Santhosh Sankar , Preeti Preeti , Kavya Ravikumar , Amrendra Kumar , Yedu Prasad , Sukriti Pal , Desirazu N. Rao , Handanahal S. Savithri , Nagasuma Chandra
{"title":"Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase","authors":"Santhosh Sankar , Preeti Preeti , Kavya Ravikumar , Amrendra Kumar , Yedu Prasad , Sukriti Pal , Desirazu N. Rao , Handanahal S. Savithri , Nagasuma Chandra","doi":"10.1016/j.crstbi.2023.100108","DOIUrl":"https://doi.org/10.1016/j.crstbi.2023.100108","url":null,"abstract":"","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X23000144/pdfft?md5=58c2a7698f99ec6ba39e7a85575af79a&pid=1-s2.0-S2665928X23000144-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138436767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cryo-EM structure of the trehalose monomycolate transporter, MmpL3, reconstituted into peptidiscs","authors":"Julie Couston , Zongxin Guo , Kaituo Wang , Pontus Gourdon , Mickaël Blaise","doi":"10.1016/j.crstbi.2023.100109","DOIUrl":"https://doi.org/10.1016/j.crstbi.2023.100109","url":null,"abstract":"<div><p>Mycobacteria have an atypical thick and waxy cell wall. One of the major building blocks of such mycomembrane is trehalose monomycolate (TMM). TMM is a mycolic acid ester of trehalose that possesses long acyl chains with up to 90 carbon atoms. TMM represents an essential component of mycobacteria and is synthesized in the cytoplasm, and then flipped over the plasma membrane by a specific transporter known as MmpL3. Over the last decade, MmpL3 has emerged as an attractive drug target to combat mycobacterial infections. Recent three-dimensional structures of MmpL3 determined by X-ray crystallography and cryo-EM have increased our understanding of the TMM transport, and the mode of action of inhibiting compounds. These structures were obtained in the presence of detergent and/or in a lipidic environment. In this study, we demonstrate the possibility of obtaining a high-quality cryo-EM structure of MmpL3 without any presence of detergent through the reconstitution of the protein into peptidiscs. The structure was determined at an overall resolution of 3.2 Å and demonstrates that the overall structure of MmpL3 is preserved as compared to previous structures. Further, the study identified a new structural arrangement of the linker that fuses the two subdomains of the transmembrane domain, suggesting the feature may serve a role in the transport process.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":"Article 100109"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X23000156/pdfft?md5=30d57577920410fae3129100020f9753&pid=1-s2.0-S2665928X23000156-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134653072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The conserved crown bridge loop at the catalytic centre of enzymes of the haloacid dehalogenase superfamily","authors":"David P. Leader, E. James Milner-White","doi":"10.1016/j.crstbi.2023.100105","DOIUrl":"10.1016/j.crstbi.2023.100105","url":null,"abstract":"<div><p>The crown bridge loop is hexapeptide motif in which the backbone carbonyl group at position 1 is hydrogen bonded to the backbone imino groups of positions 4 and 6. Residues at positions 1 and 4–6 are held in a tight substructure, but different orientations of the plane of the peptide bond between positions 2 and 3 result in two conformers: the 2,3-α<sub>R</sub>α<sub>R</sub> crown bridge loop — found in approximately 7% of proteins — and the 2,3-β<sub>R</sub>α<sub>L</sub> crown bridge loop, found in approximately 1–2% of proteins. We constructed a relational database in which we identified 60 instances of the 2,3-β<sub>R</sub>α<sub>L</sub> conformer, and find that about half occur in enzymes of the haloacid dehalogenase (HAD) superfamily, where they are located next to the catalytic aspartate residue. Analysis of additional enzymes of the HAD superfamily in the extensive SCOPe dataset showed this crown bridge loop to be a conserved feature. Examination of available structures showed that the 2,3-β<sub>R</sub>α<sub>L</sub> conformation — but not the 2,3-α<sub>R</sub>α<sub>R</sub> conformation — allows the backbone carbonyl group at position 2 to interact with the essential Mg<sup>2+</sup> ion. The possibility of interconversion between the 2,3-β<sub>R</sub>α<sub>L</sub> and 2,3-α<sub>R</sub>α<sub>R</sub> conformations during catalysis is discussed.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":"Article 100105"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/69/e8/main.PMC10541634.