1,721,077 research outputs found
Structural analysis of 30-nm chromatin fiber architecture
No full textThe folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an
important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in
chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientational
constraints of the nucleosome units that provide the geometrical conditions of helical conformations. Recently,
the elucidation of the x-ray crystal structure of a nucleosome tetramer array and the interpretation of electron
microscopy images of reconstituted nucleosome arrays suggested two different architectures of the chromatin
fiber. We approached the problem by integrating the experimental findings with geometrical, conformational
and topological restraints, under the hypothesis of the minimum distortion of the nucleosome and linker DNA
structures. Weshow that the excluded volume at linker crossing and the torsional energy limit the possible close
packing of the nucleosomes in the chromatin fiber. In particular, the torsional energy of the chromatin fiber
appears crucial in determining the kind of nucleosome packing for short nucleosome repeat lengths as in
telomeres and yeast chromatin
Interazioni specifiche tra DNA con diversa superstruttura intrinseca e ligandi del solco minore del B-DNA.
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A Statistical Thermodynamic Approach for Predicting The Sequence-Dependent Nucleosome Positioning along Genomes
No full textThe distribution of nucleosomes, the fundamental repeating units of chromatin, along the eukaryotic genome rules replication, transcription, repair, and regulation processes through modulation of DNA accessibility. Genome-wide maps provide much information about the factors that direct nucleosome positioning. However, the experimental nucleosome maps do not permit to conclude unambiguously that the DNA sequence of the eukaryotic genomes encodes nucleosome positioning and organization. A possible way to disclose this important issue is to develop theoretical models capable of predicting nucleosome positioning in terms of the DNA sequence. Toward this goal, we propose a physical model for predicting nucleosome thermodynamic stability in terms of DNA sequence. The model, based on a statistical mechanical approach, allows the calculation of the canonical ensemble free energy involved in the formation of each nucleosome along a DNA tract. The theoretical nucleosome distribution along genomes was compared with the experimental positioning maps of yeast genome. The results are comparable with those obtained with pure statistical models based on identifying some recurrent sequence features obtained from the statistical analysis of a very large pool of nucleosomal DNA sequences. However, our model based on the physical properties of the DNA such as curvature and flexibility appears universal and applicable to any genomes without rearrangements
The elastic model in the mechanics of DNA deformations.
No full textThe mechanics of DNA structural fluctuations at room temperature is generally modelled with a simple one-dimensional worm-like elastic model that approximates the energy of the DNA deformations from its intrinsic sequence-dependent curvature as proportional to the square of the curvature deviations, although this approximation should be suitable for small deformations of B-DNA canonical structure. Although the high curvature of DNA in nucleosomes exclude the first order elasticity approach, the high-resolution structures of the nucleosome show that DNA essentially retains the B conformation following an almost cylindrical super-helix. However, a few significant kinks largely independent of sequence are present; in fact, the distortion energy evaluated adopting the canonical persistence length of 50 nm is in the range of base pair stacking energies. This means that unstaking of some dinucleotide steps could occur in phase along the sequence as it appears in the X-ray nucleosome structures, probably at TA sequence positions, due to the lowest stacking energy proper of this dinucleotide. The good results in predicting the thermodynamic stability of nucleosomes obtained adopting elastic models suggest the hypothesis that the DNA super-helical distortion involved in the elastic model represents an ideal fitting, almost equivalent in energy, of the actual nucleosomal structures, which is the result of local structural arrangements optimized according to the different specific histone-DNA interactions along the sequence
Geometrical, Conformational, and Topological Restraints in Nucleosome Compaction along Chromatin Fibers
No full textCompaction of nucleosomes in chromatin is directed by their positioning along DNA. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientation constraints of the nucleosome units that provide the geometrical conditions of helical conformations. We investigated the architectures of the chromatin fiber by integrating the experimental results with geometrical, conformational and topological restraints, under the hypothesis of the minimum distortion of the nucleosome and linker DNA structures. The periodical repeats of nucleosomes can be investigated assuming the principle of conformational equivalence of the repeating units. The problem of selecting the compact architectures of the chromatin fiber for different linker lengths can be factorized in one in which only orientational parameters are taken into account and the other in which the lengths of DNA linkers are considered. The best packing of nucleosomes requires the uniformity of orientational parameters and “quasi-conformational equivalence” of the repeating units, even though linker lengths are not strictly equal. We showed that the path of the linkers in compact nucleosome packing is severely constrained by steric hindrances and topological conditions and that the excluded volume at linker crossing and the torsional energy limit the possible close packing of the nucleosomes in the chromatin fiber. In particular, the torsional energy of the chromatin fiber appears crucial in determining the kind of nucleosome packing for short nucleosome repeat lengths as in telomeres and yeast chromatin
Theoretical models for studying thermodynamic properties of biological macromolecules
