Journal of structural biology最新文献

{"title":"Studying protein–protein interactions: Latest and most popular approaches","authors":"Sama Akbarzadeh ,&nbsp;Özlem Coşkun ,&nbsp;Başak Günçer","doi":"10.1016/j.jsb.2024.108118","DOIUrl":"10.1016/j.jsb.2024.108118","url":null,"abstract":"<div><p>PPIs, or protein–protein interactions, are essential for many biological processes. According to the findings, abnormal PPIs have been linked to several diseases, such as cancer and infectious and neurological disorders. Consequently, focusing on PPIs is a path toward disease treatment and a crucial tool for producing novel medications. Many methods exist to investigate PPIs, including low- and high-throughput studies. Since many PPIs have been discovered using <em>in vitro</em> and <em>in vivo</em> experimental approaches, the use of computational methods to predict PPIs has grown due to the expanding scale of PPI data and the intrinsic complexity of interacting mechanisms. Recognizing PPI networks offers a systematic means of predicting protein functions, and pathways that are included. These investigations can help uncover the underlying molecular mechanisms of complex phenotypes and clarify the biological processes related to health and diseases. Therefore, our goal in this study is to provide an overview of the latest and most popular approaches for investigating PPIs. We also overview some important clinical approaches based on the PPIs and how these interactions can be targeted.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 4","pages":"Article 108118"},"PeriodicalIF":3.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108532","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":"Structural analysis of the human C5a-C5aR1 complex using cryo-electron microscopy","authors":"Tingting Yang ,&nbsp;Jian Li ,&nbsp;Xinyu Cheng ,&nbsp;Qiuyuan Lu ,&nbsp;Zara Farooq ,&nbsp;Ying Fu ,&nbsp;Sijia Lv ,&nbsp;Weiwei Nan ,&nbsp;Boming Yu ,&nbsp;Jingjing Duan ,&nbsp;Yuting Zhang ,&nbsp;Yang Fu ,&nbsp;Haihai Jiang ,&nbsp;Peter J McCormick ,&nbsp;Yanyan Li ,&nbsp;Jin Zhang","doi":"10.1016/j.jsb.2024.108117","DOIUrl":"10.1016/j.jsb.2024.108117","url":null,"abstract":"<div><p>The complement system is a complex network of proteins that plays a crucial role in the innate immune response. One important component of this system is the C5a-C5aR1 complex, which is critical in the recruitment and activation of immune cells. In-depth investigation of the activation mechanism as well as biased signaling of the C5a-C5aR1 system will facilitate the elucidation of C5a-mediated pathophysiology. In this study, we determined the structure of C5a-C5aR1-Gi complex at a high resolution of 3 Å using cryo-electron microscopy (Cryo-EM). Our results revealed the binding site of C5a, which consists of a polar recognition region on the extracellular side and an amphipathic pocket within the transmembrane domain. Furthermore, we found that C5a binding induces conformational changes of C5aR1, which subsequently leads to the activation of G protein signaling pathways. Notably, a key residue (M265) located on transmembrane helix 6 (TM6) was identified to play a crucial role in regulating the recruitment of β-arrestin driven by C5a. This study provides more information about the structure and function of the human C5a-C5aR1 complex, which is essential for the proper functioning of the complement system. The findings of this study can also provide a foundation for the design of new pharmaceuticals targeting this receptor with bias or specificity.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108117"},"PeriodicalIF":3.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995955","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":"Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer","authors":"Michael L. Oldham ,&nbsp;M. Zuhaib Qayyum ,&nbsp;Ravi C. Kalathur ,&nbsp;Charles O. Rock ,&nbsp;Christopher D. Radka","doi":"10.1016/j.jsb.2024.108116","DOIUrl":"10.1016/j.jsb.2024.108116","url":null,"abstract":"<div><p>Oleate hydratase (OhyA) is a bacterial peripheral membrane protein that catalyzes FAD-dependent water addition to membrane bilayer-embedded unsaturated fatty acids. The opportunistic pathogen <em>Staphylococcus aureus</em> uses OhyA to counteract the innate immune system and support colonization. Many Gram-positive and Gram-negative bacteria in the microbiome also encode OhyA. OhyA is a dimeric flavoenzyme whose carboxy terminus is identified as the membrane binding domain; however, understanding how OhyA binds to cellular