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41178270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Soluble domains of cytochrome c-556 and Rieske iron–sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis","authors":"Hiraku Kishimoto , Chihiro Azai , Tomoya Yamamoto , Risa Mutoh , Tetsuko Nakaniwa , Hideaki Tanaka , Yohei Miyanoiri , Genji Kurisu , Hirozo Oh-oka","doi":"10.1016/j.crstbi.2023.100101","DOIUrl":"https://doi.org/10.1016/j.crstbi.2023.100101","url":null,"abstract":"<div><p>In photosynthetic green sulfur bacteria, the electron transfer reaction from menaquinol:cytochrome <em>c</em> oxidoreductase to the P840 reaction center (RC) complex occurs directly without any involvement of soluble electron carrier protein(s). X-ray crystallography has determined the three-dimensional structures of the soluble domains of the <em>CT0073</em> gene product and Rieske iron-sulfur protein (ISP). The former is a mono-heme cytochrome <em>c</em> with an α-absorption peak at 556 nm. The overall fold of the soluble domain of cytochrome <em>c</em>-556 (designated as cyt <em>c</em>-556<sub><em>sol</em></sub>) consists of four α-helices and is very similar to that of water-soluble cyt <em>c</em>-554 that independently functions as an electron donor to the P840 RC complex. However, the latter's remarkably long and flexible loop between the α3 and α4 helices seems to make it impossible to be a substitute for the former. The structure of the soluble domain of the Rieske ISP (Rieske<sub><em>sol</em></sub> protein) shows a typical β-sheets-dominated fold with a small cluster-binding and a large subdomain. The architecture of the Rieske<sub><em>sol</em></sub> protein is bilobal and belongs to those of <em>b</em><sub>6</sub><em>f</em>-type Rieske ISPs. Nuclear magnetic resonance (NMR) measurements revealed weak non-polar but specific interaction sites on Rieske<sub><em>sol</em></sub> protein when mixed with cyt <em>c</em>-556<sub><em>sol</em></sub>. Therefore, menaquinol:cytochrome <em>c</em> oxidoreductase in green sulfur bacteria features a Rieske/cyt<em>b</em> complex tightly associated with membrane-anchored cyt <em>c</em>-556.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"5 ","pages":"Article 100101"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49813934","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}
Vladimir Y. Lunin , Natalia L. Lunina , Alexandre G. Urzhumtsev
{"title":"Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation","authors":"Vladimir Y. Lunin , Natalia L. Lunina , Alexandre G. Urzhumtsev","doi":"10.1016/j.crstbi.2023.100102","DOIUrl":"10.1016/j.crstbi.2023.100102","url":null,"abstract":"<div><p>In X-ray crystallography and cryo-EM, experimental maps can be heterogeneous, showing different level of details in different regions. In this work we interpret heterogeneity in terms of two parameters, assigned individually for each atom, combining the conventional atomic displacement parameter with the resolution of the atomic image in the map. We propose a local real-space procedure to estimate the values of these heterogeneity parameters, assuming that a fragment of the density map and atomic positions are given. The procedure is based on an analytic representation of the atomic image, as a function of the inhomogeneity parameters and atomic coordinates. In this article, we report the results of the tests both with maps simulated and those derived from experimental data. For simulated maps containing regions with different resolutions, the method determines the local map resolution around the atomic centers and the values of the displacement parameter with reasonable accuracy. For experimental maps, obtained as a Fourier synthesis of a given global resolution, estimated values of the local resolution are close to the global one, and the values of the estimated displacement parameters are close to the respective values of the closest atoms in the refined model. Shown successful applications of the proposed method to experimental crystallographic and cryo-EM maps can be seen as a practical proof of method.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":"Article 100102"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ff/50/main.PMC10329102.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9812483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gary X. Shaw , Lixin Fan , Scott Cherry , Genbin Shi , Joseph E. Tropea , Xinhua Ji
