Quarterly Reviews of Biophysics最新文献_第4页

A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions. DNA合作两态平衡的定量模型:实验测试、见解和预测。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-03-16 DOI: 10.1017/S0033583521000032

J Michael Schurr

{"title":"A quantitative model of a cooperative two-state equilibrium in DNA: experimental tests, insights, and predictions.","authors":"J Michael Schurr","doi":"10.1017/S0033583521000032","DOIUrl":"https://doi.org/10.1017/S0033583521000032","url":null,"abstract":"Quantitative parameters for a two-state cooperative transition in duplex DNAs were finally obtained during the last 5 years. After a brief discussion of observations pertaining to the existence of the two-state equilibrium per se, the lengths, torsion, and bending elastic constants of the two states involved and the cooperativity parameter of the model are simply stated. Experimental tests of model predictions for the responses of DNA to small applied stretching, twisting, and bending stresses, and changes in temperature, ionic conditions, and sequence are described. The mechanism and significance of the large cooperativity, which enables significant DNA responses to such small perturbations, are also noted. The capacity of the model to resolve a number of long-standing and sometimes interconnected puzzles in the extant literature, including the origin of the broad pre-melting transition studied by numerous workers in the 1960s and 1970s, is demonstrated. Under certain conditions, the model predicts significant long-range attractive or repulsive interactions between hypothetical proteins with strong preferences for one or the other state that are bound to well-separated sites on the same DNA. A scenario is proposed for the activation of the ilvPG promoter on a supercoiled DNA by integration host factor.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2021-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583521000032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25481012","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}

引用次数: 3

Current limitations to high-resolution structure determination by single-particle cryoEM. 单粒子低温电镜测定高分辨率结构的局限性。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-03-11 DOI: 10.1017/S0033583521000020

Edoardo D'Imprima, Werner Kühlbrandt

引用次数: 18

Hydrophobic interactions control the self-assembly of DNA and cellulose. 疏水相互作用控制DNA和纤维素的自组装。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-02-05 DOI: 10.1017/S0033583521000019

Björn Lindman, Bruno Medronho, Luís Alves, Magnus Norgren, Lars Nordenskiöld

{"title":"Hydrophobic interactions control the self-assembly of DNA and cellulose.","authors":"Björn Lindman, Bruno Medronho, Luís Alves, Magnus Norgren, Lars Nordenskiöld","doi":"10.1017/S0033583521000019","DOIUrl":"https://doi.org/10.1017/S0033583521000019","url":null,"abstract":"Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly studied and are well understood. On the other hand, the detailed roles of hydrogen bonding and hydrophobic interactions have remained controversial. It is found that the contributions of hydrophobic interactions in driving important processes, like the double-helix formation of DNA and the aqueous dissolution of cellulose, are dominating whereas the net contribution from hydrogen bonding is small. In reviewing the roles of different interactions for DNA and cellulose it is useful to compare with the self-assembly features of surfactants, the simplest case of amphiphilic molecules. Pertinent information on the amphiphilic character of cellulose and DNA can be obtained from the association with surfactants, as well as on modifying the hydrophobic interactions by additives.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2021-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583521000019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25334280","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}

引用次数: 38

Setting up and operating a cryo-EM laboratory. 建立和操作低温电子显微镜实验室。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-01-08 DOI: 10.1017/S003358352000013X

Deryck J Mills

{"title":"Setting up and operating a cryo-EM laboratory.","authors":"Deryck J Mills","doi":"10.1017/S003358352000013X","DOIUrl":"https://doi.org/10.1017/S003358352000013X","url":null,"abstract":"Cryo-electron microscopy (cryo-EM) has become the technique of choice for structural biology of macromolecular assemblies, after the 'resolution revolution' that has occurred in this field since 2012. With a suitable instrument, an appropriate electron detector and, last but not least, a cooperative sample it is now possible to collect images from which macromolecular structures can be determined to better than 2 Å resolution, where reliable atomic models can be built. By electron tomography and sub-tomogram averaging of cryo-samples, it is also possible to reconstruct subcellular structures to sub-nanometre resolution. This review describes the infrastructure that is needed to achieve this goal. Ideally, a cryo-EM lab will have a dedicated 300 kV electron microscope for data recording and a 200 kV instrument for screening cryo-samples, both with direct electron detectors, and at least one 120 kV EM for negative-stain screening at room temperature. Added to this should be ancillary equipment for specimen preparation, including a light microscope, carbon coater, plasma cleaner, glow discharge unit, a device for fast, robotic sample freezing, liquid nitrogen storage Dewars and a ready supply of clean liquid nitrogen. In practice, of course, the available budget will determine the number and types of microscopes and how elaborate the lab can be. The cryo-EM lab should be designed with adequate space for the electron microscopes and ancillary equipment, and should allow for sufficient storage space. Each electron microscope room should be connected to the image-processing computers by fibre-optic cables for the rapid transfer of large datasets. The cryo-EM lab should be overseen by a facility manager whose responsibilities include the day-to-day tasks to ensure that all microscopes are operating perfectly, organising service and repairs to minimise downtime, and controlling the budget. Large facilities will require additional support staff who help to oversee the operation of the facility and instruct new users.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2021-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S003358352000013X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38795828","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}

