Acta Crystallographica Section A Foundations and Advances最新文献

{"title":"Aspherical scattering factors from multipole model for X-ray and electron crystallography","authors":"Paulina M. Dominiak","doi":"10.1107/s2053273323097966","DOIUrl":"https://doi.org/10.1107/s2053273323097966","url":null,"abstract":"To interpret experimental diffraction data","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the role of a highly conserved tryptophan in the copper-binding site of Bacillus subtilis YcnI protein","authors":"Yuri R. O. Silva, Dia Zheng, Oriana S. Fisher, Stephen C. Peters","doi":"10.1107/s2053273323096432","DOIUrl":"https://doi.org/10.1107/s2053273323096432","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A modular covalent labeling system for ground-truth localization of synaptic proteins by cryo-electron tomography","authors":"Richard Held, Maia Azubel, Jiahao Liang, Axel T Brunger","doi":"10.1107/s2053273323097851","DOIUrl":"https://doi.org/10.1107/s2053273323097851","url":null,"abstract":"Neuronal synapses are micron sized cell-cell contacts that serve as sites of information transfer in the nervous system. Single synapses are densely crowded, with thousands of proteins taking part in dozens of signaling pathways. To regulate sensitivity, selectivity, and crosstalk between these pathways, synapses control the nanometer-scale topography of their proteome. Cryo - electron tomography (cryoET) — in combination with focused ion beam milling and sub-tomogram averaging — is a powerful technique to determine in situ protein structures. The positions and orientations of particles contributing to the averaged structure can then be mapped back to the original tomogram to gain insight into protein topography. However, synapses and other crowded cellular environments present challenges to accurately identifying a protein of interest. This is further exacerbated by the presence of structurally similar non -target proteins and the low resolution of individual subtomogram volumes. To realize the potential of cryoET for visualization of nanoscale protein topography, we have developed a modular system to covalently label endogenously-expressed membrane proteins with gold nanoparticles (AuNPs). AuNPs are homogenous, can be tuned in size, and are amenable to monomeric functionalization to target extracellular terminal ends or loops. We apply our labeling system to localize AMPA-type glutamate receptors within tomograms of neuronal synapses, revealing a distinctive clustered receptor topography with defined offsets from sites of neurotransmitter release. Furthermore, our system facilitates in situ quantification of receptor copy number and subunit stoichiometry— hallmarks of visual proteomics—and enables accurate particle picking for subsequent sub-tomogram averaging of receptors and associated scaffolding proteins. Our method is broadly applicable to target proteins with extracellular epitopes, can be readily implemented in most wetlabs, and should enhance cryoET as a method for both in situ structural biology and the mapping of nanoscale","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of a 10-23 deoxyribozyme captured in a precatalytic state","authors":"Evan R. Cramer, Sarah A. Starcovic, A. Robart","doi":"10.1107/s2053273323099217","DOIUrl":"https://doi.org/10.1107/s2053273323099217","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The use of CheckMyMetal for modeling metal binding sites in low-resolution protein structures","authors":"Michael Gucwa, Joanna Lenkiewicz, Michal Szcygiel, Aziza Aripova, Wladek Minor","doi":"10.1107/s2053273323096171","DOIUrl":"https://doi.org/10.1107/s2053273323096171","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA crystal improvement with definitive screening designs","authors":"B. Venkataramany, Francis A. Acquah, Syed A. Aslam, Charles W. Carter, Jr, B. Mooers","doi":"10.1107/s2053273323099448","DOIUrl":"https://doi.org/10.1107/s2053273323099448","url":null,"abstract":"When one or more crystallization leads have been obtained from prior knowledge or sparse matrix screening, the next step is determining which experimental factors are essential for crystal growth. This task is often done by varying one or two factors with evenly spaced factor levels, often at great expense in time and material. The Design of Experiments (DOE) approach offers experimental designs that can simultaneously vary from three to many factors with a relatively small number of samples. However, the interpretation of the results requires the fitting of linear models. Traditional DOE screening designs include two - level fractional factorials (introduced to protein crystallography by Carter and Carter in 1979) and optimal experimental designs where three or more factors are varied (introduced to protein crystallography by Carter and Yin in 1994). Most factors in vapor diffusion experim ents cause a non-linear response in crystal quality and size. The non -linear respo nse requires three factor levels to be detected. The newer Definitive Screening Designs (DSDs) have three factor levels (Jones and Nachtsheim 2011). We were attracted to DSDs because t hey require roughly half the samples the corresponding optimal designs require. Here, we apply these designs to identify essential factors in the crystallization of several RNAs to optimize crystal size fo r single-crystal diffraction studies with synchrotron radiation. We used the hanging drop method for crystallization by vapor diffusion. We used the longest dimension of the largest crystal in a drop as our response variable. We used Response Surface Methodology (R SM) to identify the active factors in DSD experiments with 3 to 8 factors. The DSD experiments enabled us to elim inate the unimportant factors from downstream crystal size optimization experiments, saving us time and material. We envision an efficient workflow in which we screen experimental factors by using a DSD after sparse matrix screening