membranes is not complete until the membrane-bound structure has been elucidated. All available OhyA structures depict the solution state of the protein outside its functional environment. Here, we employ liposomes to solve the cryo-electron microscopy structure of the functional unit: the OhyA•membrane complex. The protein maintains its structure upon membrane binding and slightly alters the curvature of the liposome surface. OhyA preferentially associates with 20–30 nm liposomes with multiple copies of OhyA dimers assembling on the liposome surface resulting in the formation of higher-order oligomers. Dimer assembly is cooperative and extends along a formed ridge of the liposome. We also solved an OhyA dimer of dimers structure that recapitulates the intermolecular interactions that stabilize the dimer assembly on the membrane bilayer as well as the crystal contacts in the lattice of the OhyA crystal structure. Our work enables visualization of the molecular trajectory of membrane binding for this important interfacial enzyme.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108116"},"PeriodicalIF":3.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S104784772400056X/pdfft?md5=9988fe164241cbab00e0c3e8f1b152bc&pid=1-s2.0-S104784772400056X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995954","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":"A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52","authors":"Lucas R. Struble,&nbsp;Jeffrey J. Lovelace,&nbsp;Gloria E.O. Borgstahl","doi":"10.1016/j.jsb.2024.108115","DOIUrl":"10.1016/j.jsb.2024.108115","url":null,"abstract":"<div><p>Human RAD52 protein binds DNA and is involved in genomic stability maintenance and several forms of DNA repair, including homologous recombination and single-strand annealing. Despite its importance, there are very few structural details about the variability of the RAD52 ring size and the RAD52 C-terminal protein–protein interaction domains. Even recent attempts to employ cryogenic electron microscopy (cryoEM) methods on full-length yeast and human RAD52 do not reveal interpretable structures for the C-terminal half that contains the replication protein A (RPA) and RAD51 binding domains. In this study, we employed the monodisperse purification of two RAD52 deletion constructs and small angle X-ray scattering (SAXS) to construct a structural model that includes RAD52′s RPA binding domain. This model is of interest to DNA repair specialists as well as for drug development against HR-deficient cancers.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108115"},"PeriodicalIF":3.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000558/pdfft?md5=acafec8a9e1be5b37262734c8ddbbbf6&pid=1-s2.0-S1047847724000558-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906895","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":"Relationship between thermal stability of collagens and the fraction of hydrophobic residues in their molecules","authors":"Olga V. Meshcheryakova ,&nbsp;Maxim A. Bogdanov ,&nbsp;Alexander V. Efimov","doi":"10.1016/j.jsb.2024.108114","DOIUrl":"10.1016/j.jsb.2024.108114","url":null,"abstract":"<div><p>In this study, a database of the thermal stability of collagens and their synthetic analogues has been compiled taking into account literature sources. In total, our database includes 1200 records. As a result of a comparative theoretical analysis of the collected experimental data, the relationship between the melting temperature (<em>T</em>_m) or denaturation temperature (<em>T</em>_d) of collagens and the fraction of hydrophobic residues (<em>f</em>) in their molecules has been established. It is shown that this relationship is linear: the larger the <em>f</em> value, the higher the denaturation or melting temperature of a given collagen.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108114"},"PeriodicalIF":3.0,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878944","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 structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538","authors":"Yasmin Bay ,&nbsp;Federico Javier Miguez Cabello ,&nbsp;Chloe C. Koens ,&nbsp;Stine M. Frantsen ,&nbsp;Darryl S. Pickering ,&nbsp;Karla Frydenvang ,&nbsp;Pierre Francotte ,&nbsp;Bernard Pirotte ,&nbsp;Anders S. Kristensen ,&nbsp;Derek Bowie ,&nbsp;Jette Sandholm Kastrup","doi":"10.1016/j.jsb.2024.108113","DOIUrl":"10.1016/j.jsb.2024.108113","url":null,"abstract":"<div><p>Kainate receptors play an important role in the central nervous system by mediating postsynaptic excitatory