Pub Date : 2025-01-27DOI: 10.1016/j.jsb.2025.108172
Lev Kapnulin , Ayelet Heimowitz , Nir Sharon
The process of particle picking, a crucial step in cryo-electron microscopy (cryo-EM) image analysis, often encounters challenges due to outliers, leading to inaccuracies in downstream processing. In response to this challenge, this research introduces an additional automated step to reduce the number of outliers identified by the particle picker. The proposed method enhances both the accuracy and efficiency of particle picking, thereby reducing the overall running time and the necessity for expert intervention in the process. Experimental results demonstrate the effectiveness of the proposed approach in mitigating outlier inclusion and its potential to enhance cryo-EM data analysis pipelines significantly. This work contributes to the ongoing advancement of automated cryo-EM image processing methods, offering novel insights and solutions to challenges in structural biology research.
{"title":"Outlier removal in cryo-EM via radial profiles","authors":"Lev Kapnulin , Ayelet Heimowitz , Nir Sharon","doi":"10.1016/j.jsb.2025.108172","DOIUrl":"10.1016/j.jsb.2025.108172","url":null,"abstract":"<div><div>The process of particle picking, a crucial step in cryo-electron microscopy (cryo-EM) image analysis, often encounters challenges due to outliers, leading to inaccuracies in downstream processing. In response to this challenge, this research introduces an additional automated step to reduce the number of outliers identified by the particle picker. The proposed method enhances both the accuracy and efficiency of particle picking, thereby reducing the overall running time and the necessity for expert intervention in the process. Experimental results demonstrate the effectiveness of the proposed approach in mitigating outlier inclusion and its potential to enhance cryo-EM data analysis pipelines significantly. This work contributes to the ongoing advancement of automated cryo-EM image processing methods, offering novel insights and solutions to challenges in structural biology research.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108172"},"PeriodicalIF":3.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066404","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}
Pub Date : 2025-01-20DOI: 10.1016/j.jsb.2025.108170
Chaoyi Chen , Yidan Yan , Jingpeng Wu , Wen-Biao Gan
Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mitochondrial morphology and function. To address the challenge of segmenting small mitochondrial compartments in vEM images, we propose an automated mitochondrial segmentation method called GCTransNet. This method employs grayscale migration technology to preprocess images, effectively reducing intensity distribution differences across EM images. By utilizing 3D Global Context Vision Transformers (GC-ViT) combined with global context self-attention modules and local self-attention modules, GCTransNet precisely models long-range and short-range spatial interactions. The long-range interactions enable the model to capture the global structural relationships within the mitochondrial segmentation network, while the short-range interactions refine local details and boundaries. In our approach, the encoder of the 3D U-Net network, a classical multi-scale learning architecture that retains high-resolution features through skip connections and combines multi-scale features for precise segmentation, is replaced by a 3D GC-ViT. The GC-ViT leverages shifted window-based self-attention, capturing long-range dependencies and offering improved segmentation accuracy compared to traditional U-Net encoders. In the MitoEM mitochondrial segmentation challenge, GCTransNet achieved state-of-the-art results, demonstrating its superiority in automated mitochondrial segmentation. The code and its documentation are publicly available at https://github.com/GanLab123/GCTransNet.
{"title":"GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers","authors":"Chaoyi Chen , Yidan Yan , Jingpeng Wu , Wen-Biao Gan","doi":"10.1016/j.jsb.2025.108170","DOIUrl":"10.1016/j.jsb.2025.108170","url":null,"abstract":"<div><div>Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mitochondrial morphology and function. To address the challenge of segmenting small mitochondrial compartments in vEM images, we propose an automated mitochondrial segmentation method called GCTransNet. This method employs grayscale migration technology to preprocess images, effectively reducing intensity distribution differences across EM images. By utilizing 3D Global Context Vision Transformers (GC-ViT) combined with global context self-attention modules and local self-attention modules, GCTransNet precisely models long-range and short-range spatial interactions. The long-range interactions enable the model to capture the global structural relationships within the mitochondrial segmentation network, while the short-range interactions refine local details and boundaries. In our approach, the encoder of the 3D U-Net network, a classical multi-scale learning architecture that retains high-resolution features through skip connections and combines multi-scale features for precise segmentation, is replaced by a 3D GC-ViT. The GC-ViT leverages shifted window-based self-attention, capturing long-range dependencies and offering improved segmentation accuracy compared to traditional U-Net encoders. In the MitoEM mitochondrial segmentation challenge, GCTransNet achieved state-of-the-art results, demonstrating its superiority in automated mitochondrial segmentation. The code and its documentation are publicly available at <span><span>https://github.com/GanLab123/GCTransNet</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108170"},"PeriodicalIF":3.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143023913","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}
Despite sharing ∼ 43 % sequence identity and structurally similar individual domains, botulinum neurotoxin (BoNT) serotypes A and E have differences in their properties and domain positioning. BoNT/E has a faster onset of action than BoNT/A. This difference is proposed to be due to conformational differences between BoNT/E and the other BoNT serotypes. Where most serotypes have the light chain (LC) and binding domain (BD) on opposite sides of the translocation domain (TD), BoNT/E forms a more compact shape with direct interactions between residues of the LC and BD. To elucidate the structural basis for the different properties of BoNT/A and BoNT/E, biophysical studies including molecular dynamic (MD) simulations, circular dichroism (CD) and small-angle X-ray scattering (SAXS) were applied to BoNT/A, for comparison against previous work on BoNT/E.
