Journal of Structural Biology: X最新文献_第6页

Recent advances in the structural biology of encapsulin bacterial nanocompartments 细菌纳米室的结构生物学研究进展

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100062

Timothy Wiryaman , Navtej Toor

引用次数: 3

Colloid assembly and transformation (CAT): The relationship of PILP to biomineralization 胶体组装和转化(CAT): PILP与生物矿化的关系

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2021.100059

Laurie Gower, Jeremy Elias

{"title":"Colloid assembly and transformation (CAT): The relationship of PILP to biomineralization","authors":"Laurie Gower, 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":"6 ","pages":"Article 100059"},"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}

引用次数: 5

Hydrogens and hydrogen-bond networks in macromolecular MicroED data 大分子MicroED数据中的氢和氢键网络

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100078

Max T.B. Clabbers , Michael W. Martynowycz , Johan Hattne , Tamir Gonen

{"title":"Hydrogens and hydrogen-bond networks in macromolecular MicroED data","authors":"Max T.B. Clabbers , Michael W. Martynowycz , Johan Hattne , 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":"6 ","pages":"Article 100078"},"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}

引用次数: 3

The role of C-terminal helix in the conformational transition of an arginine binding protein c端螺旋在精氨酸结合蛋白构象转变中的作用

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100071

Vinothini Santhakumar, Nahren Manuel Mascarenhas

{"title":"The role of C-terminal helix in the conformational transition of an arginine binding protein","authors":"Vinothini Santhakumar, 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":"6 ","pages":"Article 100071"},"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}

引用次数: 0

SAA fibrils involved in AA amyloidosis are similar in bulk and by single particle reconstitution: A MAS solid-state NMR study 参与AA淀粉样变性的SAA原纤维在体积和单颗粒重构方面相似:一项MAS固态核磁共振研究

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100069

Arpita Sundaria , Falk Liberta , Dilan Savran , Riddhiman Sarkar , Natalia Rodina , Carsten Peters , Nadine Schwierz , Christian Haupt , Matthias Schmidt , Bernd Reif

{"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 , Falk Liberta , Dilan Savran , Riddhiman Sarkar , Natalia Rodina , Carsten Peters , Nadine Schwierz , Christian Haupt , Matthias Schmidt , 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":"6 ","pages":"Article 100069"},"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}

引用次数: 0

Solid-state NMR analysis of unlabeled fungal cell walls from Aspergillus and Candida species 曲霉和念珠菌未标记真菌细胞壁的固态NMR分析

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100070

Liyanage D. Fernando , Malitha C. Dickwella Widanage , S. Chandra Shekar , Frederic Mentink-Vigier , Ping Wang , Sungsool Wi , Tuo Wang

{"title":"Solid-state NMR analysis of unlabeled fungal cell walls from Aspergillus and Candida species","authors":"Liyanage D. Fernando , Malitha C. Dickwella Widanage , S. Chandra Shekar , Frederic Mentink-Vigier , Ping Wang , Sungsool Wi , Tuo Wang","doi":"10.1016/j.yjsbx.2022.100070","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2022.100070","url":null,"abstract":"<div><p>Fungal infections cause high mortality in immunocompromised individuals, which has emerged as a significant threat to human health. The efforts devoted to the development of antifungal agents targeting the cell wall polysaccharides have been hindered by our incomplete picture of the assembly and remodeling of fungal cell walls. High-resolution solid-state nuclear magnetic resonance (ss NMR) studies have substantially revised our understanding of the polymorphic structure of polysaccharides and the nanoscale organization of cell walls in <em>Aspergillus fumigatus</em> and multiple other fungi. However, this approach requires <sup>13</sup>C/<sup>15</sup>N-enrichment of the sample being studied, severely restricting its application. Here we employ the dynamic nuclear polarization (DNP) technique to compare the unlabeled cell wall materials of <em>A. fumigatus</em> and <em>C. albicans</em> prepared using both liquid and solid media. For each fungus, we have identified a highly conserved carbohydrate core for the cell walls of conidia and mycelia, and from liquid and solid cultures. Using samples prepared in different media, the recently identified function of α-glucan, which packs with chitin to form the mechanical centers, has been confirmed through conventional ss NMR measurements of polymer dynamics. These timely efforts not only validate the structural principles recently discovered for <em>A. fumigatus</em> cell walls in different morphological stages, but also open up the possibility of extending the current investigation to other fungal materials and cellular systems that are challenging to label.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"6 ","pages":"Article 100070"},"PeriodicalIF":2.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152422000113/pdfft?md5=08b4743ce96c14d7bba9c36752d2ebfe&pid=1-s2.0-S2590152422000113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72075254","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}

引用次数: 10

AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction AreTomo:一个集成的软件包，用于自动无标记，运动校正冷冻电子断层扫描校准和重建

