Pub Date : 2024-02-05DOI: 10.1134/s106377452360093x
T. N. Safonova, A. N. Antipov, V. P. Veiko, N. N. Mordkovich, N. A. Okorokova, P. V. Dorovatovskii, K. M. Polyakov
Abstract
Crystals of the enzyme purine nucleoside phosphorylase from the extremophilic bacterium Halomonas Chromatireducens AGD 8-3, suitable for X-ray diffraction, were grown by the vapor-diffusion method. The X-ray diffraction data were collected from these crystals at the Belok beamline of the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”) at 100 K to 1.80 Å resolution. The X-ray diffraction data were processed in the space groups P1, P2, P21, and P622. The structure was solved by the molecular replacement method taking into account the twinning in the space groups P21 and P1 with one and two hexamers of the enzyme per asymmetric unit, respectively.
摘要通过蒸发扩散法从嗜极细菌 Halomonas Chromatireducens AGD 8-3 中生长出适合 X 射线衍射的嘌呤核苷磷酸化酶晶体。这些晶体的 X 射线衍射数据是在库尔恰托夫同步辐射源（国家研究中心 "库尔恰托夫研究所"）的 Belok 光束线以 100 K 的分辨率 1.80 Å 采集的。X 射线衍射数据在空间群 P1、P2、P21 和 P622 中进行了处理。考虑到 P21 和 P1 空间群中的孪生结构，每个不对称单元分别有一个和两个酶的六聚体，因此采用分子置换法对该结构进行了求解。
{"title":"Preliminary X-ray Diffraction Analysis of Purine Nucleoside Phosphorylase from the Haloalkaliphilic Bacterium Halomonas chromatireducens","authors":"T. N. Safonova, A. N. Antipov, V. P. Veiko, N. N. Mordkovich, N. A. Okorokova, P. V. Dorovatovskii, K. M. Polyakov","doi":"10.1134/s106377452360093x","DOIUrl":"https://doi.org/10.1134/s106377452360093x","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Crystals of the enzyme purine nucleoside phosphorylase from the extremophilic bacterium <i>Halomonas Chromatireducens</i> AGD 8-3, suitable for X-ray diffraction, were grown by the vapor-diffusion method. The X-ray diffraction data were collected from these crystals at the Belok beamline of the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”) at 100 K to 1.80 Å resolution. The X-ray diffraction data were processed in the space groups <i>P</i>1, <i>P</i>2, <i>P</i>2<sub>1</sub>, and <i>P</i>622. The structure was solved by the molecular replacement method taking into account the twinning in the space groups <i>P</i>2<sub>1</sub> and <i>P</i>1 with one and two hexamers of the enzyme per asymmetric unit, respectively.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523600928
N. V. Lekontseva, A. D. Nikulin
Abstract
The structure of the Hfq protein from the bacterium Chromobacterium haemolyticum, which forms crystals in two different spatial groups, has been determined. In both cases, the protein has a specific quaternary hexamer-ring structure. The obtained structure showed a previously undescribed interaction between the C-terminal unstructured part of Hfq and the amino acid residues of the proximal RNA-binding site of the protein. This contact may contribute to the regulation of the binding of RNA molecules to the Hfq protein.
{"title":"The Structure of the Hfq Protein from Chromobacterium haemolyticum Revealed a New Variant of Regulation of RNA Binding with the Protein","authors":"N. V. Lekontseva, A. D. Nikulin","doi":"10.1134/s1063774523600928","DOIUrl":"https://doi.org/10.1134/s1063774523600928","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The structure of the Hfq protein from the bacterium <i>Chromobacterium haemolyticum</i>, which forms crystals in two different spatial groups, has been determined. In both cases, the protein has a specific quaternary hexamer-ring structure. The obtained structure showed a previously undescribed interaction between the C-terminal unstructured part of Hfq and the amino acid residues of the proximal RNA-binding site of the protein. This contact may contribute to the regulation of the binding of RNA molecules to the Hfq protein.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523601065
A. S. Ivanovsky, I. A. Kolesnikov, Yu. V. Kordonskaya, A. V. Ermakov, M. A. Marchenkova, V. I. Timofeev, Yu. V. Pisarevsky, Yu. A. Dyakova, M. V. Kovalchuk
Abstract
Based on the spike protein of the SARS-CoV-2 virus, a protein capable of causing an immune answer has been predicted. The protein stability in solution is confirmed by the molecular dynamics simulation. Immunomodulation has shown that this protein causes an immune reaction and, correspondingly, may serve a vaccine prototype.