neurotransmission and modulating the release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. To date, only three structures of the ligand-binding domain (LBD) of the kainate receptor subunit GluK1 in complex with positive allosteric modulators have been determined by X-ray crystallography, all belonging to class II modulators. Here, we report a high-resolution structure of GluK1-LBD in complex with kainate and BPAM538, which belongs to the full-spanning class III. One BPAM538 molecule binds at the GluK1 dimer interface, thereby occupying two allosteric binding sites simultaneously. BPAM538 stabilizes the active receptor conformation with only minor conformational changes being introduced to the receptor. Using a calcium-sensitive fluorescence-based assay, a 5-fold potentiation of the kainate response (100 μM) was observed in presence of 100 μM BPAM538 at GluK1(<em>Q</em>)_b, whereas no potentiation was observed at GluK2(<em>VCQ</em>)_a. Using electrophysiology recordings of outside-out patches excised from HEK293 cells, BPAM538 increased the peak response of GluK1(<em>Q</em>)_b co-expressed with NETO2 to rapid application of 10 mM L-glutamate with 130 ± 20 %, and decreased desensitization determined as the steady-state/peak response ratio from 23 ± 2 % to 90 ± 4 %. Based on dose–response relationship experiments on GluK1(<em>Q</em>)_b the EC₅₀ of BPAM538 was estimated to be 58 ± 29 μM.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108113"},"PeriodicalIF":3.0,"publicationDate":"2024-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000534/pdfft?md5=fd36f2c650fe072db6eace68cdb0888f&pid=1-s2.0-S1047847724000534-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855872","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":"From viruses to humans – Exploring the structure–function relationship of the Kesv protein for the future of biomedicine","authors":"Purva Asrani ,&nbsp;Guiscard Seebohm ,&nbsp;Raphael Stoll","doi":"10.1016/j.jsb.2024.108112","DOIUrl":"10.1016/j.jsb.2024.108112","url":null,"abstract":"<div><p>Viruses often use ion channel proteins to initialise host infections. Defects in ion channel proteins are also linked to several metabolic disorders in humans. In that instance, modulation of ion channel activities becomes central to development of antiviral therapies and drug design. Kesv, a potassium-selective ion channel protein expressed by <em>Ectocarpus siliculosus</em> virus (EsV), possesses remarkable properties which can help to characterise the molecular basis of the functional processes relevant to virus biology and human physiology. The small structural features of this ion channel could serve as a fundamental primer to study more complex ion channels from humans. Therefore, in spite of their evolutionary distance, the potential link between viral and human ion channel proteins could provide opportunities for therapeutic and biotechnological applications.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108112"},"PeriodicalIF":3.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000522/pdfft?md5=d5c6725038e68f38ea3d69444ec53849&pid=1-s2.0-S1047847724000522-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788454","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":"3D quantification of the lacunocanalicular network on human femoral diaphysis through synchrotron radiation-based nanoCT","authors":"Boliang Yu ,&nbsp;Remy Gauthier ,&nbsp;Cécile Olivier ,&nbsp;Julie Villanova ,&nbsp;Hélène Follet ,&nbsp;David Mitton ,&nbsp;Francoise Peyrin","doi":"10.1016/j.jsb.2024.108111","DOIUrl":"10.1016/j.jsb.2024.108111","url":null,"abstract":"<div><p>Osteocytes are the major actors in bone mechanobiology. Within bone matrix, they are trapped close together in a submicrometric interconnected network: the lacunocanalicular network (LCN). The interstitial fluid circulating within the LCN transmits the mechanical information to the osteocytes that convert it into a biochemical signal. Understanding the interstitial fluid dynamics is necessary to better understand the bone mechanobiology. Due to the submicrometric dimensions of the LCN, making it difficult to experimentally investigate fluid dynamics, numerical models appear as a relevant tool for such investigation. To develop such models, there is a need for geometrical and morphological data on the human LCN. This study aims at providing morphological data on the human LCN from measurement of 27 human femoral diaphysis bone samples using synchrotron radiation nano-computed tomography with an isotropic voxel size of 100 nm. Except from the canalicular diameter, the canalicular morphological parameters presented a high variability within one sample. Some differences in terms of both lacunar and canalicular morphology were observed between the male and female populations. But it has to be highlighted that all the canaliculi cannot be detected with a voxel size of 100 nm. Hence, in the current study, only a specific population of large canaliculi that could be characterize. Still, to the authors knowledge, this is the first time such a data set was introduced to the community. Further processing will be achieved in order to provide new insight on the LCN permeability.