Journal of structural biology最新文献

{"title":"Exploring the folding landscape of leptin: Insights into threading pathways","authors":"Fernando Bruno da Silva ,&nbsp;Jennifer M. Simien ,&nbsp;Rafael G. Viegas ,&nbsp;Ellinor Haglund ,&nbsp;Vitor Barbanti Pereira Leite","doi":"10.1016/j.jsb.2023.108054","DOIUrl":"10.1016/j.jsb.2023.108054","url":null,"abstract":"<div><p><span><span>The discovery of new protein topologies with entanglements and loop-crossings have shown the impact of local </span>amino acid arrangement and global three-dimensional structures. This phenomenon plays a crucial role in understanding how protein structure relates to folding and function, affecting the global stability, and biological activity. Protein entanglements encompassing knots and non-trivial topologies add complexity to their folding free energy landscapes. However, the initial native contacts driving the threading event for entangled proteins remains elusive. The Pierced Lasso Topology (PLT) represents an entangled topology where a covalent linker creates a loop in which the polypeptide backbone is threaded through. Compared to true knotted topologies, PLTs are simpler topologies where the covalent-loop persists in all conformations. In this work, the PLT protein leptin, is used to visualize and differentiate the preference for slipknotting over plugging transition pathways along the folding route. We utilize the Energy Landscape Visualization Method (ELViM), a multidimensional projection technique, to visualize and distinguish early threaded conformations that cannot be observed in an </span><em>in vitro</em> experiment. Critical contacts for the leptin threading mechanisms were identified where the competing pathways are determined by the formation of a hairpin loop in the unfolded basin. Thus, prohibiting the dominant slipknotting pathway. Furthermore, ELViM offers insights into distinct folding pathways associated with slipknotting and plugging providing a novel tool for <em>de novo</em> design and <em>in vitro</em> experiments with residue specific information of threading events <em>in silico</em>.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108054"},"PeriodicalIF":3.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138520711","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":"Journal of Structural Biology – Paper of the Year 2022","authors":"Xinzheng Zhang","doi":"10.1016/j.jsb.2023.108032","DOIUrl":"10.1016/j.jsb.2023.108032","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108032"},"PeriodicalIF":3.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41176549","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":"The 3D organization of the mineralized scales of the sturgeon has structures reminiscent of dentin and bone: A FIB-SEM study","authors":"Joshua Milgram ,&nbsp;Katya Rehav ,&nbsp;Jamal Ibrahim ,&nbsp;Ron Shahar ,&nbsp;Stephen Weiner","doi":"10.1016/j.jsb.2023.108045","DOIUrl":"10.1016/j.jsb.2023.108045","url":null,"abstract":"<div><p>Scales are structures composed of mineralized collagen fibrils embedded in the skin of fish. Here we investigate structures contributing to the bulk of the scale material of the sturgeon (<em>Acipencer guldenstatii</em><span>) at the millimeter, micrometer and nanometer length scales. Polished and fracture surfaces were prepared in each of the three anatomic planes for imaging with light and electron microscopy<span><span>, as well as focused ion beam – scanning electron microscopy (FIB-SEM). The scale is composed of three layers, upper and lower layers forming the bulk of the scale, as well as a thin surface layer. </span>FTIR shows that the scale is composed mainly of collagen and carbonated hydroxyapatite. Lacunae are present throughout the structure. Fracture surfaces of all three layers are characterized by large diameter collagen fibril bundles (CFBs) emanating from a plane comprising smaller diameter CFBs orientated in different directions. Fine lineations seen in polished surfaces of both major layers are used to define planes called here the striation planes. FIB-SEM image stacks of the upper and lower layers acquired in planes aligned with the striation planes, show that CFBs are oriented in various directions within the striation plane, with larger CFBs emanating from the striation plane. Fibril bundles oriented in different directions in the same plane is reminiscent of a similar organization in orthodentin. The large collagen fibril bundles emanating out of this plane are analogous to von Korff fibrils found in developing dentin with respect to size and orientation. Scales of the sturgeon are unusual in that their mineralized collagen fibril organization contains structural elements of both dentin and bone. The sturgeon scale may be an example of an early evolved mineralized material which is neither bone nor dentin but contains characteristics of both materials, however, the fossil data required to confirm this is missing.