No full textThe three-dimensional organization of biological macromolecules as well as their superstructural transitions appears to be a complex problem involving static and large scale dynamic effects. However, in many cases some features dominate over the others; the possibility of identifying these determinants allows considerable simplifications of the models, because a lower number of variables have to be considered. In the case of the superstructural transformations of DNA, the dominant effect seems to be the elastic energy involved in the continuous deformations of the structure. The aim of this work is the development of an analytical model to study the transitions of circular DNAs toward supercoiled states, commonly referred as writhe transitions. Although there are several papers in the literature concerning experimental electrophoretic studies of natural DNAs, the current results have been compared with Monte Carlo data by different authors, for a more straightforward comparison. This is because electrophoretic experiments just reveal the DNA behaviour averaged over a conformation ensemble, whereas Monte Carlo data are split into the contributions of the forms with different topological numbers. The comparison of the elastic ground-state energy and entropy of a 468 bp isotropic chain, calculated with the present model, and the ensemble average energy evaluated by Monte Carlo simulations (Gebe & Schurr, 1996) shows a straightforward correlation. The two sets of data differ for a strictly constant quantity, supporting the initial hypothesis of the equivalence of the interactions with the solvent and/or counterions, and the independence of the fluctuations of the writhing number in the whole set of the possible transformations. The application of the model to intrinsically curved DNAs has shown that curvature always seems to stabilize the supercoiled DNA forms, shifting the transitions to lower linking number differences. Also the bent of the DNA axis due to protein binding seems to favour the occurrence of writhe transitions, as in the case of the catabolite gene activator protein (CAP). These findings suggest a new role of the sequence in determining the mechanical behaviour of DNA, either determining its intrinsic curvature or directing the binding of bent-inducing proteins. In the latter half of this work, the same topological approach has been extended to the study of the tertiary organization of globular proteins. In particular, a new algorithm is proposed to identify proteins domains, based on the statistical analysis of the distribution of the local axes of the polypeptide chain, evaluated on topological basis. A polypeptide chain can be modelled as a ribbon and, therefore, can be studied in terms of topological quantities. The complexity of a space curve is conveniently described by its writhing number, which represents the number of self-crossings in the curve projections onto a unit sphere. Each crossing is taken to be positive or negative depending if it is right- or left-handed. Consequently, the summation of the absolute values of the writhing-number contributions, here referred as absolute writhing number, can conveniently describe the three-dimensional organization of a non-directional space curve. It is interesting that the absolute writhing number of 71 crystallographic and NMR structures from the Protein Data Bank (Bernstein et al., 1977) shows a very good correlation (R = 0.996) with the number of amino acid residues. For a more straightforward comparison, the absolute writhing number was calculated for a set of random coils. They show the same dependence of the native proteins with respect to the amino-acids number, but they appear much more spread out (R = 0.953) and the fitting line lies below that relative to the native proteins. The result is consistent with the fact that random coils are generally less compact of native proteins. This finding supports the hypothesis that topological requirements should be satisfied in the process of protein folding and in the final organization of the tertiary structures
Peptides with regular enantiomeric sequences: A wide class of modular self-assembling architectures
No full textOrganic trans-annular assemblies constitute an expanding class of structures with promising applications for the design of nanotechnological devices. Among the strategies developed for the engineering of organic nanotubes, those characterized by regular alternating enantiomeric amino acid sequences have been proven particularly useful. In fact, cyclic peptides with an even number of regularly alternating D- and L-amino acids have the tendency to adopt local beta-conformation that are capable of forming trans-annular self-assembling architectures, hydrogen bond directed. The formation of such structures is the result of the conformational equivalence of the monomer units, a general principle that associates stereo-chemical to chemical equivalence in a polymer chain. For configurationally alternating sequences the conformational equivalence produces cyclic structures, where a monomer unit is related to the adjacent along the chain by a roto-reflection axis, S-n,. A slight relaxation of the conformational equivalence can formally transform a cyclic structure into a conformationally quasi-equivalent helical structures characterized by the presence of polar inner channels, which allow the transient binding for an activated flow of specific ions. To prove our early predictions, we synthesized different alternating polypeptide and the corresponding linear and cyclic oligopeptides and investigated their conformations by NMR and CID spectroscopy as well as the formation of self-assembling structures by increasing the concentration in solution. Moreover, their predicted ability to behave as an ion-channel across bilayer membranes are investigated and experimental evidence of single molecule conducting events are reported. Finally, the possibility is suggested to obtain self-assembled trans-annular structures by chemically bridging the amino acid side chains stabilized using different strategies. A complex construct with good perspective for nano-technological applications is proposed in which cyclic DL-lysine side chains are bridged by the formation of salycilaldimmine metal chelates
Albumin binding onto synthetic vesicles
No full textVesicular entities were obtained by mixing didodecyldimethylammonium bromide and sodium dodecylsulfate in non-stoichiometric ratios. The vesicles bear a positive surface charge, due to the cationic species being in excess, and adsorb significant amounts of protein, presumably by electrostatic interactions. We modulated the net charge of bovine serum albumin by pH and observed its binding onto the above vesicles. Binding is controlled by the net charge of vesicles and albumin: it is substantial when albumin has negative charges in excess and is negligible, or non-existent, below its iso-electric point. For pH values >6.0, the binding efficiency increases in proportion to protein charge. Surface coverage changes in proportion to pH when the number of charges neutralized upon binding remains the same. The size of protein-vesicle lipo-plexes was inferred by dynamic light scattering and their charge by zeta-potential. The structure of albumin was evaluated by circular dichroism spectroscopy and estimates of alpha-helix, beta-strand and random coil contents were achieved. Increasing the beta-strand and random coil contents subsequent to binding suggests a significant interaction between vesicles and albumin. Attempts to determine the binding efficiency were made by elaborating zeta-potential values. The results were interpreted in terms of a Gibbs adsorption isotherm. Accordingly, it is possible to estimate the binding energy under different pH conditions
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