{"title":"Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design","authors":"Gary X. Shaw , Lixin Fan , Scott Cherry , Genbin Shi , Joseph E. Tropea , Xinhua Ji","doi":"10.1016/j.crstbi.2023.100095","DOIUrl":"https://doi.org/10.1016/j.crstbi.2023.100095","url":null,"abstract":"<div><p>Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. <em>Helicobacter pylori</em> infection occurs in human stomach of over 50% of the world population, but first-line therapies for the infection are facing rapidly increasing resistance. Novel antibiotics are urgently needed, toward which structural information on potential targets is critical. We have determined the crystal structure of <em>H. pylori</em> DHNA (HpDHNA) in complex with a pterin molecule (HpDHNA:Pterin) at 1.49-Å resolution. The HpDHNA:Pterin complex forms a tetramer in crystal. The tetramer is also observed in solution by dynamic light scattering and confirmed by small-angle X-ray scattering. To date, all but one reported DHNA structures are octameric complexes. As the only exception, ligand-free <em>Mycobacterium tuberculosis</em> DHNA (apo-MtDHNA) forms a tetramer in crystal, but its active sites are only partially formed. In contrast, the tetrameric HpDHNA:Pterin complex has well-formed active sites. Each active site accommodates one pterin molecule, but the exit of active site is blocked by two amino acid residues exhibiting a contact distance of 5.2 Å. In contrast, the corresponding contact distance in <em>Staphylococcus aureus</em> DHNA (SaDHNA) is twice the size, ranging from 9.8 to 10.5 Å, for ligand-free enzyme, the substrate complex, the product complex, and an inhibitor complex. This large contact distance indicates that the active site of SaDHNA is wide open. We propose that this isozyme-specific contact distance (ISCD) is a characteristic feature of DHNA active site. Comparative analysis of HpDHNA and SaDHNA structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"5 ","pages":"Article 100095"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49773028","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}
Lucas de Freitas Pedrosa , Paul de Vos , João Paulo Fabi
{"title":"Nature's soothing solution: Harnessing the potential of food-derived polysaccharides to control inflammation","authors":"Lucas de Freitas Pedrosa , Paul de Vos , João Paulo Fabi","doi":"10.1016/j.crstbi.2023.100112","DOIUrl":"https://doi.org/10.1016/j.crstbi.2023.100112","url":null,"abstract":"<div><p>Reducing inflammation by diet is a major goal for prevention or lowering symptoms of a variety of diseases, such as auto-immune reactions and cancers. Natural polysaccharides are increasingly gaining attention due to their potential immunomodulating capacity. Structures of those molecules are highly important for their effects on the innate immune system, cytokine production and secretion, and enzymes in immune cells. Such polysaccharides include β-glucans, pectins, fucoidans, and fructans. To better understand the potential of these immunomodulatory molecules, it is crucial to enhance dedicated research in the area. A bibliometric analysis was performed to set a starting observation point. Major pillars of inflammation, such as pattern recognition receptors (PRRs), enzymatic production of inflammatory molecules, and involvement in specific pathways such as Nuclear-factor kappa-B (NF-kB), involved in cell transcription, survival, and cytokine production, and mitogen-activated protein kinase (MAPK), a regulator of genetic expression, mitosis, and cell differentiation. Therefore, the outcomes from polysaccharide applications in those scenarios are discussed.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":"Article 100112"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X23000181/pdfft?md5=ec0180249c9abf086a14417e3c082f0c&pid=1-s2.0-S2665928X23000181-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134653073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK","authors":"Aditi Maulik , Devleena Bandopadhyay , Mahavir Singh","doi":"10.1016/j.crstbi.2023.100099","DOIUrl":"10.1016/j.crstbi.2023.100099","url":null,"abstract":"<div><p>Long Intergenic Non-coding RNAs (lincRNAs) are the largest class of long non-coding RNAs in eukaryotes, originating from the genome's intergenic regions. A ∼4 kb long lincRNA-p21 is derived from a transcription unit next to the p21/Cdkn1a gene locus. LincRNA-p21 plays regulatory roles in p53-dependent transcriptional and translational repression through its physical association with proteins such as hnRNPK and HuR. It is also involved in the aberrant gene expression in different cancers. In this study, we have carried out a bioinformatics-based gene analysis and annotation of lincRNA-p21 to show that it is highly conserved in primates and identified two conserved domains in its sequence at the 5′ and 3′ terminal regions. hnRNPK has previously been shown to interact specifically with the 5′ conserved region of lincRNA-p21. hnRNPK is known to bind preferentially to the pyrimidine-rich (poly C) nucleotide sequences in RNAs. Interestingly, we observed a single occurrence of a cytosine-rich patch (C-patch) consisting of a CUCCCGC sequence in the 5′ conserved region of human lincRNA-p21, making it a putative hnRNPK binding motif. Using NMR and ITC experiments, we showed that the single-stranded C-patch containing RNA sequence motif interacts specifically with the KH3 domain of hnRNPK.