引用次数: 8

Macromolecular room temperature crystallography. 大分子室温结晶学。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-01-08 DOI: 10.1017/S0033583520000128

Marcus Fischer

引用次数: 20

Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism - CORRIGENDUM. 遗传密码和基因组域的能量映射:密码进化和分子达尔文主义的含义-勘误。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2020-12-10 DOI: 10.1017/S0033583520000116

Horst H Klump, Jens Völker, Kenneth J Breslauer

引用次数: 1

Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases - ERRATUM. 阿尔茨海默病和帕金森病体内模型中蛋白质错误折叠和聚集的生物物理学研究-勘误。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2020-11-18 DOI: 10.1017/S0033583520000104

Tessa Sinnige, Karen Stroobants, Christopher M Dobson, Michele Vendruscolo

{"title":"Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases - ERRATUM.","authors":"Tessa Sinnige, Karen Stroobants, Christopher M Dobson, Michele Vendruscolo","doi":"10.1017/S0033583520000104","DOIUrl":"https://doi.org/10.1017/S0033583520000104","url":null,"abstract":"Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD. Because biophysical methods have enabled an accurate quantification and a detailed understanding of the molecular mechanisms underlying protein misfolding and aggregation in vitro, we expect that the further development of these methods to probe directly the corresponding mechanisms in vivo will open effective routes for diagnostic and therapeutic interventions.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2020-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583520000104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38613457","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}

引用次数: 1

Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives. 淀粉样蛋白的单分子研究:从生物物理性质到诊断观点。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2020-11-05 DOI: 10.1017/S0033583520000086

Jinming Wu, Chan Cao, Rolf Antonie Loch, Ann Tiiman, Jinghui Luo

{"title":"Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives.","authors":"Jinming Wu, Chan Cao, Rolf Antonie Loch, Ann Tiiman, Jinghui Luo","doi":"10.1017/S0033583520000086","DOIUrl":"https://doi.org/10.1017/S0033583520000086","url":null,"abstract":"In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2020-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583520000086","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38566627","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}

引用次数: 6

Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism. 遗传密码和基因组域的能量映射:密码进化和分子达尔文主义的含义。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2020-11-04 DOI: 10.1017/S0033583520000098

Horst H Klump, Jens Völker, Kenneth J Breslauer

{"title":"Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism.","authors":"Horst H Klump, Jens Völker, Kenneth J Breslauer","doi":"10.1017/S0033583520000098","DOIUrl":"https://doi.org/10.1017/S0033583520000098","url":null,"abstract":"When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to 'evolve' from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven 'molecular Darwinism'. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2020-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583520000098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38658152","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}

引用次数: 8

Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis. 用波动有限元分析探讨轴突内鞭毛动力蛋白的动态。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2020-08-10 DOI: 10.1017/S0033583520000062

Robin A Richardson, Benjamin S Hanson, Daniel J Read, Oliver G Harlen, Sarah A Harris

{"title":"Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis.","authors":"Robin A Richardson, Benjamin S Hanson, Daniel J Read, Oliver G Harlen, Sarah A Harris","doi":"10.1017/S0033583520000062","DOIUrl":"https://doi.org/10.1017/S0033583520000062","url":null,"abstract":"Flagellar dyneins are the molecular motors responsible for producing the propagating bending motions of cilia and flagella. They are located within a densely packed and highly organised super-macromolecular cytoskeletal structure known as the axoneme. Using the mesoscale simulation technique Fluctuating Finite Element Analysis (FFEA), which represents proteins as viscoelastic continuum objects subject to explicit thermal noise, we have quantified the constraints on the range of molecular conformations that can be explored by dynein-c within the crowded architecture of the axoneme. We subsequently assess the influence of crowding on the 3D exploration of microtubule-binding sites, and specifically on the axial step length. Our calculations combine experimental information on the shape, flexibility and environment of dynein-c from three distinct sources; negative stain electron microscopy, cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET). Our FFEA simulations show that the super-macromolecular organisation of multiple protein complexes into higher-order structures can have a significant influence on the effective flexibility of the individual molecular components, and may, therefore, play an important role in the physical mechanisms underlying their biological function.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2020-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583520000062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38244889","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}

引用次数: 7