{"title":"Application of the Crystal Structure of the SARS-CoV-2 Spike Protein for the Development of a Peptide Vaccine against Virus","authors":"A. S. Ivanovsky, I. A. Kolesnikov, Yu. V. Kordonskaya, A. V. Ermakov, M. A. Marchenkova, V. I. Timofeev, Yu. V. Pisarevsky, Yu. A. Dyakova, M. V. Kovalchuk","doi":"10.1134/s1063774523601065","DOIUrl":"https://doi.org/10.1134/s1063774523601065","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Based on the spike protein of the SARS-CoV-2 virus, a protein capable of causing an immune answer has been predicted. The protein stability in solution is confirmed by the molecular dynamics simulation. Immunomodulation has shown that this protein causes an immune reaction and, correspondingly, may serve a vaccine prototype.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523600916
S. A. Shilova, I. O. Matyuta, E. Y. Bezsudnova, M. E. Minyaev, A. Y. Nikolaeva, V. O. Popov, K. M. Boyko
Abstract
D-cycloserine inhibits pyridoxal 5'-phosphate (PLP)-dependent enzymes both reversibly and irreversibly. As an alanine racemase inhibitor, D-cycloserine is used in drug therapy in the treatment of tuberculosis. Several products of the interaction of D-cycloserine and PLP in the active site of the enzyme are known. The crystal structure of the complex of PLP-dependent D-amino acid transaminase from the bacteria Aminobacterium colombiense (Amico) with D-cycloserine obtained at a resolution of 1.9 Å is presented, in which the ring-opened adduct of PLP and D-cycloserine was discovered. In addition, the interaction of D-cycloserine with Amico has been characterized by the kinetic and spectral methods, various products of the interaction of D-cycloserine and PLP in the active site of transaminase have been determined, and the coordination of D-cycloserine and PLP adducts in the Amico active site has been analyzed. It is established that the products of the interaction of D-cycloserine with PLP in the Amico active site are several compounds, including PLP and DCS adducts in the cyclic and open forms, oxime formed by PMP and β-aminooxy-D-alanine, and PMP and β-aminooxypyruvate.
{"title":"3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine","authors":"S. A. Shilova, I. O. Matyuta, E. Y. Bezsudnova, M. E. Minyaev, A. Y. Nikolaeva, V. O. Popov, K. M. Boyko","doi":"10.1134/s1063774523600916","DOIUrl":"https://doi.org/10.1134/s1063774523600916","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>D-cycloserine inhibits pyridoxal 5'-phosphate (PLP)-dependent enzymes both reversibly and irreversibly. As an alanine racemase inhibitor, D-cycloserine is used in drug therapy in the treatment of tuberculosis. Several products of the interaction of D-cycloserine and PLP in the active site of the enzyme are known. The crystal structure of the complex of PLP-dependent D-amino acid transaminase from the bacteria <i>Aminobacterium colombiense</i> (Amico) with D-cycloserine obtained at a resolution of 1.9 Å is presented, in which the ring-opened adduct of PLP and D-cycloserine was discovered. In addition, the interaction of D-cycloserine with Amico has been characterized by the kinetic and spectral methods, various products of the interaction of D-cycloserine and PLP in the active site of transaminase have been determined, and the coordination of D-cycloserine and PLP adducts in the Amico active site has been analyzed. It is established that the products of the interaction of D-cycloserine with PLP in the Amico active site are several compounds, including PLP and DCS adducts in the cyclic and open forms, oxime formed by PMP and β-aminooxy-D-alanine, and PMP and β-aminooxypyruvate.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523601119
A. E. Tishin, A. V. Gladysheva, L. A. Pyatavina, S. E. Olkin, A. A. Gladysheva, I. R. Imatdionov, A. V. Vlaskina, A. Yu. Nikolaeva, V. R. Samygina, A. P. Agafonov
Abstract
Human rhinovirus picornain 3C is a high-value commercial cysteine protease, which is widely used to remove affinity tags and fusion proteins during the purification of the target proteins. A variant of rhinovirus A28 picornain 3C produced in this study is not annotated in the NCBI databases, shares 79% sequence identity in the PDB, and was not previously used in the protein engineering. A protocol was developed for the isolation and purification of the protein to use it in structural studies. The initial crystallization conditions were found. The determination and analysis of the structure of rhinovirus A28 picornain 3C will provide new possibilities for performing basic research on the evolution of proteolytic enzymes and for the design of the optimal variant of this protease.