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100068

Shawn Zheng , Georg Wolff , Garrett Greenan , Zhen Chen , Frank G.A. Faas , Montserrat Bárcena , Abraham J. Koster , Yifan Cheng , David A. Agard

{"title":"AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction","authors":"Shawn Zheng , Georg Wolff , Garrett Greenan , Zhen Chen , Frank G.A. Faas , Montserrat Bárcena , Abraham J. Koster , Yifan Cheng , 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":"6 ","pages":"Article 100068"},"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}

引用次数: 42

Neurons as a model system for cryo-electron tomography 神经元作为低温电子断层扫描的模型系统

IF 2.9

Journal of Structural Biology: X Pub Date : 2022-01-01 DOI: 10.1016/j.yjsbx.2022.100067

Benoît Zuber , Vladan Lučić

引用次数: 3

Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM 单粒子低温电镜超分辨成像及放大倍率选择的实验评价

IF 2.9

Journal of Structural Biology: X Pub Date : 2021-01-01 DOI: 10.1016/j.yjsbx.2021.100047

J. Ryan Feathers , Katherine A. Spoth , J. Christopher Fromme

{"title":"Experimental evaluation of super-resolution imaging and magnification choice in single-particle cryo-EM","authors":"J. Ryan Feathers , Katherine A. Spoth , J. Christopher Fromme","doi":"10.1016/j.yjsbx.2021.100047","DOIUrl":"10.1016/j.yjsbx.2021.100047","url":null,"abstract":"<div><p>The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physical Nyquist limit by increasing sampling frequency, yet there are few reports of reconstructions that do so. Here we directly examine the contribution of super-resolution information, obtained with the K3 direct electron detector using a 2-condenser microscope, to single-particle cryo-EM reconstructions surpassing the physical Nyquist limit. We also present a comparative analysis of a sample imaged at four different magnifications. This analysis demonstrates that lower magnifications can be beneficial, despite the loss of higher resolution signal, due to the increased number of particle images obtained. To highlight the potential utility of lower magnification data collection, we produced a 3.5 Å reconstruction of jack bean urease with particles from a single micrograph.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"5 ","pages":"Article 100047"},"PeriodicalIF":2.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2021.100047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25576100","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}

引用次数: 8

Structural basis of enzyme activity regulation by the propeptide of l-lysine α-oxidase precursor from Trichoderma viride 绿色木霉l-赖氨酸α-氧化酶前体前体肽调节酶活性的结构基础

IF 2.9

Journal of Structural Biology: X Pub Date : 2021-01-01 DOI: 10.1016/j.yjsbx.2021.100044

Masaki Kitagawa , Nanako Ito , Yuya Matsumoto , Masaya Saito , Takashi Tamura , Hitoshi Kusakabe , Kenji Inagaki , Katsumi Imada

{"title":"Structural basis of enzyme activity regulation by the propeptide of l-lysine α-oxidase precursor from Trichoderma viride","authors":"Masaki Kitagawa , Nanako Ito , Yuya Matsumoto , Masaya Saito , Takashi Tamura , Hitoshi Kusakabe , Kenji Inagaki , Katsumi Imada","doi":"10.1016/j.yjsbx.2021.100044","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2021.100044","url":null,"abstract":"<div><p>Harmuful proteins are usually synthesized as inactive precursors and are activated by proteolytic processing. <span>l</span>-Amino acid oxidase (LAAO) is a flavoenzyme that catalyzes the oxidative deamination of <span>l</span>-amino acid to produce a 2-oxo acid with ammonia and highly toxic hydrogen peroxide and, therefore, is expressed as a precursor. The LAAO precursor shows significant variation in size and the cleavage pattern for activation. However, the molecular mechanism of how the propeptide suppresses the enzyme activity remains unclear except for deaminating/decarboxylating <em>Pseudomonas</em> <span>l</span>-phenylalanine oxidase (PAO), which has a short N-terminal propeptide composed of 14 residues. Here we show the inactivation mechanism of the <span>l</span>-lysine oxidase (LysOX) precursor (prLysOX), which has a long N-terminal propeptide composed of 77 residues, based on the crystal structure at 1.97 Å resolution. The propeptide of prLysOX indirectly changes the active site structure to inhibit the enzyme activity. prLysOX retains weak enzymatic activity with strict specificity for <span>l</span>-lysine and shows raised activity in acidic conditions. The structures of prLysOX crystals that soaked in a solution with various concentrations of <span>l</span>-lysine have revealed that prLysOX can adopt two conformations; one is the inhibitory form, and the other is very similar to mature LysOX. The propeptide region of the latter form is disordered, and <span>l</span>-lysine is bound to the latter form. These results indicate that prLysOX uses a different strategy from PAO to suppress the enzyme activity and suggest that prLysOX can be activated quickly in response to the environmental change without proteolytic processing.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"5 ","pages":"Article 100044"},"PeriodicalIF":2.9,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2021.100044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72075947","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}

引用次数: 5