</span></span></p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108045"},"PeriodicalIF":3.0,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136397922","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":"MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template","authors":"Gaoxin Hou ,&nbsp;Zhidong Yang ,&nbsp;Dawei Zang ,&nbsp;Jose-Jesus Fernández ,&nbsp;Fa Zhang ,&nbsp;Renmin Han","doi":"10.1016/j.jsb.2023.108044","DOIUrl":"10.1016/j.jsb.2023.108044","url":null,"abstract":"<div><p>Fiducial marker detection in electron micrographs becomes an important and challenging task with the development of large-field electron microscopy. The fiducial marker detection plays an important role in several steps during the process of electron micrographs, such as the alignment and parameter calibrations. However, limited by the conditions of low signal-to-noise ratio (SNR) in the electron micrographs, the performance of fiducial marker detection is severely affected. In this work, we propose the MarkerDetector, a novel algorithm for detecting fiducial markers in electron micrographs. The proposed MarkerDetector is built upon the following contributions: Firstly, a wavelet-based template generation algorithm is devised in MarkerDetector. By adopting a shape-based criterion, a high-quality template can be obtained. Secondly, a robust marker determination strategy is devised by utilizing statistic-based filtering, which can guarantee the correctness of the detected fiducial markers. The average running time of our algorithm is 1.67 seconds with promising accuracy, indicating its practical feasibility for applications in electron micrographs.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 1","pages":"Article 108044"},"PeriodicalIF":3.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134649182","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":"Classification of helical polymers with deep-learning language models","authors":"Daoyi Li,&nbsp;Wen Jiang","doi":"10.1016/j.jsb.2023.108041","DOIUrl":"10.1016/j.jsb.2023.108041","url":null,"abstract":"<div><p>Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classification methods are effective at separating particles of interest from contaminants, but they do not effectively differentiate between polymorphs, resulting in heterogeneity in the 2D classes. As such, it is crucial to develop a method that can computationally divide a dataset of polymorphic helical structures into homogenous subsets. In this work, we utilized deep-learning language models to embed the filaments as vectors in hyperspace and group them into clusters. Tests with both simulated and experimental datasets have demonstrated that our method – HLM (<strong>H</strong>elical classification with <strong>L</strong>anguage <strong>M</strong>odel) can effectively distinguish different types of filaments, in the presence of many contaminants and low signal-to-noise ratios. We also demonstrate that HLM can isolate homogeneous subsets of particles from a publicly available dataset, resulting in the discovery of a previously unreported filament variant with an extra density around the tau filaments.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108041"},"PeriodicalIF":3.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71521911","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":"From in-silico screening to in-vitro evaluation: Enhancing the detection of Microcystins with engineered PP1 mutant variants","authors":"Ezequiel J. Alba-Posse ,&nbsp;Carlos David Bruque ,&nbsp;Yamila Gándola ,&nbsp;Javier Gasulla ,&nbsp;Alejandro D. Nadra","doi":"10.1016/j.jsb.2023.108043","DOIUrl":"10.1016/j.jsb.2023.108043","url":null,"abstract":"<div><p>Cyanotoxins produced during harmful algal blooms (CyanoHABs) have become a worldwide issue of concern. Microcystins (MC) are the most ubiquitous group of cyanotoxins and have known carcinogenic and hepatotoxic effects. The protein phosphatase inhibition assays (PPIAs), based on the inhibition of Protein Phosphatase 1/2A (PP1/PP2A) by MC, are one of the most cost-effective options for detecting MC. In this work, we aimed to design <em>in-silico</em> and evaluate <em>in-vitro</em> mutant variants of the PP1 protein, in order to enhance their capabilities as a MC biosensor.</p><p>To this end, we performed an <em>in-silico</em> active site-saturated mutagenesis screening, followed by stability and docking affinity calculation with the MCLR cyanotoxin. Candidates with improved both affinity and stability were further tested in a fully flexible active-site docking. The best-scored mutations (19) were individually analysed regarding their locations and interactions. Four of them (p.D197F; p.Q249Y; p.S129W; p.D220Q) were selected for <em>in-vitro</em> expression and evaluation. Mutant p.D197F, exhibited a significant increment in inhibition by MCLR with respect to the WT, while showing a non-significant difference in stability nor activity. This successful PP1 inhibition enhancement suggests the potential of the p.D197F variant for practical MC detection applications.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108043"},"PeriodicalIF":3.0,"publicationDate":"2023-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71482870","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":"Predicting virus Fitness: Towards a structure-based computational model","authors":"Shivani Thakur ,&nbsp;Kasper Planeta Kepp ,&nbsp;Rukmankesh Mehra","doi":"10.1016/j.jsb.2023.108042","DOIUrl":"10.1016/j.jsb.2023.108042","url":null,"abstract":"<div><p>Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108042"},"PeriodicalIF":3.