Journal of Structural Biology: X最新文献

{"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":null,"pages":null},"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":"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":null,"pages":null},"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}

{"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":null,"pages":null},"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":null,"pages":null},"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":"Recent advances in the structural biology of encapsulin bacterial nanocompartments","authors":"Timothy Wiryaman ,&nbsp;Navtej Toor","doi":"10.1016/j.yjsbx.2022.100062","DOIUrl":"10.1016/j.yjsbx.2022.100062","url":null,"abstract":"<div><p>Large capsid-like nanocompartments called encapsulins are common in bacteria and archaea and contain cargo proteins with diverse functions. Advances in cryo-electron microscopy have enabled structure determination of many encapsulins in recent years. Here we summarize findings from recent encapsulin structures that have significant implications for their biological roles. We also compare important features such as the E-loop, cargo-peptide binding site, and the fivefold axis channel in different structures. In addition, we describe the discovery of a flavin-binding pocket within the encapsulin shell that may reveal a role for this nanocompartment in iron metabolism.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"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/6d/f3/main.PMC8802124.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10643654","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":"Colloid assembly and transformation (CAT): The relationship of PILP to biomineralization","authors":"Laurie Gower,&nbsp;Jeremy Elias","doi":"10.1016/j.yjsbx.2021.100059","DOIUrl":"10.1016/j.yjsbx.2021.100059","url":null,"abstract":"<div><p>The field of biomineralization has undergone a revolution in the past 25 years, which paralleled the discovery by Gower of a polymer-induced liquid-precursor (PILP) mineralization process. She proposed this <em>in vitro</em> model system might be useful for studying the role biopolymers play in biomineralization; however, the ramifications of this pivotal discovery were slow to be recognized. This was presumably because it utilized simple polypeptide additives, and at that time it was not recognized that the charged proteins intimately associated with biominerals are often intrinsically disordered proteins (IDPs). Over the years, many enigmatic biomineral features have been emulated with this model system, too many to be mere coincidence. Yet the PILP system continues to be underacknowledged, probably because of its namesake, which indicates a “liquid precursor”, while we now know the phase appears to have viscoelastic character. Another factor is the confusing semantics that arose from the discovery of multiple “non-classical crystallization” pathways. This review suggests a more relevant terminology for the polymer-modulated reactions is “colloid assembly and transformation (CAT)”, which we believe more accurately captures the key stages involved in both biomineralization and the PILP process. The PILP model system has helped to decipher the key role that biopolymers, namely the IDPs, play in modulating biomineralization processes, which was not readily accomplished in living biological systems. Some remaining challenges in understanding the organic–inorganic interactions involved in biomineralization are discussed, which further highlight how the PILP model system may prove invaluable for studying the simple, yet complex, CAT crystallization pathway.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"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/4a/88/main.PMC8749173.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39688133","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":"AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction","authors":"Shawn Zheng ,&nbsp;Georg Wolff ,&nbsp;Garrett Greenan ,&nbsp;Zhen Chen ,&nbsp;Frank G.A. Faas ,&nbsp;Montserrat Bárcena ,&nbsp;Abraham J. Koster ,&nbsp;Yifan Cheng ,&nbsp;David A. Agard","doi":"10.1016/j.yjsbx.2022.100068","DOIUrl":"10.1016/j.yjsbx.2022.100068","url":null,"abstract":"<div><p>AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ± 80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"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/d4/bb/main.PMC9117686.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9901772","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":"Hydrogens and hydrogen-bond networks in macromolecular MicroED data","authors":"Max T.B. Clabbers ,&nbsp;Michael W. Martynowycz ,&nbsp;Johan Hattne ,&nbsp;Tamir Gonen","doi":"10.1016/j.yjsbx.2022.100078","DOIUrl":"10.1016/j.yjsbx.2022.100078","url":null,"abstract":"<div><p>Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the <em>ab initio</em> structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9731847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10779799","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":"SAA fibrils involved in AA amyloidosis are similar in bulk and by single particle reconstitution: A MAS solid-state NMR study","authors":"Arpita Sundaria ,&nbsp;Falk Liberta ,&nbsp;Dilan Savran ,&nbsp;Riddhiman Sarkar ,&nbsp;Natalia Rodina ,&nbsp;Carsten Peters ,&nbsp;Nadine Schwierz ,&nbsp;Christian Haupt ,&nbsp;Matthias Schmidt ,&nbsp;Bernd Reif","doi":"10.1016/j.yjsbx.2022.100069","DOIUrl":"10.1016/j.yjsbx.2022.100069","url":null,"abstract":"<div><p>AA amyloidosis is one of the most prevalent forms of systemic amyloidosis and affects both humans and other vertebrates. In this study, we compare MAS solid-state NMR data with a recent cryo-EM study of fibrils involving full-length murine SAA1.1. We address the question whether the specific requirements for the reconstitution of an amyloid fibril structure by cryo-EM can potentially yield a bias towards a particular fibril polymorph. We employ fibril seeds extracted from <em>in to vivo</em> material to imprint the fibril structure onto the biochemically produced protein. Sequential assignments yield the secondary structure elements in the fibril state. Long-range DARR and PAR experiments confirm largely the topology observed in the <em>ex-vivo</em> cryo-EM study. We find that the β-sheets identified in the NMR experiments are similar to the β-sheets found in the cryo-EM study, with the exception of amino acids 33–42. These residues cannot be assigned by solid-state NMR, while they adopt a stable β-sheet in the cryo-EM structure. We suggest that the differences between MAS solid-state NMR and cryo-EM data are a consequence of a second conformer involving residues 33–42. Moreover, we were able to characterize the dynamic C-terminal tail of SAA in the fibril state. The C-terminus is flexible, remains detached from the fibrils, and does not affect the SAA fibril structure as confirmed further by molecular dynamics simulations. As the C-terminus can potentially interact with other cellular components, binding to cellular targets can affect its accessibility for protease digestion.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"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/53/e2/main.PMC9340516.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40599857","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":"The role of C-terminal helix in the conformational transition of an arginine binding protein","authors":"Vinothini Santhakumar,&nbsp;Nahren Manuel Mascarenhas","doi":"10.1016/j.yjsbx.2022.100071","DOIUrl":"10.1016/j.yjsbx.2022.100071","url":null,"abstract":"<div><p>The <em>thermotoga maritima</em> arginine binding protein (TmArgBP) is a periplasmic binding protein that has a short helix at the C-terminal end (CTH), which is swapped between the two chains. We apply a coarse-grained structure-based model (SBM) and all-atom MD simulation on this protein to understand the mechanism and the role of CTH in the conformational transition. When the results of SBM simulations of TmArgBP in the presence and absence of CTH are compared, we find that CTH is strategically located at the back of the binding pocket restraining the open-state conformation thereby disengaging access to the closed-state. We also ran all-atom MD simulations of open-state TmArgBP with and without CTH and discovered that in the absence of CTH the protein could reach the closed-state within 250 ns, while in its presence, the protein remained predominantly in its open-state conformation. In the simulation started from unliganded closed-state conformation without CTH, the protein exhibited multiple transitions between the two states, suggesting CTH as an essential structural element to stabilize the open-state conformation. In another simulation that began with an unliganded closed-state conformation with CTH, the protein was able to access the open-state. In this simulation the CTH was observed to reorient itself to interact with the protein emphasizing its role in assisting the conformational change. Based on our findings, we believe that CTH not only acts as a structural element that constraints the protein in its open-state but it may also guide the protein back to its open-state conformation upon ligand unbinding.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9402392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33444617","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}