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"5 ","pages":"Article 100099"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9c/41/main.PMC10023864.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9155549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural modelling and dynamics of full-length of TLR10 sheds light on possible modes of dimerization, ligand binding and mechanism of action","authors":"Vikas Tiwari, R. Sowdhamini","doi":"10.1016/j.crstbi.2023.100097","DOIUrl":"10.1016/j.crstbi.2023.100097","url":null,"abstract":"<div><p>Toll like receptors (TLRs) play a pivotal role in innate and adaptive immunity. There are 10 TLRs in the human genome, of which TLR10 is the least characterized. Genetic polymorphism of TLR10 has been shown to be associated with multiple diseases including tuberculosis and rheumatoid arthritis. TLR10 consists of an extracellular domain (ECD), a single-pass transmembrane (TM) helix and intracellular TIR (Toll/Interleukin-1 receptor) domain. ECD is employed for ligand recognition and the intracellular domain interacts with other TIR domain-containing adapter proteins for signal transduction. Experimental structure of ECD or TM domain is not available for TLR10. In this study, we have modelled multiple forms of TLR10-ECD dimers, such as closed and open forms, starting from available structures of homologues. Subsequently, multiple full-length TLR10 homodimer models were generated by utilizing homology modelling and protein-protein docking. The dynamics of these models in membrane-aqueous environment revealed the global motion of ECD and TIR domain towards membrane bilayer. The TIR domain residues exhibited high root mean square fluctuation compared to ECD. The ‘closed form’ model was observed to be energetically more favorable than ‘open form’ model. The evaluation of persistent interchain interactions, along with their conservation score, unveiled critical residues for each model. Further, the binding of dsRNA to TLR10 was modelled by defined and blind docking approaches. Differential binding of dsRNA to the protomers of TLR10 was observed upon simulation that could provide clues on ligand disassociation. Dynamic network analysis revealed that the ‘open form’ model can be the functional form while ‘closed form’ model can be the apo form of TLR10.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"5 ","pages":"Article 100097"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/18/2e/main.PMC9996232.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9157311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pragyan P. Parida, Deepa Saraswathi, Subbarao M.V. Mopidevi, Sreejith Raran-Kurussi
{"title":"Advancing large-scale production of TEV protease through an innovative NT* tag-based fusion construct","authors":"Pragyan P. Parida, Deepa Saraswathi, Subbarao M.V. Mopidevi, Sreejith Raran-Kurussi","doi":"10.1016/j.crstbi.2023.100106","DOIUrl":"10.1016/j.crstbi.2023.100106","url":null,"abstract":"<div><p>Tobacco etch virus Protease (TEVp), a cysteine protease, is renowned for its remarkable specific proteolysis, making it an invaluable tool for removing fusion tags from recombinant proteins. However, TEV protease's inherent insolubility limits its broad application. Fusion constructs like an N-terminal MBP fusion, known for its improved solubility, have been employed for TEVp production to address this issue. In this study, we fused the TEVp with the N-terminal domain of the spider silk protein, specifically utilizing a charge-reversed mutant (D40K/K65D) of the N-terminal domain of major ampullate spidroin-1 protein from <em>Euprosthenops australis</em>, referred to as NT*. This fusion construct contains a TEVp cleavage site, enabling intracellular self-processing and the release of a His<sub>7</sub>-tagged protease. The significant increase in soluble protein expression allowed us to purify approximately 90–100 mg of TEVp from a 1-L <em>E. coli</em> culture, surpassing previous findings by a considerable margin. The enzyme remained stable and catalytically active even after several months of storage in a deep freezer (−80 °C).</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"6 ","pages":"Article 100106"},"PeriodicalIF":2.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9e/23/main.PMC10563009.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41194127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}