipocalin 2 (Lcn2) scaffold proved particularly successful for the design of binding proteins with novel specificities and, over the years, more than 20 crystal structures of Lcn2-based Anticalins have been elucidated. In this graphical structural biology review we illustrate the conformational variability that emerged in the loop region of these functionally diverse artificial binding proteins in comparison with the natural scaffold. Our present analysis provides picturesque evidence of the high structural plasticity around the binding site of the lipocalins which explains the proven tolerance toward excessive mutagenesis, thus demonstrating remarkable resemblance to the complementarity-determining region of antibodies (immunoglobulins).</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100054"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d9/65/main.PMC8693463.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtomogram analysis: The sum of a tomogram’s particles reveals molecular structure in situ","authors":"Friedrich Förster","doi":"10.1016/j.yjsbx.2022.100063","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2022.100063","url":null,"abstract":"<div><p>Cryo-electron tomography is uniquely suited to provide insights into the molecular architecture of cells and tissue in the native state. While frozen hydrated specimens tolerate sufficient electron doses to distinguish different types of particles in a tomogram, the accumulating beam damage does not allow resolving their detailed molecular structure individually. Statistical methods for subtomogram averaging and classification that coherently enhance the signal of particles corresponding to copies of the same type of macromolecular allow obtaining much higher resolution insights into macromolecules. Here, I review the developments in subtomogram analysis at Wolfgang Baumeister’s laboratory that make the dream of structural biology in the native cell become reality.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100063"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152422000046/pdfft?md5=609a521d1a590ad494462d2a057cfdd3&pid=1-s2.0-S2590152422000046-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72075253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtomogram averaging for biophysical analysis and supramolecular context","authors":"Lauren Ann Metskas ,&nbsp;Rosalie Wilfong ,&nbsp;Grant J. Jensen","doi":"10.1016/j.yjsbx.2022.100076","DOIUrl":"10.1016/j.yjsbx.2022.100076","url":null,"abstract":"<div><p>Recent advances in hardware, software and computing power have led to increasingly ambitious applications of cryo-electron tomography and subtomogram averaging. It is now possible to reveal both structures and biophysical relationships like protein binding partners and small molecule occupancy in these experiments. However, some data processing choices require the user to prioritize structure or biophysical context. Here, we present a modified subtomogram averaging approach that preserves both capabilities. By increasing the accuracy of particle-picking, performing alignment and averaging on all subtomograms, and decreasing reliance on symmetry and tight masks, the usability of tomography and subtomogram averaging data for biophysical analyses is greatly increased without negatively impacting structural refinements.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100076"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/01/ea/main.PMC9596874.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10644661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological solid-state NMR: Integrative across different scientific disciplines","authors":"Marc Baldus","doi":"10.1016/j.yjsbx.2022.100075","DOIUrl":"10.1016/j.yjsbx.2022.100075","url":null,"abstract":"<div><p>For almost five decades, solid-state NMR (ssNMR) has been used to study complex biomolecular systems. This article gives a view on how ssNMR methods and applications have evolved during this time period in a broader structural biology context. It also discusses possible directions for additional developments and the future role of ssNMR in a life science context and beyond.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100075"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9523391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40389445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does dentine mineral change with anatomical location, microscopic site and patient age?","authors":"Arosha T. Weerakoon ,&nbsp;Crystal Cooper ,&nbsp;Ian A. Meyers ,&nbsp;Nicholas Condon ,&nbsp;Christopher Sexton ,&nbsp;David Thomson ,&nbsp;Pauline J. Ford ,&nbsp;Anne L. Symons","doi":"10.1016/j.yjsbx.2022.100060","DOIUrl":"10.1016/j.yjsbx.2022.100060","url":null,"abstract":"<div><h3>Objective</h3><p>To determine the effect of patient age (young or mature), anatomical location (shallow/deep and central/peripheral) and microscopic site (intertubular/peritubular) on dentine mineral density, distribution and composition.