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108111"},"PeriodicalIF":3.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1047847724000510/pdfft?md5=d757da53596e50cc6e6dd899a64cf4be&pid=1-s2.0-S1047847724000510-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141766423","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":"Quantitative 3D electron microscopy characterization of mitochondrial structure, mitophagy, and organelle interactions in murine atrial fibrillation","authors":"Pavithran Guttipatti ,&nbsp;Najla Saadallah ,&nbsp;Ruiping Ji ,&nbsp;Uma Mahesh R. Avula ,&nbsp;Christopher N. Goulbourne ,&nbsp;Elaine Y. Wan","doi":"10.1016/j.jsb.2024.108110","DOIUrl":"10.1016/j.jsb.2024.108110","url":null,"abstract":"<div><p>Atrial fibrillation (AF) is the most common clinical arrhythmia, however there is limited understanding of its pathophysiology including the cellular and ultrastructural changes rendered by the irregular rhythm, which limits pharmacological therapy development. Prior work has demonstrated the importance of reactive oxygen species (ROS) and mitochondrial dysfunction in the development of AF. Mitochondrial structure, interactions with other organelles such as sarcoplasmic reticulum (SR) and T-tubules (TT), and degradation of dysfunctional mitochondria via mitophagy are important processes to understand ultrastructural changes due to AF. However, most analysis of mitochondrial structure and interactome in AF has been limited to two-dimensional (2D) modalities such as transmission electron microscopy (EM), which does not fully visualize the morphological evolution of the mitochondria during mitophagy. Herein, we utilize focused ion beam-scanning electron microscopy (FIB-SEM) and perform reconstruction of three-dimensional (3D) EM from murine left atrial samples and measure the interactions of mitochondria with SR and TT. We developed a novel 3D quantitative analysis of FIB-SEM in a murine model of AF to quantify mitophagy stage, mitophagosome size in cardiomyocytes, and mitochondrial structural remodeling when compared with control mice. We show that in our murine model of spontaneous and continuous AF due to persistent late sodium current, left atrial cardiomyocytes have heterogenous mitochondria, with a significant number which are enlarged with increased elongation and structural complexity. Mitophagosomes in AF cardiomyocytes are located at Z-lines where they neighbor large, elongated mitochondria. Mitochondria in AF cardiomyocytes show increased organelle interaction, with 5X greater contact area with SR and are 4X as likely to interact with TT when compared to control. We show that mitophagy in AF cardiomyocytes involves 2.5X larger mitophagosomes that carry increased organelle contents. In conclusion, when oxidative stress overcomes compensatory mechanisms, mitophagy in AF faces a challenge of degrading bulky complex mitochondria, which may result in increased SR and TT contacts, perhaps allowing for mitochondrial Ca²⁺ maintenance and antioxidant production.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108110"},"PeriodicalIF":3.0,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620264","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":"Exploring α-synuclein stability under the external electrostatic field: Effect of repeat unit","authors":"Javokhir Khursandov ,&nbsp;Rasulbek Mashalov ,&nbsp;Mukhriddin Makhkamov ,&nbsp;Farkhad Turgunboev ,&nbsp;Avez Sharipov ,&nbsp;Jamoliddin Razzokov","doi":"10.1016/j.jsb.2024.108109","DOIUrl":"10.1016/j.jsb.2024.108109","url":null,"abstract":"<div><p>Parkinson’s disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field’s effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"216 3","pages":"Article 108109"},"PeriodicalIF":3.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141534667","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}