{"title":"Preparation and Crystallization of Picornain 3C of Rhinovirus A28","authors":"A. E. Tishin, A. V. Gladysheva, L. A. Pyatavina, S. E. Olkin, A. A. Gladysheva, I. R. Imatdionov, A. V. Vlaskina, A. Yu. Nikolaeva, V. R. Samygina, A. P. Agafonov","doi":"10.1134/s1063774523601119","DOIUrl":"https://doi.org/10.1134/s1063774523601119","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Human rhinovirus picornain 3C is a high-value commercial cysteine protease, which is widely used to remove affinity tags and fusion proteins during the purification of the target proteins. A variant of rhinovirus A28 picornain 3C produced in this study is not annotated in the NCBI databases, shares 79% sequence identity in the PDB, and was not previously used in the protein engineering. A protocol was developed for the isolation and purification of the protein to use it in structural studies. The initial crystallization conditions were found. The determination and analysis of the structure of rhinovirus A28 picornain 3C will provide new possibilities for performing basic research on the evolution of proteolytic enzymes and for the design of the optimal variant of this protease.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523600965
Y. A. Abramchik, E. A. Zayats, V. I. Timofeev, M. B. Shevtsov, M. A. Kostromina, I. V. Fateev, D. O. Yurovskaya, A. A. Karanov, I. D. Konstantinova, I. P. Kuranova, R. S. Esipov
Abstract
A highly effective producer strain Escherichia coli C3030/pET23d+-EcHGPRT, allowing production of recombinant hypoxanthine‒guanine phosphoribosyltransferase from E. coli (EcHGPRT) in a soluble form, has been created. A method for isolating and purifying the recombinant protein has been developed. The specific activity against the natural substrate and pyrazine-2-carboxamide derivatives has been determined. Crystals of the EcHGPRT complexes with 3-hydroxypyrazine-2-carboxamide (T-1105) and 6-fluoro-3-hydroxypyrazine-2-carboxamide (T-705), suitable for X-ray diffraction analysis, have been grown by capillary counter diffusion. X-ray diffraction sets with a resolution of up to 2.4 and 2.5 Å have been collected at the ESRF synchrotron (France, station ID23-1) at a temperature of 100 K. The crystals belong to the sp. gr. P3(1)21; the independent part of the cell contains two enzyme molecules.
摘要 高效生产菌株大肠杆菌 C3030/pET23d+-EcHGPRT，可生产可溶性重组大肠杆菌次黄嘌呤-鸟嘌呤磷酸核糖转移酶（EcHGPRT）。还开发了一种分离和纯化重组蛋白的方法。对天然底物和吡嗪-2-甲酰胺衍生物的特异性活性已经确定。通过毛细管反向扩散法，培育出了适合 X 射线衍射分析的 EcHGPRT 与 3-羟基吡嗪-2-甲酰胺（T-1105）和 6-氟-3-羟基吡嗪-2-甲酰胺（T-705）的复合物晶体。这些晶体属于 P3(1)21；细胞的独立部分包含两个酶分子。
{"title":"Preliminary X-ray Study of Crystals Obtained by Co-Crystallization of Hypoxanthine‒Guanine Phosphoribosyltransferase from Escherichia coli and Pyrazine-2-Carboxamide Derivatives","authors":"Y. A. Abramchik, E. A. Zayats, V. I. Timofeev, M. B. Shevtsov, M. A. Kostromina, I. V. Fateev, D. O. Yurovskaya, A. A. Karanov, I. D. Konstantinova, I. P. Kuranova, R. S. Esipov","doi":"10.1134/s1063774523600965","DOIUrl":"https://doi.org/10.1134/s1063774523600965","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>A highly effective producer strain <i>Escherichia coli</i> C3030/pET23d<sup>+</sup>-<i>Ec</i>HGPRT, allowing production of recombinant hypoxanthine‒guanine phosphoribosyltransferase from <i>E. coli</i> (<i>Ec</i>HGPRT) in a soluble form, has been created. A method for isolating and purifying the recombinant protein has been developed. The specific activity against the natural substrate and pyrazine-2-carboxamide derivatives has been determined. Crystals of the <i>Ec</i>HGPRT complexes with 3-hydroxypyrazine-2-carboxamide (T-1105) and 6-fluoro-3-hydroxypyrazine-2-carboxamide (T-705), suitable for X-ray diffraction analysis, have been grown by capillary counter diffusion. X-ray diffraction sets with a resolution of up to 2.4 and 2.5 Å have been collected at the ESRF synchrotron (France, station ID23-1) at a temperature of 100 K. The crystals belong to the sp. gr. <i>P</i>3(1)21; the independent part of the cell contains two enzyme molecules.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523601132
