Current Research in Structural Biology最新文献

{"title":"Comparative computational and experimental analyses of some natural small molecules to restore transcriptional activation function of p53 in cancer cells harbouring wild type and p53Ser46 mutant","authors":"Seyad Shefrin ,&nbsp;Anissa Nofita Sari ,&nbsp;Vipul Kumar ,&nbsp;Huayue Zhang ,&nbsp;Hazna Noor Meidinna ,&nbsp;Sunil C. Kaul ,&nbsp;Renu Wadhwa ,&nbsp;Durai Sundar","doi":"10.1016/j.crstbi.2022.09.002","DOIUrl":"10.1016/j.crstbi.2022.09.002","url":null,"abstract":"<div><p>Genetic mutations in p53 are frequently associated with many types of cancers that affect its stability and activity through multiple ways. The Ser46 residue present in the transactivation domain2 (TAD2) domain of p53 undergoes phosphorylation that blocks its degradation by MDM2 and leads to cell cycle arrest/apoptosis/necrosis upon intrinsic or extrinsic stresses. On the other hand, unphosphorylated p53 mutants escape cell arrest or death triggered by these molecular signaling axes and lead to carcinogenesis. Phosphorylation of Ser in the TAD2 domain of p53 mediates its interactions with transcription factor p62, yielding transcriptional activation of downstream pro-apoptotic genes. The p53 phosphorylation causes string-like elongated conformation that increases its binding affinity with the PH domain of p62. On the other hand, lack of phosphorylation causes helix-like motifs and low binding affinity to p62. We undertook molecular simulation analyses to investigate the potential of some natural small molecules (Withanone (Wi-N) &amp; Withaferin-A (Wi-A) from Ashwagandha; Cucurbitacin-B (Cuc-B) from bitter Cucumber; and Caffeic acid phenethyl ester (CAPE) and Artepillin C (ARC) from honeybee propolis) to interact with p62-binding region of p53 and restore its wild-type activity. We found that Wi-N, Wi-A, and Cuc-B have the potential to restore p53-p62 interaction for phosphorylation-deficient p53 mutants. Wi-N, in particular, caused a reversal of the α-helical structure into an elongated string-like conformation similar to the wild-type p53. These data suggested the use of these natural compounds for the treatment of p53^Ser46 mutant harbouring cancers. We also compared the efficiency of Wi-N, Wi-A, Cuc-B, CAPE, and ARC to abrogate Mortalin-p53 binding resulting in nuclear translocation and reactivation of p53 function and provide experimental evidence to the computational analysis. Taken together, the use of these small molecules for reactivation of p53 in cancer cells is suggested.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 320-331"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9507986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40377922","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":"Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B","authors":"Jinyu Liu ,&nbsp;Michael Kothe ,&nbsp;Jianxin Zhang ,&nbsp;Eliud Oloo ,&nbsp;Svetlana Stegalkina ,&nbsp;Sophia T. Mundle ,&nbsp;Lu Li ,&nbsp;Jinrong Zhang ,&nbsp;Leah E. Cole ,&nbsp;Lucianna Barone ,&nbsp;Hans-Peter Biemann ,&nbsp;Harry Kleanthous ,&nbsp;Natalie G. Anosova ,&nbsp;Stephen F. Anderson","doi":"10.1016/j.crstbi.2022.03.003","DOIUrl":"10.1016/j.crstbi.2022.03.003","url":null,"abstract":"<div><p><em>Clostridium difficile</em> toxins are the primary causative agents for hospital-acquired diarrhea and pseudomembranous colitis. Numerous monoclonal antibodies (mAbs) targeting different domains of <em>Clostridium difficile</em> toxin have been reported. Here we report the crystal structures of two mAbs, B1 and B2, in complex with the glycosyltransferase domain (GTD) of the <em>Clostridium difficile</em> toxin B (TcdB). B2 bound to the N-terminal 4 helix bundle of the GTD, a conserved membrane localization domain (MLD) found in the large clostridial glycosylating toxin family implicated in targeting plasma membrane. B1 bound to a distinct epitope at the hinge region between the MLD and the catalytic subdomain of the GTD. Functional studies revealed the potency of these mAbs <em>in vitro</em> and <em>in vivo</em> to be synergistic when given in combination.