MD simulations at six pH values across the toxin’s activation barrier (pH ∼ 5.5), followed by one extra repeat for the pH values below 5.5, revealed a rare event at pH 5 and 5.5 where interactions between a previously identified switch region of BoNT/A and the BD were lost. This hinted at an increased freedom of movement, thus allowing the region to change from α-helical to a β-hairpin. In good agreement with previous work, CD showed a gradual and small loss of helicity as the pH decreased below pH 5.5, stabilising at pH 4.5. Combined with the relative scarcity of structural changes observed by MD in the switch region required for activity, these results may explain the slower onset of action for BoNT/A compared to BoNT/E.
{"title":"Inter-Domain interactions Slow BoNT/A’s onset of action","authors":"C.J. Lalaurie , M. Zloh , D.R. Higazi , K.A. Bunting , P.A. Dalby","doi":"10.1016/j.jsb.2025.108171","DOIUrl":"10.1016/j.jsb.2025.108171","url":null,"abstract":"<div><div>Despite sharing ∼ 43 % sequence identity and structurally similar individual domains, botulinum neurotoxin (BoNT) serotypes A and E have differences in their properties and domain positioning. BoNT/E has a faster onset of action than BoNT/A. This difference is proposed to be due to conformational differences between BoNT/E and the other BoNT serotypes. Where most serotypes have the light chain (LC) and binding domain (BD) on opposite sides of the translocation domain (TD), BoNT/E forms a more compact shape with direct interactions between residues of the LC and BD. To elucidate the structural basis for the different properties of BoNT/A and BoNT/E, biophysical studies including molecular dynamic (MD) simulations, circular dichroism (CD) and small-angle X-ray scattering (SAXS) were applied to BoNT/A, for comparison against previous work on BoNT/E.</div><div>MD simulations<!--> <!-->at six pH values across the toxin’s activation barrier (pH ∼ 5.5), followed by one extra repeat for the pH values below 5.5, revealed a rare event at pH 5 and 5.5 where interactions between a previously identified switch region of BoNT/A<!--> <!-->and the BD were lost.<!--> <!-->This hinted<!--> <!-->at an increased freedom of movement, thus allowing the region to change from α-helical to a β-hairpin. In good agreement with previous work, CD showed a gradual and small loss of helicity as the pH decreased below pH 5.5, stabilising at pH 4.5. Combined with the relative scarcity of structural changes observed by MD in the switch region required for activity, these results may explain the slower onset of action for BoNT/A compared to BoNT/E.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108171"},"PeriodicalIF":3.0,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007389","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}
Transmission electron microscopy, especially at cryogenic temperature, is largely used for studying biological macromolecular complexes. A main difficulty of TEM imaging of biological samples is the weak amplitude contrasts due to electron diffusion on light elements that compose biological organisms. Achieving high-resolution reconstructions implies therefore the acquisition of a huge number of TEM micrographs followed by a time-consuming image analysis. This TEM constraint could be overcome by extracting the phase shift of the electron beam having interacted with a “low contrast” sample. This can be achieved by off-axis electron holography, an electron interferometric technique used in material science, but rarely in biology due to lack of sensitivity. Here, we took advantage of recent technological advances on a dedicated 300 keV TEM to re-evaluate the performance of off-axis holography on unstained T4 and T5 bacteriophages at room temperature and in cryogenic conditions. Our results demonstrate an improvement in contrast and signal-to-noise ratio at both temperatures compared to bright field TEM images, with some limitations in spatial resolution. In addition, we show that the electron beam phase shift gives information on charge variations, paving the way to electrostatic potential studies of biological objects at the nanometer scale.
