Quarterly Reviews of Biophysics最新文献

{"title":"Copper chaperone blocks amyloid formation via ternary complex.","authors":"Istvan Horvath,&nbsp;Tony Werner,&nbsp;Ranjeet Kumar,&nbsp;Pernilla Wittung-Stafshede","doi":"10.1017/S0033583518000045","DOIUrl":"https://doi.org/10.1017/S0033583518000045","url":null,"abstract":"<p><p>Protein misfolding in cells is avoided by a network of protein chaperones that detect misfolded or partially folded species. When proteins escape these control systems, misfolding may result in protein aggregation and amyloid formation. We here show that aggregation of the amyloidogenic protein α-synuclein (αS), the key player in Parkinson's disease, is controlled by the copper transport protein Atox1 in vitro. Copper ions are not freely available in the cellular environment, but when provided by Atox1, the resulting copper-dependent ternary complex blocks αS aggregation. Because the same inhibition was found for a truncated version of αS, lacking the C-terminal part, it appears that Atox1 interacts with the N-terminal copper site in αS. Metal-dependent chaperoning may be yet another manner in which cells control its proteome.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37092600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anticipating innovations in structural biology.","authors":"Helen M Berman, Catherine L Lawson, Brinda Vallat, Margaret J Gabanyi","doi":"10.1017/S0033583518000057","DOIUrl":"10.1017/S0033583518000057","url":null,"abstract":"<p><p>In this review, we describe how the interplay among science, technology and community interests contributed to the evolution of four structural biology data resources. We present the method by which data deposited by scientists are prepared for worldwide distribution, and argue that data archiving in a trusted repository must be an integral part of any scientific investigation.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":7.2,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438187/pdf/nihms-996514.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37266770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.","authors":"Giulia Palermo,&nbsp;Janice S Chen,&nbsp;Clarisse G Ricci,&nbsp;Ivan Rivalta,&nbsp;Martin Jinek,&nbsp;Victor S Batista,&nbsp;Jennifer A Doudna,&nbsp;J Andrew McCammon","doi":"10.1017/S0033583518000070","DOIUrl":"10.1017/S0033583518000070","url":null,"abstract":"<p><p>Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 - a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution - reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1-3 regions 'sense' nucleic acids, 'regulate' the HNH conformational transition, and ultimately 'lock' the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1-3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36830164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The enigmatic ribosomal stalk.","authors":"Anders Liljas,&nbsp;Suparna Sanyal","doi":"10.1017/S0033583518000100","DOIUrl":"https://doi.org/10.1017/S0033583518000100","url":null,"abstract":"<p><p>The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000100","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37092596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RecA kinetically selects homologous DNA by testing a five- or six-nucleotide matching sequence and deforming the second DNA.","authors":"Masayuki Takahashi","doi":"10.1017/S0033583518000094","DOIUrl":"https://doi.org/10.1017/S0033583518000094","url":null,"abstract":"<p><p>RecA family proteins pair two DNAs with the same sequence to promote strand exchange during homologous recombination. To understand how RecA proteins search for and recognize homology, we sought to determine the length of homologous sequence that permits RecA to start its reaction. Specifically, we analyzed the effect of sequence heterogeneity on the association rate of homologous DNA with RecA/single-stranded DNA complex. We assumed that the reaction can start with equal likelihood at any point in the DNA, and that sequence heterogeneity abolishes some possible initiation sites. This analysis revealed that the effective recognition size is five or six nucleotides, larger than the three nucleotides recognized by a RecA monomer. Because the first DNA is elongated 1.5-fold by intercalation of amino acid residues of RecA every three bases, the second bound DNA must be elongated to pair with the first. Because this length is similar to estimates based on the strand-exchange reaction or DNA pair formation, the homology test is likely to occur primarily at the association step. The energetic difference due to the absence of hydrogen bonding is too small to discriminate single-nucleotide heterogeneity over a five- or six-nucleotide sequence. The selection is very likely to be made kinetically, and probably involves some structural factor other than Watson-Crick hydrogen bonding. It would be valuable to determine whether this is also the case for other biological reactions involving DNA base complementarity, such as replication, transcription, and translation.