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71482871","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":"Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM","authors":"Mart G.F. Last ,&nbsp;Willem E.M. Noteborn ,&nbsp;Lenard M. Voortman ,&nbsp;Thomas H. Sharp","doi":"10.1016/j.jsb.2023.108040","DOIUrl":"10.1016/j.jsb.2023.108040","url":null,"abstract":"<div><p>Correlated super-resolution cryo-fluorescence and cryo-electron microscopy (cryoEM) has been gaining popularity as a method to investigate biological samples with high resolution and specificity. A concern in this combined method (called SR–cryoCLEM), however, is whether and how fluorescence imaging prior to cryoEM acquisition is detrimental to sample integrity. In this report, we investigated the effect of high-dose laser light (405, 488, and 561 nm) irradiation on apoferritin samples prepared for cryoEM with excitation wavelengths commonly used in fluorescence microscopy, and compared these samples to controls that were kept in the dark. We found that laser illumination, of equal duration and intensity as used in cryo-single molecule localization microscopy (cryoSMLM) and in the presence of high concentrations of fluorescent protein, did not affect the achievable resolution in cryoEM, with final reconstructions reaching resolutions of ∼ 1.8 Å regardless of the laser illumination. The finding that super-resolution fluorescence imaging of cryosamples prior to cryoEM data acquisition does not limit the achievable resolution suggests that super-resolution cryo-fluorescence microscopy and in situ structural biology using cryoEM are entirely compatible.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108040"},"PeriodicalIF":3.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S104784772300103X/pdfft?md5=ca38b0f0bb54e6b6b46ebbea157a82f8&pid=1-s2.0-S104784772300103X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71424505","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":"Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases","authors":"Quentin Bertrand ,&nbsp;Sandrine Coquille ,&nbsp;Antonio Iorio ,&nbsp;Fabio Sterpone ,&nbsp;Dominique Madern","doi":"10.1016/j.jsb.2023.108039","DOIUrl":"10.1016/j.jsb.2023.108039","url":null,"abstract":"<div><p>In this work, we investigated the lactate dehydrogenase (LDH) from <em>Selenomonas ruminantium</em> (<em>S. rum</em>), an enzyme that differs at key amino acid positions from canonical allosteric LDHs. The wild type (Wt) of this enzyme recognises pyuvate as all LDHs. However, introducing a single point mutation in the active site loop (I85R) allows <em>S. Rum</em> LDH to recognize the oxaloacetate substrate as a typical malate dehydrogenase (MalDH), whilst maintaining homotropic activation as an LDH. We report the tertiary structure of the Wt and I85R<!--> <!-->LDH mutant.</p><p>The Wt <em>S. rum</em> enzyme structure binds NADH and malonate, whilst also resembling the typical compact R-active state of canonical LDHs. The structure of the mutant with I85R was solved in the Apo State (without ligand), and shows no large conformational reorganization such as that observed with canonical allosteric LDHs in Apo state. This is due to a local structural feature typical of <em>S. rum</em> LDH that prevents large-scale conformational reorganization. The <em>S. rum</em> LDH was also studied using Molecular Dynamics simulations, probing specific local deformations of the active site that allow the <em>S. rum</em> LDH to sample the T-inactive state. We propose that, with respect to the LDH/MalDH superfamily, the <em>S. rum</em> enzyme possesses a specific<!--> <!-->structural and dynamical way to ensure homotropic activation.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108039"},"PeriodicalIF":3.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54229744","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":"Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG","authors":"José P. Leite ,&nbsp;Frederico Lourenço ,&nbsp;Rute Oliveira ,&nbsp;Sérgio F. Sousa ,&nbsp;Marta V. Mendes ,&nbsp;Luís Gales","doi":"10.1016/j.jsb.2023.108038","DOIUrl":"10.1016/j.jsb.2023.108038","url":null,"abstract":"<div><p>Transcription of specific genes in bacteria under environmental stress is frequently initiated by extracytoplasmic function (ECF) σ factors. ECFs σ factors harbour two conserved domains, σ₂ and σ₄, for transcription initiation by recognition of the promoter region and recruitment of RNA polymerase (RNAP). The crystal structure of <em>Streptomyces tsukubaensis</em> SigG1, an ECF56-family σ factor, was determined revealing σ₂, σ₄ and the additional carboxi-terminal domain SnoaL_2 tightly packed in a compact conformation. The structure of anti-sigma RsfG was also determined by X-ray crystallography and shows a rare β-barrel fold. Analysis of the metal binding motifs inside the protein barrel are consistent with Fe(III) binding, which is in agreement with previous findings that the <em>Streptomyces tsukubaensis</em> ECF56 SigG1-RsfG system is involved in metal-ion homeostasis.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"215 4","pages":"Article 108038"},"PeriodicalIF":3.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49678811","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}