{"title":"Off-axis electron holography of unstained bacteriophages: Towards electrostatic potential measurement of biological samples","authors":"Elio Karim , Christophe Gatel , Amélie Leforestier , Stéphanie Balor , Vanessa Soldan , Célia Plisson-Chastang , Pierre-Emmanuel Gleizes , Etienne Snoeck","doi":"10.1016/j.jsb.2025.108169","DOIUrl":"10.1016/j.jsb.2025.108169","url":null,"abstract":"<div><div>Transmission electron microscopy, especially at cryogenic temperature, is largely used for studying biological macromolecular complexes. A main difficulty of TEM imaging of biological samples is the weak amplitude contrasts due to electron diffusion on light elements that compose biological organisms. Achieving high-resolution reconstructions implies therefore the acquisition of a huge number of TEM micrographs followed by a time-consuming image analysis. This TEM constraint could be overcome by extracting the phase shift of the electron beam having interacted with a “low contrast” sample. This can be achieved by off-axis electron holography, an electron interferometric technique used in material science, but rarely in biology due to lack of sensitivity. Here, we took advantage of recent technological advances on a dedicated 300 keV TEM to re-evaluate the performance of off-axis holography on unstained T4 and T5 bacteriophages at room temperature and in cryogenic conditions. Our results demonstrate an improvement in contrast and signal-to-noise ratio at both temperatures compared to bright field TEM images, with some limitations in spatial resolution. In addition, we show that the electron beam phase shift gives information on charge variations, paving the way to electrostatic potential studies of biological objects at the nanometer scale.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108169"},"PeriodicalIF":3.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007383","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}
Pub Date : 2025-01-12DOI: 10.1016/j.jsb.2025.108168
Yongli Wang , Yankai Chang , Fangyuan Yin , Chunliu Kang , Yao Meng , Fukang Xu , Yiran Liu , Yunxia Zhang , Changjing Wu , Shuhua Fan , Junlong Zhao
Cryptosporidium has gained much attention as a major cause of diarrhea worldwide. Here, we present the first structure of H-2Kb complexed with a decapeptide from Cryptosporidium parvum Gp40/15 protein (Gp40/15-VTF10). In contrast to all published structures, the aromatic residue P3-Phe of Gp40/15-VTF10 is anchored in pocket C rather than the canonical Y/F at P5 or P6 reported for octapeptides and nonapeptides. The results of in vitro refolding assays and circular dichroism experiments showed that the side chains of P3 and P5 play key roles in Gp40/15-VTF10 peptide binding. However, functional analysis of decapeptide epitopes revealed that the Gp40/15-VTF10 peptide did not elicit a strong CD8+T immune response, whereas the decapeptide epitope MEDLE2-INF10 induced a significant CD8+ T-cell response in peptide-immunized C57BL/6 mice. Using a model structure of H-2Kb-INF10 complex, we found that the antigenic decapeptide INF10 exhibits a completely different conformation, with the aromatic anchors P3F and P7F docked into the D and C pockets, respectively, while similar peptide conformation and hydrogen bond interactions between the peptide and major histocompatibility complex were found in the resolved H-2Kb-SVF9 complex. As the H-2Kb molecule predominantly prefers octapeptides with a strong anchor of P5 Y/F (or P6 Y/F for nonapeptides) binding to the C pocket, we propose that P7 Y/F in the C pocket may represent a novel binding mode for decapeptides. The results should increase the accuracy of T-cell epitope prediction and support the development of T-cell epitope vaccines against cryptosporidiosis.