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37092599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Former QRB Editor Richard Henderson awarded the Nobel Prize.","authors":"Bengt Nordén,&nbsp;David Lilley","doi":"10.1017/S003358351800001X","DOIUrl":"https://doi.org/10.1017/S003358351800001X","url":null,"abstract":"","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S003358351800001X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37092598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Solid and fluid segments within the same molecule of stratum corneum ceramide lipid.","authors":"Quoc Dat Pham,&nbsp;Enamul H Mojumdar,&nbsp;Gert S Gooris,&nbsp;Joke A Bouwstra,&nbsp;Emma Sparr,&nbsp;Daniel Topgaard","doi":"10.1017/S0033583518000069","DOIUrl":"https://doi.org/10.1017/S0033583518000069","url":null,"abstract":"<p><p>The outer layer of the skin, stratum corneum (SC) is an efficient transport barrier and it tolerates mechanical deformation. At physiological conditions, the majority of SC lipids are solid, while the presence of a small amount of fluid lipids is considered crucial for SC barrier and material properties. Here we use solid-state and diffusion nuclear magnetic resonance to characterize the composition and molecular dynamics of the fluid lipid fraction in SC model lipids, focusing on the role of the essential SC lipid CER EOS, which is a ceramide esterified omega-hydroxy sphingosine linoleate with very long chain. We show that both rigid and mobile structures are present within the same CER EOS molecule, and that the linoleate segments undergo fast isotropic reorientation while exhibiting extraordinarily slow self-diffusion. The characterization of this unusual self-assembly in SC lipids provides deepened insight into the molecular arrangement in the SC extracellular lipid matrix and the role of CER EOS linoleate in the healthy and diseased skin.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37091134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase - CORRIGENDUM.","authors":"Amirhossein Taghavi,&nbsp;Paul van der Schoot,&nbsp;Joshua T Berryman","doi":"10.1017/S0033583517000142","DOIUrl":"https://doi.org/10.1017/S0033583517000142","url":null,"abstract":"","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583517000142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35716971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design.","authors":"Vaida Linkuvienė,&nbsp;Asta Zubrienė,&nbsp;Elena Manakova,&nbsp;Vytautas Petrauskas,&nbsp;Lina Baranauskienė,&nbsp;Audrius Zakšauskas,&nbsp;Alexey Smirnov,&nbsp;Saulius Gražulis,&nbsp;John E Ladbury,&nbsp;Daumantas Matulis","doi":"10.1017/S0033583518000082","DOIUrl":"https://doi.org/10.1017/S0033583518000082","url":null,"abstract":"<p><p>The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583518000082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37092594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Secondary nucleation of monomers on fibril surface dominates α-synuclein aggregation and provides autocatalytic amyloid amplification.","authors":"Ricardo Gaspar,&nbsp;Georg Meisl,&nbsp;Alexander K Buell,&nbsp;Laurence Young,&nbsp;Clemens F Kaminski,&nbsp;Tuomas P J Knowles,&nbsp;Emma Sparr,&nbsp;Sara Linse","doi":"10.1017/S0033583516000172","DOIUrl":"https://doi.org/10.1017/S0033583516000172","url":null,"abstract":"<p><p>Parkinson's disease (PD) is characterized by proteinaceous aggregates named Lewy Bodies and Lewy Neurites containing α-synuclein fibrils. The underlying aggregation mechanism of this protein is dominated by a secondary process at mildly acidic pH, as in endosomes and other organelles. This effect manifests as a strong acceleration of the aggregation in the presence of seeds and a weak dependence of the aggregation rate on monomer concentration. The molecular mechanism underlying this process could be nucleation of monomers on fibril surfaces or fibril fragmentation. Here, we aim to distinguish between these mechanisms. The nature of the secondary processes was investigated using differential sedimentation analysis, trap and seed experiments, quartz crystal microbalance experiments and super-resolution microscopy. The results identify secondary nucleation of monomers on the fibril surface as the dominant secondary process leading to rapid generation of new aggregates, while no significant contribution from fragmentation was found. The newly generated oligomeric species quickly elongate to further serve as templates for secondary nucleation and this may have important implications in the spreading of PD.</p>","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583516000172","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35245190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}