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 96-105"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000071/pdfft?md5=4a4136597a850e24f49d0aeffaad03e7&pid=1-s2.0-S2665928X22000071-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46043093","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":"Insight into the nucleoside transport and inhibition of human ENT1","authors":"Zhixiang Wu ,&nbsp;Zhongjie Han ,&nbsp;Wenxue Zhou ,&nbsp;Xiaohan Sun ,&nbsp;Lei Chen ,&nbsp;Shuang Yang ,&nbsp;Jianping Hu ,&nbsp;Chunhua Li","doi":"10.1016/j.crstbi.2022.05.005","DOIUrl":"10.1016/j.crstbi.2022.05.005","url":null,"abstract":"<div><p>The human equilibrative nucleoside transporter 1 (hENT1) is an effective controller of adenosine signaling by regulating its extracellular and intracellular concentration, and has become a solid drug target of clinical used adenosine reuptake inhibitors (AdoRIs). Currently, the mechanisms of adenosine transport and inhibition for hENT1 remain unclear, which greatly limits the in-depth understanding of its inner workings as well as the development of novel inhibitors. In this work, the dynamic details of hENT1 underlie adenosine transport and the inhibition mechanism of the non-nucleoside AdoRIs dilazep both were investigated by comparative long-time unbiased molecular dynamics simulations. The calculation results show that the conformational transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. One of the trimethoxyphenyl rings in dilazep serves as the adenosyl moiety of the endogenous adenosine substrate to competitively occupy the orthosteric site of hENT1. Due to extensive and various <em>VDW</em> interactions with N30, M33, M84, P308 and F334, the other trimethoxyphenyl ring is stuck in the opportunistic site near the extracellular side preventing the complete occlusion of thin gate simultaneously. Obviously, dilazep shows significant inhibitory activity by disrupting the local induce-fit action in substrate binding cavity and blocking the transport cycle of whole protein. This study not only reveals the nucleoside transport mechanism by hENT1 at atomic level, but also provides structural guidance for the subsequent design of novel non-nucleoside AdoRIs with enhanced pharmacologic properties.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 192-205"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X22000174/pdfft?md5=e1c75ea5b8ad5a522cd8b2abcc83a0c3&pid=1-s2.0-S2665928X22000174-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46964148","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":"Multifaceted membrane binding head of the SARS-CoV-2 spike protein","authors":"Anh Tran,&nbsp;Troy A. Kervin,&nbsp;Michael Overduin","doi":"10.1016/j.crstbi.2022.05.001","DOIUrl":"10.1016/j.crstbi.2022.05.001","url":null,"abstract":"<div><p>The SARS-CoV-2 spike protein presents a surface with enormous membrane binding potential to host tissues and organelles of infected cells. Its exposed trimeric head binds not only the angiotensin-converting enzyme 2 (ACE2), but also host phospholipids which are missing from all existing structures. Hence, the membrane interaction surfaces that mediate viral fusion, entry, assembly and egress remain unclear. Here the spike:membrane docking sites are identified based on membrane optimal docking area (MODA) analysis of 3D structures of spike proteins in closed and open conformations at endocytic and neutral pH levels as well as ligand complexes. This reveals multiple membrane binding sites in the closed spike head that together prefer convex membranes and are modulated by pH, fatty acids and post-translational modifications including glycosylation. The exposure of the various membrane interaction sites adjusts upon domain repositioning within the trimer, allowing formation of intermediate bilayer complexes that lead to the prefusion state while also enabling ACE2 receptor recognition. In contrast, all antibodies that target the spike head would block the membrane docking process that precedes ACE2 recognition. Together this illuminates the engagements of the spike protein with plasma, endocytic, ER or exocytic vesicle membranes that help to drive the cycle of viral infection, and offers novel sites for intervention.