and before optimizing the factors' levels with an optimal design or grid screens. After optimization, we replicate","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"X-ray restrained wavefunction approach: latest achievements and future challenges","authors":"A. Genoni","doi":"10.1107/s2053273323099795","DOIUrl":"https://doi.org/10.1107/s2053273323099795","url":null,"abstract":"Nowadays, quantum crystallography can be considered as an emerging field of science with the aim of investigating properties and phenomena of the crystalline state that can be explained only through the laws of quantum mechanics [1]. To achieve this goal, several techniques have been proposed over the years [2,3]. Among them it is worth mentioning the multipole models for the determination of experimental electron densities from X-ray diffraction data [4], but also the more modern Hirshfeld atom refinement (HAR) [5] and Xray restrained wavefunction (XRW) [6] methods, which are two approaches strongly based on the traditional methods of quantum chemistry. Here the focus will be on the XRW strategy, a technique that has the objective of determining wavefunctions that not only minimize the electronic energy of the investigated system but that also simultaneously maximize the agreement between calculated and experimental X-ray structure factor amplitudes. Initially proposed at Hartree-Fock level [6], the method has recently known a broad and rapid development through the extension of the formalism to other kind of wavefunction ansatz [7-10]. Moreover, different groups have also extensively studied and proved the capabilities of the X-ray restrained wavefunction technique in successfully extracting electron correlation and crystal effects on the electron density [11,12]. These results paved the way towards the possible future exploitation of the XRW method in the framework of density functional theory (DFT). In the first part of the presentation, a general overview of the X-ray restrained wavefunction approach will be given, with a particular emphasis on the more recent multi-determinant XRW strategies [9,10], which are strictly rooted in valence bond theory and allowed the extraction of chemically meaningful information from X-ray diffraction experiments. The focus will afterwards shift to the investigations that were conducted to assess to what extent the XRW method can capture electron correlation and crystal effects intrinsically included in theoretically generated or experimental X-ray diffraction data [11,12]. Starting from those results, the first attempts of extracting DFT exchange-correlation potentials through inversion of the X-ray restrained wavefunction equations will be also shown. Moreover, future directions of the ongoing work will be discussed.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"C—H...O bonds involving Trp sidechain in protein structures","authors":"Michal Szczygiel, Wladek Minor, Zygmunt Derewenda","doi":"10.1107/s2053273323099540","DOIUrl":"https://doi.org/10.1107/s2053273323099540","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and biophysical characterization of the Vibrio cholerae ferrous iron transport protein B (FeoB)","authors":"Mark A. Lee, Aaron T. Smith","doi":"10.1107/s2053273323096572","DOIUrl":"https://doi.org/10.1107/s2053273323096572","url":null,"abstract":"The acquisition and transport of ferrous iron (Fe2+) is essential for the survival and the virulence of many infectious prokaryotes. While bacteria possess several methods to acquire Fe2+, the ferrous iron transport (Feo) system is the most important Fe2+ transport complex, and the Feo system has strong ties to bacterial pathogenesis. The most conserved component of the Feo system is FeoB, a polytopic transmembrane protein containing a soluble N-terminal domain (termed NFeoB) that has been shown to have GTP hydrolysis activity. Intriguingly, some studies have revealed that a select number of FeoBs hydrolyze both GTP and ATP, making them NTPases rather than strict GTPases. While sequence analyses suggest key differences between GTPase and NTPase FeoBs, there is a lack of structural information defining the nucleotide promiscuity of these G-protein like domains. In this work, we report the crystallization of apo Vibrio cholerae NFeoB (VcNFeoB), which was previously defined as an NTPase. Comparisons to other GTPase and NTPase type NFeoBs reveal key differences that are hypothesized to play a role in nucleotide discrimination. These results give insight into ferrous iron acquisition of this problematic pathogen, which could be leveraged for future therapeutic developments.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An automated approach to MicroED enables structure determination of complex samples","authors":"J. Unge, Jieye Lin, Sara J. Weaver, Callie Saeher, Tamir Gonen","doi":"10.1107/s2053273323098273","DOIUrl":"https://doi.org/10.1107/s2053273323098273","url":null,"abstract":"One of the advantages of MicroED is that a structure can be determined from a few submicro-meter sized crystals only. Nevertheless, collecting a large number of data sets can improve the data substantially in cases where diffraction is not ideal, or the sample contains several compounds. An automated approach to MicroED is presented using the commonly used SerialEM software. This allows unattended data collection after initial setup of typically 1000 data sets per day, where typically 20-30 data sets would be collected manually. Also, a MicroED accostumized processing pipeline that includes all steps from image conversion and data processing to structure determination is presented. The processing pipeline EffortLess merges the successful data sets in any useful combination and finally the structure or the best merged data is presented. The protocols and pipelines together with examples and applications of using an automated approach to MicroED is presented.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}