{"title":"Structural analyses of Cryptosporidium parvum epitopes reveal a novel scheme of decapeptide binding to H-2Kb","authors":"Yongli Wang , Yankai Chang , Fangyuan Yin , Chunliu Kang , Yao Meng , Fukang Xu , Yiran Liu , Yunxia Zhang , Changjing Wu , Shuhua Fan , Junlong Zhao","doi":"10.1016/j.jsb.2025.108168","DOIUrl":"10.1016/j.jsb.2025.108168","url":null,"abstract":"<div><div><em>Cryptosporidium</em> has gained much attention as a major cause of diarrhea worldwide. Here, we present the first structure of H-2K<sup>b</sup> complexed with a decapeptide from <em>Cryptosporidium parvum</em> Gp40/15 protein (Gp40/15-VTF10). In contrast to all published structures, the aromatic residue P3-Phe of Gp40/15-VTF10 is anchored in pocket C rather than the canonical Y/F at P5 or P6 reported for octapeptides and nonapeptides. The results of <em>in vitro</em> refolding assays and circular dichroism experiments showed that the side chains of P3 and P5 play key roles in Gp40/15-VTF10 peptide binding. However, functional analysis of decapeptide epitopes revealed that the Gp40/15-VTF10 peptide did not elicit a strong CD8<sup>+</sup>T immune response, whereas the decapeptide epitope MEDLE2-INF10 induced a significant CD8<sup>+</sup> T-cell response in peptide-immunized C57BL/6 mice. Using a model structure of H-2K<sup>b</sup>-INF10 complex, we found that the antigenic decapeptide INF10 exhibits a completely different conformation, with the aromatic anchors P3F and P7F docked into the D and C pockets, respectively, while similar peptide conformation and hydrogen bond interactions between the peptide and major histocompatibility complex were found in the resolved H-2K<sup>b</sup>-SVF9 complex. As the H-2K<sup>b</sup> molecule predominantly prefers octapeptides with a strong anchor of P5 Y/F (or P6 Y/F for nonapeptides) binding to the C pocket, we propose that P7 Y/F in the C pocket may represent a novel binding mode for decapeptides. The results should increase the accuracy of T-cell epitope prediction and support the development of T-cell epitope vaccines against cryptosporidiosis.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108168"},"PeriodicalIF":3.0,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983830","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}
Pub Date : 2025-01-05DOI: 10.1016/j.jsb.2025.108166
Minh H. Tran , Cristina E. Martina , Rocco Moretti , Marcus Nagel , Kevin L. Schey , Jens Meiler
High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function and enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually. By incorporating HDX data as both distance restraints and a scoring term in the RosettaDock algorithm, RosettaHDX successfully generated near-native models (interface root-mean square deviation ≤ 4 Å) for all 9 benchmark complexes examined, averaging 3.6 times more near-native models than Rosetta alone. Near-native models among the top 10 scoring were identified in 3/9 cases, compared to 1/9 with Rosetta alone. Additionally, we developed a predictive metric based on docking results with HDX restraints to identify allosteric peptides in HDX datasets.
{"title":"RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data","authors":"Minh H. Tran , Cristina E. Martina , Rocco Moretti , Marcus Nagel , Kevin L. Schey , Jens Meiler","doi":"10.1016/j.jsb.2025.108166","DOIUrl":"10.1016/j.jsb.2025.108166","url":null,"abstract":"<div><div>High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function and enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually. By incorporating HDX data as both distance restraints and a scoring term in the RosettaDock algorithm, RosettaHDX successfully generated near-native models (interface root-mean square deviation ≤ 4 Å) for all 9 benchmark complexes examined, averaging 3.6 times more near-native models than Rosetta alone. Near-native models among the top 10 scoring were identified in 3/9 cases, compared to 1/9 with Rosetta alone. Additionally, we developed a predictive metric based on docking results with HDX restraints to identify allosteric peptides in HDX datasets.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108166"},"PeriodicalIF":3.0,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007386","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}
Pub Date : 2025-01-05DOI: 10.1016/j.jsb.2025.108167
José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain
Cry proteins, commonly found in Gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and insect vectors. Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran Anthonomus grandis (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.
{"title":"Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium","authors":"José D. Antonino , Shalini Chaudhary , Mark Lubberts , Brendan J. McConkey , Camilla A.S. Valença , Marcus V. de Aragão Batista , Patricia Severino , Marcelo da Costa Mendonça , Eliana B. Souto , Silvio S. Dolabella , Sona Jain","doi":"10.1016/j.jsb.2025.108167","DOIUrl":"10.1016/j.jsb.2025.108167","url":null,"abstract":"<div><div>Cry proteins, commonly found in Gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and insect vectors<em>.</em> Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran <em>Anthonomus grandis</em> (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108167"},"PeriodicalIF":3.0,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971462","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}
Pub Date : 2024-12-26DOI: 10.1016/j.jsb.2024.108165
Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz
The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein–mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components—aragonite, protein and chitin—of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone Haliotis rufescens, with the (001) crystal surface of aragonite and the chitin molecule. We report the results of atomistic molecular-modelling calculations and molecular-dynamics simulations of the peptide interacting with both the aragonite surface and the chitin polymer. The peptide shows an energetically favourable binding to the aragonite surface. The interaction of the carboxylic groups of the glutamic unit with the crystalline surface is essential to reproduce the characteristic elastomeric properties of this peptide in nacre.