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 146-157"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9109970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49007296","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":"Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation","authors":"Ramachandira Prabu ,&nbsp;Amaresh Mohanty ,&nbsp;Susmida Seni Balakrishnan ,&nbsp;G. Jayalakshmi ,&nbsp;Kothandapani Sundar","doi":"10.1016/j.crstbi.2022.03.002","DOIUrl":"10.1016/j.crstbi.2022.03.002","url":null,"abstract":"<div><p>Intercellular adhesion (IcaADBC) operon is necessary for PNAG (Polyβ-1,6-N-acetyl-D-glucosamine) biosynthesis of biofilm formation in <em>Staphylococcus epidermidis</em>. IcaC protein has a wide range of functions in terms of growth phase variation, migration, transposon insertion, PNAG modification, biofilm formation. Unusual TTTA signature motifs were identified from nucleotide sequence. Asparagine-linked glycosylation consensus motifs were identified at position 169 and 240. <em>S</em>. <em>epidermidis</em> was a close evolutionary association with <em>S</em>. <em>haemolyticus</em> and other <em>Staphylococcus</em> spp. Due to the non-availability of crystal structure, protein threading procedure was selected for constructing a full length IcaC three-dimensional structure. QMEANBrane structure quality assessment with model scores −100000 range within predicted integral membrane structure. IcaC motif constitutes 18 transmembrane helix, 37 helix-helix interaction, 8 beta turn, 2 gamma turn. Binding free energy was calculated with their succinate ligand docking form hydrogen bond with critical amino acids showed ΔG score −2.574 ​kJ/mol using Schrödinger. Serine (Ser96), Glutamic acid (Glu99), Tryptophan (Trp191) were active site amino acids form the catalytic core required for O-succinyltransferase function. Molecular dynamics simulation (MDS) was performed to evaluate the stability of IcaC protein and IcaC-Succinate binding complexes with the active site amino acids throughout trajectories captured with time scale 100 ns simulation period using GROMACS 4.5.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 78-86"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665928X2200006X/pdfft?md5=b2be9e8a0290b02be1d65323939b1627&pid=1-s2.0-S2665928X2200006X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42035642","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":"Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions","authors":"Payam Arghavani,&nbsp;Mitra Pirhaghi,&nbsp;Faezeh Moosavi-Movahedi,&nbsp;Fatemeh Mamashli,&nbsp;Elnaz Hosseini,&nbsp;Ali Akbar Moosavi-Movahedi","doi":"10.1016/j.crstbi.2022.11.002","DOIUrl":"10.1016/j.crstbi.2022.11.002","url":null,"abstract":"<div><p>Protein oligomerization has two notable aspects: it is crucial for the performing cellular and molecular processes accurately, and it produces amyloid fibril precursors. Although a clear explanation for amyloidosis as a whole is lacking, most studies have emphasized the importance of protein misfolding followed by formation of cytotoxic oligomer structures, which are responsible for disorders as diverse as neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, and metabolic disorders, such as type 2 diabetes. Constant surveillance by oligomeric protein structures known as molecular chaperones enables cells to overcome the challenge of misfolded proteins and their harmful assemblies. These molecular chaperones encounter proteins in cells, and benefit cell survival as long as they perform correctly. Thus, this review highlights the roles of structural aspects of chaperone protein oligomers in determining cell fate—either succumbing to amyloid oligomers or survival—as well as experimental approaches used to investigate these entities.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 356-364"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9747510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10713287","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":"Putting on molecular weight: Enabling cryo-EM structure determination of sub-100-kDa proteins","authors":"Koen Wentinck ,&nbsp;Christos Gogou ,&nbsp;Dimphna H. Meijer","doi":"10.1016/j.crstbi.2022.09.005","DOIUrl":"10.1016/j.crstbi.2022.09.005","url":null,"abstract":"<div><p>Significant advances in the past decade have enabled high-resolution structure determination of a vast variety of proteins by cryogenic electron microscopy single particle analysis. Despite improved sample preparation, next-generation imaging hardware, and advanced single particle analysis algorithms, small proteins remain elusive for reconstruction due to low signal-to-noise and lack of distinctive structural features. Multiple efforts have therefore been directed at the development of size-increase techniques for small proteins. Here we review the latest methods for increasing effective molecular weight of proteins &lt;100 ​kDa through target protein binding or target protein fusion - specifically by using nanobody-based assemblies, fusion tags, and symmetric scaffolds. Finally, we summarize these state-of-the-art techniques into a decision-tree to facilitate the design of tailored future approaches, and thus for further exploration of ever-smaller proteins that make up the largest part of the human genome.