A. D. Burtseva, T. N. Baymukhametov, I. O. Ilyasov, M. A. Bolshakov, A. A. Moskalenko, K. M. Boyko, A. A. Ashikhmin
Abstract
The primary processes of photosynthesis for purple photosynthesising bacteria occur in light-harvesting (LH) complexes. The LH2 complex contains polypeptides; bacteriochlorophyll; and, in most cases, carotenoids. There are three known spatial structures of LH2 complexes from purple nonsulfur bacteria; however, high-resolution structures have not been established for purple sulfur bacteria. The results of the structural study of two light-harvesting complexes LH2 from purple sulfur bacteria Ectothiorhodospira haloalkaliphila by cryoelectronic microscopy are reported. Images of carotenoid-containing (LH2+) and carotenoidless (LH2–) variants of the complex, demonstrating a characteristic architecture of the objects of this type, are obtained. A 3D reconstruction of LH2+ is performed with a resolution of 4.5 Å; it coincides with the previously established crystal structure. The presence of particles of different morphology is shown for LH2–.
{"title":"Structural Study of the Light-Harvesting Complex LH2 from the Purple Sulfur Bacteria Ectothiorhodospira haloalkaliphila by Cryoelectronic Microscopy","authors":"A. D. Burtseva, T. N. Baymukhametov, I. O. Ilyasov, M. A. Bolshakov, A. A. Moskalenko, K. M. Boyko, A. A. Ashikhmin","doi":"10.1134/s1063774523601132","DOIUrl":"https://doi.org/10.1134/s1063774523601132","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The primary processes of photosynthesis for purple photosynthesising bacteria occur in light-harvesting (LH) complexes. The LH2 complex contains polypeptides; bacteriochlorophyll; and, in most cases, carotenoids. There are three known spatial structures of LH2 complexes from purple nonsulfur bacteria; however, high-resolution structures have not been established for purple sulfur bacteria. The results of the structural study of two light-harvesting complexes LH2 from purple sulfur bacteria <i>Ectothiorhodospira haloalkaliphila</i> by cryoelectronic microscopy are reported. Images of carotenoid-containing (LH2+) and carotenoidless (LH2–) variants of the complex, demonstrating a characteristic architecture of the objects of this type, are obtained. A 3D reconstruction of LH2+ is performed with a resolution of 4.5 Å; it coincides with the previously established crystal structure. The presence of particles of different morphology is shown for LH2–.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523600308
A. M. Azieva, E. V. Yastremsky, D. A. Kirillova, T. D. Patsaev, A. A. Mikhutkin, R. V. Sharikov, R. A. Kamyshinsky, K. I. Lukanina, N. A. Sharikova, T. E. Grigoriev, A. L. Vasiliev
Abstract
The adhesive properties of scaffolds, which primarily depend on the chemical and structural features of their surface, play an important role in the tissue engineering. The cell adhesion of dissociated primary neuronal culture to isotropic and anisotropic nonwoven and sponge polylactide scaffolds was studied by fluorescence and environmental scanning electron microscopy. Neurons extracted from neonatal mouse brain showed improved adhesion on all types of scaffolds after the plasma treatment. The most pronounced effect was observed for non-oriented scaffolds.