{"title":"Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface","authors":"Elena Macias-Sánchez , Yumeida Meruvia-Rojas , Julyan H.E. Cartwright , Antonio G. Checa , C.Ignacio Sainz-Díaz","doi":"10.1016/j.jsb.2024.108165","DOIUrl":"10.1016/j.jsb.2024.108165","url":null,"abstract":"<div><div>The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein–mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components—aragonite, protein and chitin—of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone <em>Haliotis rufescens</em>, with the (001) crystal surface of aragonite and the chitin molecule. We report the results of atomistic molecular-modelling calculations and molecular-dynamics simulations of the peptide interacting with both the aragonite surface and the chitin polymer. The peptide shows an energetically favourable binding to the aragonite surface. The interaction of the carboxylic groups of the glutamic unit with the crystalline surface is essential to reproduce the characteristic elastomeric properties of this peptide in nacre.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108165"},"PeriodicalIF":3.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895584","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}
Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are bioactive lysophospholipids derived from cell membranes that activate the endothelial differentiation gene family of G protein-coupled receptors. Activation of these receptors triggers multiple downstream signaling cascades through G proteins such as Gi/o, Gq/11, and G12/13. Therefore, LPA and S1P mediate several physiological processes, including cytoskeletal dynamics, neurite retraction, cell migration, cell proliferation, and intracellular ion fluxes. The basis for the G-protein coupling selectivity of EDG receptors, however, remains unknown. Here, we present cryo-electron microscopy structures of LPA-activated LPA1 in complexes with Gi, Gq, and G13 heterotrimers. Comparison of the three LPA1-G protein structures shows clearly different conformations of intracellular loop 2 (ICL2) and ICL3 that are likely induced by the different Gα protein interfaces. Interestingly, this G-protein interface interaction is a common feature of LPA and S1P receptors. Our findings provide clues to understanding the promiscuity of G-protein coupling in the endothelial differentiation gene family.
{"title":"Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins","authors":"Shota Suzuki , Kotaro Tanaka , Akiko Kamegawa , Kouki Nishikawa , Hiroshi Suzuki , Atsunori Oshima , Yoshinori Fujiyoshi","doi":"10.1016/j.jsb.2024.108164","DOIUrl":"10.1016/j.jsb.2024.108164","url":null,"abstract":"<div><div>Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are bioactive lysophospholipids derived from cell membranes that activate the endothelial differentiation gene family of G protein-coupled receptors. Activation of these receptors triggers multiple downstream signaling cascades through G proteins such as Gi/o, Gq/11, and G12/13. Therefore, LPA and S1P mediate several physiological processes, including cytoskeletal dynamics, neurite retraction, cell migration, cell proliferation, and intracellular ion fluxes. The basis for the G-protein coupling selectivity of EDG receptors, however, remains unknown. Here, we present cryo-electron microscopy structures of LPA-activated LPA1 in complexes with G<sub>i</sub>, G<sub>q</sub>, and G<sub>13</sub> heterotrimers<sub>.</sub> Comparison of the three LPA1-G protein structures shows clearly different conformations of intracellular loop 2 (ICL2) and ICL3 that are likely induced by the different Gα protein interfaces. Interestingly, this G-protein interface interaction is a common feature of LPA and S1P receptors. Our findings provide clues to understanding the promiscuity of G-protein coupling in the endothelial differentiation gene family.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 1","pages":"Article 108164"},"PeriodicalIF":3.0,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895602","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}
Pub Date : 2024-12-20DOI: 10.1016/j.jsb.2024.108163
Jose Inacio Costa-Filho , Liam Theveny , Marilina de Sautu , Tom Kirchhausen
Cryogenic electron tomography (cryo-ET) has rapidly advanced as a high-resolution imaging tool for visualizing subcellular structures in 3D with molecular detail. Direct image inspection remains challenging due to inherent low signal-to-noise ratios (SNR). We introduce CryoSamba, a self-supervised deep learning-based model designed for denoising cryo-ET images. CryoSamba enhances single consecutive 2D planes in tomograms by averaging motion-compensated nearby planes through deep learning interpolation, effectively mimicking increased exposure. This approach amplifies coherent signals and reduces high-frequency noise, substantially improving tomogram contrast and SNR. CryoSamba operates on 3D volumes without needing pre-recorded images, synthetic data, labels or annotations, noise models, or paired volumes. CryoSamba suppresses high-frequency information less aggressively than do existing cryo-ET denoising methods, while retaining real information, as shown both by visual inspection and by Fourier Shell Correlation (FSC) analysis of icosahedrally symmetric virus particles. Thus, CryoSamba enhances the analytical pipeline for direct 3D tomogram visual interpretation.
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