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 332-337"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9562432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33516105","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":"Mutations in human SARS-CoV-2 spike proteins, potential drug binding and epitope sites for COVID-19 therapeutics development","authors":"Kunchur Guruprasad","doi":"10.1016/j.crstbi.2022.01.002","DOIUrl":"10.1016/j.crstbi.2022.01.002","url":null,"abstract":"<div><p>The comparison of 303,250 human SARS-CoV-2 spike protein sequences with the reference protein sequence Wuhan-Hu-1, showed ∼96.5% of the spike protein sequence has undergone the mutations till date, since outbreak of the COVID-19 pandemic disease that was first reported in December 2019. A total of 1,269,629 mutations were detected corresponding to 1,229 distinct mutation sites in the spike proteins comprising 1,273 amino acid residues. Thereby, ∼3.5% of the human SARS-CoV-2 spike protein sequence has remained invariant in the past two years. Considering different mutations occur at the same mutation site, a total of 4,729 distinct mutations were observed and are catalogued in the present work. The WHO/CDC, U.S.A., classification and definitions for the current variants being monitored (VBM) and variant of concern (VOC) are assigned to the SARS-CoV-2 spike protein mutations identified in the present work along with a list of other amino acid substitutions observed for the variants. All 195 amino acid residues in receptor binding domain (Thr333-Pro527) were associated with mutations in SARS-CoV-2 spike protein sequence including Lys417, Tyr449, Tyr453, Ala475, Asn487, Thr500, Asn501 and Gly502 that make interactions with the ACE-2 receptor ≤3.2 ​Å distance as observed in the crystal structure complex available in the Protein Data Bank (PDB code:<span>6LZG</span><svg><path></path></svg>). However, not all these residues were mutated in the same spike protein. Especially, Gly502 mutated only in two spike protein sequences and Tyr449 mutated only in seven spike protein sequences among the spike protein sequences analysed constitute potential sites for the design of suitable inhibitors/drugs. Further, forty-four invariant residues were observed that correspond to ten domains/regions in the SARS-CoV-2 spike protein and some of the residues exposed to the protein surface amongst these may serve as epitope targets to develop monoclonal antibodies.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 41-50"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/16/87/main.PMC8824715.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39622806","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":"Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins","authors":"Maxim N. Brodmerkel ,&nbsp;Emiliano De Santis ,&nbsp;Charlotte Uetrecht ,&nbsp;Carl Caleman ,&nbsp;Erik G. Marklund","doi":"10.1016/j.crstbi.2022.10.001","DOIUrl":"10.1016/j.crstbi.2022.10.001","url":null,"abstract":"<div><p>Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution <em>in silico</em> can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Pages 338-348"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40515049","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 biology - Painting the mechanistic landscape of biomolecules","authors":"Tom L. Blundell,&nbsp;Peter E. Wright","doi":"10.1016/j.crstbi.2022.05.004","DOIUrl":"10.1016/j.crstbi.2022.05.004","url":null,"abstract":"","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"4 ","pages":"Page iv"},"PeriodicalIF":2.8,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e9/09/main.PMC9795323.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10471102","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}