Understanding DNA Calladine, C. R; Drew, Horace R
1997, 2004, 2004-12-31
eBook, Book
The functional properties of any molecule are directly related to, and affected by, its structure. This is especially true for DNA, the molecular that carries the code for all life on earth. The ...third edition of Understanding DNA has been entirely revised and updated, and expanded to cover new advances in our understanding. It explains, step by step, how DNA forms specific structures, the nature of these structures and how they fundamentally affect the biological processes of transcription and replication.Written in a clear, concise and lively fashion, Understanding DNA is essential reading for all molecular biology, biochemistry and genetics students, to newcomers to the field from other areas such as chemistry or physics, and even for seasoned researchers, who really want to understand DNA.
* Describes the basic units of DNA and how these form the double helix, and the various types of DNA double helix* Outlines the methods used to study DNA structure* Contains over 130 illustrations, some in full color, as well as exercises and further readings to stimulate student comprehension
The buckling behaviour of thin shell structures under load has been a persistent challenge to engineering designers and researchers over many decades. In this article I consider two unusual ...experimental studies on the buckling of thin-walled elastic cylindrical shells, each of which sheds intriguing light on the buckling phenomena. The classical theory of buckling of thin cylindrical shells under axial compression predicts that the buckling stress will be proportional to t/R– the ratio of thickness to radius – other things being equal. But collected results of experimental studies from many laboratories, when plotted on log–log scales, show clearly that the buckling stress is actually proportional to (t/R)1.5, with the measured buckling stresses being scattered through a factor of about 4 for shells with R/t > 200. Such scatter is commonly judged to be in accord with Koiter’s theory of ‘imperfection sensitivity’. But that theory lays no claim to an understanding of the empirical 1.5-power law. I claim that a key to this situation is the experimental performance of some small-scale open-topped silicone rubber shells, buckling under their own weight, which clearly demonstrates a 1.5-power law, but with very little scatter. The buckling mode of these shells involves almost entirely inextensional deformation, with a single small dimple growing near the base, separated from the rest of the shell by a narrow boundary layer that accounts for almost all of the dimple’s elastic strain energy. A straightforward, simple analysis of the mechanics of the dimple is consistent with the experimental 1.5-power law. As noted above, experimental buckling loads of shells that are closed at both ends also show the empirical 1.5-power law, but now with significant statistical scatter. A second aim of the paper is to throw light on that phenomenon. I venture to attribute it to the effect of the boundary conditions of the shell. I adduce support for this view from experimental observations on the buckling of a shell with special, frictional end-fittings. That feature produces significantly higher collapse loads, and with much smaller scatter, than for corresponding shells with fixed boundaries; and it permits striking pre-buckled deformations to occur, of a kind not previously noted. It will be appreciated that neither of the two parts of this article depends on the widely accepted theory of imperfection-sensitivity; hence my choice of title. It is a pleasure for me to submit this article to a special publication in honour of Michael Rotter, with whom I have discussed matters of this sort through three decades.
Davies Gilbert's work on the catenary is notable on two counts. First, it influenced Thomas Telford in formulating his final design for the Menai Strait suspension bridge (1826); and second, it ...established for the first time the form of the 'catenary of equal strength'. The classical catenary is a uniform flexible chain or cable hanging freely under gravity between supports. The 'catenary of equal strength' is the form of a cable whose cross-sectional area is made proportional to the tension at each point, so that the tensile stress is uniform throughout. In this paper I provide a sketch of the lives and achievements of Gilbert and Telford, and of their interaction over the Menai Bridge. There follows a commentary on Gilbert's 1826 paper, and on his two related publications; and a brief sketch of the earlier history of the catenary. I then describe the development of the suspension bridge up to the present time. Finally, I discuss relations between mathematical analysts and practical engineers. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of ...bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
Display omitted
•Cryo-EM can resolve the atomic structures of supercoiled flagellar filaments•Supercoiled atomic structures show 11 states in bacteria and 10 states in archaea•Distinctly different structures have evolved to form similar supercoils
Although lacking homology between their structural components, archaeal and bacterial flagellar filaments achieve the supercoiling that powers locomotion through analogous mechanisms.
The evolution of archaeal flagellar filaments Kreutzberger, Mark A B; Cvirkaite-Krupovic, Virginija; Liu, Ying ...
Proceedings of the National Academy of Sciences - PNAS,
07/2023, Letnik:
120, Številka:
28
Journal Article
Recenzirano
Odprti dostop
Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from
with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
The corkscrew-like flagellar filaments emerging from the surface of bacteria such as Salmonella typhimurium propel the cells toward nutrient and away from repellents. This kind of motility depends ...upon the ability of the flagellar filaments to adopt a range of distinct helical forms. A filament is typically constructed from ~30,000 identical flagellin molecules, which self-assemble into a tubular structure containing 11 near-longitudinal protofilaments. A “mechanical” model, in which the flagellin building block has the capacity to switch between two principal interfacial states, predicts that the filament can assemble into a “canonical” family of 12 distinct helical forms, each having unique curvature and twist: these include two “extreme” straight forms having left- and right-handed twists, respectively, and 10 intermediate helical forms. Measured shapes of the filaments correspond well with predictions of the model. This report is concerned with two unanswered questions. First, what properties of the flagellin determine which of the 12 discrete forms is preferred? Second, how does the interfacial “switch” work, at a molecular level? Our proposed solution of these problems is based mainly on a detailed examination of differences between the available electron cryo-microscopy structures of the straight L and R filaments, respectively.