</p></div><div><h3>Methods</h3><p>Extracted posterior teeth from young (aged 19–20 years, N = 4) and mature (aged 54–77 years, N = 4) subjects were prepared to shallow and deep slices. The dentine surface elemental composition was investigated in a SEM using Backscattered Electron (BSE) micrographs, Energy Dispersive X-ray Spectroscopy, and Integrated Mineral Analysis. Qualitative comparisons and quantitative measures using machine learning were used to analyse the BSE images. Quantitative outcomes were compared using quantile or linear regression models with bootstrapping to account for the multiple measures per sample. Subsequently, a Xenon Plasma Focussed Ion Beam Scanning Electron Microscopy (Xe PFIB-SEM) was used to mill large area (100 µm) cross-sections to investigate morphology through the dentine tubules using high resolution secondary electron micrographs.</p></div><div><h3>Results</h3><p>With age, dentine mineral composition remains stable, but density changes with anatomical location and microscopic site. Microscopically, accessory tubules spread into intertubular dentine (ITD) from the main tubule lumens. Within the lumens, mineral deposits form calcospherites in the young that eventually coalesce in mature tubules and branches. The mineral occlusion in mature dentine increases overall ITD density to reflect peritubular dentine (PTD) infiltrate. The ITD observed in micrographs remained consistent for age and observation plane to suggest tubule deposition affects overall dentine density. Mineral density depends on the relative distribution of PTD to ITD that varies with anatomical location.</p></div><div><h3>Significance</h3><p>Adhesive materials may interact differently within a tooth as well as in different age groups.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100060"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/91/16/main.PMC8818708.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39613919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multimodal imaging reveals membrane skeleton reorganisation during reticulocyte maturation and differences in dimple and rim regions of mature erythrocytes","authors":"Adam J. Blanch ,&nbsp;Juan Nunez-Iglesias ,&nbsp;Arman Namvar ,&nbsp;Sebastien Menant ,&nbsp;Oliver Looker ,&nbsp;Vijay Rajagopal ,&nbsp;Wai-Hong Tham ,&nbsp;Leann Tilley ,&nbsp;Matthew W.A. Dixon","doi":"10.1016/j.yjsbx.2021.100056","DOIUrl":"10.1016/j.yjsbx.2021.100056","url":null,"abstract":"<div><p>The red blood cell (RBC) is remarkable in its ability to deform as it passages through the vasculature. Its deformability derives from a spectrin-actin protein network that supports the cell membrane and provides strength and flexibility, however questions remain regarding the assembly and maintenance of the skeletal network. Using scanning electron microscopy (SEM) and atomic force microscopy (AFM) we have examined the nanoscale architecture of the cytoplasmic side of membrane discs prepared from reticulocytes and mature RBCs. Immunofluorescence microscopy was used to probe the distribution of spectrin and other membrane skeleton proteins. We found that the cell surface area decreases by up to 30% and the spectrin-actin network increases in density by approximately 20% as the reticulocyte matures. By contrast, the inter-junctional distance and junctional density increase only by 3–4% and 5–9%, respectively. This suggests that the maturation-associated reduction in surface area is accompanied by an increase in spectrin self-association to form higher order oligomers. We also examined the mature RBC membrane in the edge (rim) and face (dimple) regions of mature RBCs and found the rim contains about 1.5% more junctional complexes compared to the dimple region. A 2% increase in band 4.1 density in the rim supports these structural measurements.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100056"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/3d/main.PMC8688873.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39780147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In-cell DNP NMR reveals multiple targeting effect of antimicrobial peptide","authors":"Frances Separovic ,&nbsp;Vinzenz Hofferek ,&nbsp;Anthony P. Duff ,&nbsp;Malcom J. McConville ,&nbsp;Marc-Antoine Sani","doi":"10.1016/j.yjsbx.2022.100074","DOIUrl":"10.1016/j.yjsbx.2022.100074","url":null,"abstract":"<div><p>Dynamic nuclear polarization NMR spectroscopy was used to investigate the effect of the antimicrobial peptide (AMP) maculatin 1.1 on <em>E. coli</em> cells. The enhanced ¹⁵N NMR signals from nucleic acids, proteins and lipids identified a number of unanticipated physiological responses to peptide stress, revealing that membrane-active AMPs can have a multi-target impact on <em>E. coli</em> cells. DNP-enhanced ¹⁵N-observed ³¹P-dephased REDOR NMR allowed monitoring how Mac1 induced DNA condensation and prevented intermolecular salt bridges between the main <em>E. coli</em> lipid phosphatidylethanolamine (PE) molecules. The latter was supported by similar results obtained using <em>E. coli</em> PE lipid systems. Overall, the ability to monitor the action of antimicrobial peptides <em>in situ</em> will provide greater insight into their mode of action.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100074"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2c/60/main.PMC9486116.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33478817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}