{"title":"Effect of Plasma Treatment of Biomedical Scaffolds on Neuronal Cell Adhesion","authors":"A. M. Azieva, E. V. Yastremsky, D. A. Kirillova, T. D. Patsaev, A. A. Mikhutkin, R. V. Sharikov, R. A. Kamyshinsky, K. I. Lukanina, N. A. Sharikova, T. E. Grigoriev, A. L. Vasiliev","doi":"10.1134/s1063774523600308","DOIUrl":"https://doi.org/10.1134/s1063774523600308","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The adhesive properties of scaffolds, which primarily depend on the chemical and structural features of their surface, play an important role in the tissue engineering. The cell adhesion of dissociated primary neuronal culture to isotropic and anisotropic nonwoven and sponge polylactide scaffolds was studied by fluorescence and environmental scanning electron microscopy. Neurons extracted from neonatal mouse brain showed improved adhesion on all types of scaffolds after the plasma treatment. The most pronounced effect was observed for non-oriented scaffolds.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140882584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523601016
V. A. Grigorev, P. V. Konarev, V. V. Volkov
Abstract
The modified “simulated annealing” algorithm implemented in the DAMMINV software allows one to obtain 10 to 15 different nanoparticle models fitting small-angle X-ray scattering data. This method is based on the mode of intermittent weights of the objective function, which balances between minimization of the penalty coefficients, responsible for the model meaningfulness, and the discrepancy between the experimental and model scattering data. The effect of noise on the scattering curves on the quality of three-dimensional helix shape reconstruction has been investigated, and the results are compared with the data obtained using standard programs. The method has been verified on noise-free model data and data with superimposed Poisson noise by the example of a helix particle with a thickness of turns comparable to the characteristic size of the space between them. A comparative analysis of the reconstructed models and the three-dimensional shapes obtained using standard modes of the “simulated annealing” algorithm has been performed.
{"title":"Determination of the Shape of a Helix Particle Based on Small-Angle X-ray Scattering Data: Modification of the “Simulated Annealing” Algorithm","authors":"V. A. Grigorev, P. V. Konarev, V. V. Volkov","doi":"10.1134/s1063774523601016","DOIUrl":"https://doi.org/10.1134/s1063774523601016","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The modified “simulated annealing” algorithm implemented in the DAMMINV software allows one to obtain 10 to 15 different nanoparticle models fitting small-angle X-ray scattering data. This method is based on the mode of intermittent weights of the objective function, which balances between minimization of the penalty coefficients, responsible for the model meaningfulness, and the discrepancy between the experimental and model scattering data. The effect of noise on the scattering curves on the quality of three-dimensional helix shape reconstruction has been investigated, and the results are compared with the data obtained using standard programs. The method has been verified on noise-free model data and data with superimposed Poisson noise by the example of a helix particle with a thickness of turns comparable to the characteristic size of the space between them. A comparative analysis of the reconstructed models and the three-dimensional shapes obtained using standard modes of the “simulated annealing” algorithm has been performed.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139689236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1134/s1063774523601077
I. A. Kolesnikov, V. I. Timofeev, A. V. Ermakov, A. S. Ivanovsky, Yu. A. Dyakova, Yu. V. Pisarevsky, M. V. Kovalchuk
Abstract
The spatial structure of the envelope protein of African swine fever (ASF) virus is modeled; its topology relative to the cell membrane is calculated; the B- and T-cell epitopes are predicted for this protein; and their immunogenecity, allergenicity, and toxicity are estimated. The variability of protein amino acids and the conservativity of the found epitopes are studied. It is shown that a new peptide vaccine against ASF can be developed based on the found epitopes.
{"title":"Search for Potential Epitopes in the Envelope Protein of the African Swine Fever Virus","authors":"I. A. Kolesnikov, V. I. Timofeev, A. V. Ermakov, A. S. Ivanovsky, Yu. A. Dyakova, Yu. V. Pisarevsky, M. V. Kovalchuk","doi":"10.1134/s1063774523601077","DOIUrl":"https://doi.org/10.1134/s1063774523601077","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The spatial structure of the envelope protein of African swine fever (ASF) virus is modeled; its topology relative to the cell membrane is calculated; the B- and T-cell epitopes are predicted for this protein; and their immunogenecity, allergenicity, and toxicity are estimated. The variability of protein amino acids and the conservativity of the found epitopes are studied. It is shown that a new peptide vaccine against ASF can be developed based on the found epitopes.</p>","PeriodicalId":527,"journal":{"name":"Crystallography Reports","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140889905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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