Display omitted
► Detailed mechanics of polymorphism in bacterial flagellar filaments. ► Selection of helical forms by amino acid substitution, mechanical torque and other factors. ► Identification of bi-stable switch at interaction between α-helices from adjacent subunits.
The Southwell plot is a well-known technique for determining experimentally the elastic critical load of a structure, without having to subject the structure to loading in the vicinity of critical. ...But several authors have suggested that when the structure is a beam which undergoes
lateral-torsional buckling, a modified version of the Southwell plot is called for. In this paper we demonstrate that the modified form of the Southwell plot is not needed, and that the standard version is indeed satisfactory. We do this by plotting and re-plotting some experimental data; by drawing attention to some very clear work by Meck; and by explaining the practical coupling between the variables describing the lateral deflection and the rotation when lateral-torsional buckling occurs. Finally, we examine an argument based on symmetry which appears to support the idea that a modification of the standard Southwell plot is needed in the case of lateral-torsional buckling: but we show that a correct deployment of the argument from symmetry leads to the conclusion that the modified form of the Southwell plot is valid only for special, unrealistic cases.
The Scottish populations of salmonids are important both ecologically and economically. Game fisheries for Atlantic salmon Salmo salar, sea trout Salmo trutta trutta and brown trout Salmo trutta fari ...are all highly acclaimed and generate substantial levels of income for Scotland, but many populations are in decline and efforts are being made to ensure the future sustainability of these species. These declines have led to a focus on the impact of piscivorous bird predation on fish populations. The purpose of our review was to assess the evidence for population-level impacts on salmonid populations, and/or economic impacts on Scottish game fisheries of predation by the four primary UK freshwater piscivorous bird species: cormorant Phalacrocorax carbo, goosander Mergus merganser, red-breasted merganser Mergus serrator and grey heron Ardea cinerea. There is evidence that these birds can, in some situations, remove large numbers of fish from stocked and natural fisheries. However, a lack of information on fish population levels, the numbers and species composition of feeding birds, and robust calculations of fish consumption has hampered the conversion of the results of the existing studies into useful quantitative measures of impact. As a consequence, few studies have demonstrated any reductions in numbers of breeding fish or fish productivity due to predation by piscivorous birds, or direct economic loss to fisheries in Scotland. We support a previous recommendation for a reiterative procedure of modelling, experimentation and remodelling to assess the impacts of piscivorous birds on fisheries. Wide-scale studies of the movements of piscivorous birds, their feeding locations in relation to river characteristics, and the factors that make fish particularly vulnerable to predation are seen as important areas for future research.
Crystallised "naked" DNA oligomers in the B form show significant conformational mobility, particularly at CA/TG and TA/TA steps: there is a range in Roll angle of some 15 degrees between consecutive ...base-pairs, and Slide and Twist are directly coupled to Roll. We call such motions "mode I". They are sufficient to enable DNA to curve gently around proteins such as histone octamers in the nucleosome particle. When DNA bends around other proteins, such as CAP and TBP, its distortion is much more severe. Although the DNA in close contact with these proteins includes the CA/TG and TA/TA steps, respectively, the mode I flexibility is not deployed: instead, a more severe "mode II" manoeuvre is observed in DNA/protein co-crystals. Mode II has several distinctive physical features. First, its range of Roll angle is much wider than for mode I. Second, the major-groove width remains more-or-less constant as Roll increases, whereas it decreases significantly as Roll increases in mode I; and this enables the major groove of the DNA to accommodate a protein moiety in its severely bent conformation. Third, the value of Slide remains more-or-less constant as Roll increases, whereas it decreases in mode I. In general, in both modes I and II, the major-groove width appears to be closely related to the Slide between base-pairs. In mode II there appears to be a definite "point pivot" on the major-groove side of the two base-pairs that constitute a dinucleotide step, formed either by the steric interlocking of propeller-twisted base-pairs or by a bifurcated hydrogen bond. Distortion of DNA in mode II seems to be an intrinsic property of the double-helical structure, since it occurs whether protein is bound on the major-groove side (e.g. CAP) or on the minor-groove side (e.g. TBP). Mode II distortion occurs in a wider range of steps than those that show the largest mode-I variation; nevertheless, "access" to mode II deformation appears to be gained via mode I distortion at particular steps CA/TG and TA/TA.
PDF
