Quarterly Reviews of Biophysics最新文献_第5页

The mechanics of mitotic chromosomes. 有丝分裂染色体的机制。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-09-17 DOI: 10.1017/S0033583521000081

T Man, H Witt, E J G Peterman, G J L Wuite

{"title":"The mechanics of mitotic chromosomes.","authors":"T Man, H Witt, E J G Peterman, G J L Wuite","doi":"10.1017/S0033583521000081","DOIUrl":"https://doi.org/10.1017/S0033583521000081","url":null,"abstract":"Condensation and faithful separation of the genome are crucial for the cellular life cycle. During chromosome segregation, mechanical forces generated by the mitotic spindle pull apart the sister chromatids. The mechanical nature of this process has motivated a lot of research interest into the mechanical properties of mitotic chromosomes. Although their fundamental mechanical characteristics are known, it still remains unclear how these characteristics emerge from the structure of the mitotic chromosome. Recent advances in genomics, computational and super-resolution microscopy techniques have greatly promoted our understanding of the chromosomal structure and have motivated us to review the mechanical characteristics of chromosomes in light of the current structural insights. In this review, we will first introduce the current understanding of the chromosomal structure, before reviewing characteristic mechanical properties such as the Young's modulus and the bending modulus of mitotic chromosomes. Then we will address the approaches used to relate mechanical properties to the structure of chromosomes and we will also discuss how mechanical characterization can aid in elucidating their structure. Finally, future challenges, recent developments and emergent questions in this research field will be discussed.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"54 ","pages":"e10"},"PeriodicalIF":6.1,"publicationDate":"2021-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39423350","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: 4

A molecular view of DNA flexibility. DNA柔韧性的分子观。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-07-06 DOI: 10.1017/S0033583521000068

Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero

{"title":"A molecular view of DNA flexibility.","authors":"Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero","doi":"10.1017/S0033583521000068","DOIUrl":"https://doi.org/10.1017/S0033583521000068","url":null,"abstract":"DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"54 ","pages":"e8"},"PeriodicalIF":6.1,"publicationDate":"2021-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583521000068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39151818","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: 19

Where in the cell is my protein? 我的蛋白质在细胞的什么地方?

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-06-21 DOI: 10.1017/S003358352100007X

David J DeRosier

{"title":"Where in the cell is my protein?","authors":"David J DeRosier","doi":"10.1017/S003358352100007X","DOIUrl":"https://doi.org/10.1017/S003358352100007X","url":null,"abstract":"The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule localization microscopy (SMLM), we can achieve much better localization. The introduction of cryo-SMLM increased the yield of photons from fluorophores, which can benefit localization efforts. Dahlberg and Moerner (2021, Annual Review of Physical Chemistry, 72, 253-278) have a recent broad and elegant review of super-resolution cryo-CLEM. This paper focuses on cryo(F)PALM/STORM for the cryo-electron tomography community. I explore the current challenges to increase the accuracy of localization by SMLM and the mapping of those positions onto cryo-EM images and maps. There is much to consider: we need to know if the excitation of fluorophores damages the structures we seek to visualize. We need to determine if higher numerical aperture (NA) objectives, which add complexity to image analysis but increase resolution and the efficiency of photon collection, are better than lower NA objectives, which pose fewer problems. We need to figure out the best way to determine the axial position of fluorophores. We need to have better ways of aligning maps determined by FM with those determined by EM. We need to improve the instrumentation to be easier to use, more accurate, and ice-contamination free. The bottom line is that we have more work to do.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"54 ","pages":"e9"},"PeriodicalIF":6.1,"publicationDate":"2021-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S003358352100007X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39022097","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: 10

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

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-05-18 DOI: 10.1017/S0033583521000056

J Michael Schurr

引用次数: 0

Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. 用单粒子电子冷冻显微镜测定膜蛋白结构的两亲环境。

IF 6.1 2区生物学

Quarterly Reviews of Biophysics Pub Date : 2021-03-31 DOI: 10.1017/S0033583521000044

Christel Le Bon, Baptiste Michon, Jean-Luc Popot, Manuela Zoonens

{"title":"Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy.","authors":"Christel Le Bon, Baptiste Michon, Jean-Luc Popot, Manuela Zoonens","doi":"10.1017/S0033583521000044","DOIUrl":"https://doi.org/10.1017/S0033583521000044","url":null,"abstract":"Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.","PeriodicalId":20828,"journal":{"name":"Quarterly Reviews of Biophysics","volume":"54 ","pages":"e6"},"PeriodicalIF":6.1,"publicationDate":"2021-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0033583521000044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25532624","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: 12

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":"54 ","pages":"e5"},"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":"54 ","pages":"e3"},"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":"54 ","pages":"e2"},"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