No abstract

This paper reports the synthesis of a novel soluble poly(thienylene methylene) by a straightforward process based on the methanesulfonic acid-catalyzed self-condensation of 2-acetoxymethyl-3,4-dimethylthiophene. These macromolecules were found to generate in situ conjugated sequences consisting of thiophene and exounsaturated 2,5-dihydrothiophene moieties. The kinetics of these polycondensations, in which both the temperature and the monomer-to-catalyst molar ratio were varied, were followed by HPLC, as regards the rate of monomer consumption, and by GPC, as regards the evolution of the molecular weight of the growing chains. The ensuing polymers were characterized by FTIR, 1 H NMR, UV-vis spectroscopy, DSC, and TGA. † This contribution is dedicated to the fond memory of our dear friend and colleague Giovanna Costa, who died while this investigation was in progress.

No abstract

No abstract

This work is the first in a series devoted to applying mode coupling diffusion theory to the derivation of local dynamics properties of proteins in solution. The first-order mode-coupling approximation, or optimized Rouse-Zimm local dynamics (ORZLD), is applied here to derive the rotational dynamics of the bonds and compare the calculated with the experimental nmr 15N spin-lattice relaxation time behavior of the vnd/NK-2 homeodomain from Drosophila melanogaster. The starting point for the calculations is the experimental three-dimensional structure of the homeodomain determined by multidimensional nmr spectroscopy. The results of the computations are compared with experimentally measured 15N spin-lattice relaxation times T1, at 34.5 and 60.8 MHz, to check the first-order approximation. To estimate the relative importance of internal and overall rotation, both rigid and fluctuating dynamic models are examined, with fluctuations evaluated using molecular dynamics (MD) simulations. The correlation times for the fundamental bond vector time correlation function and for the second-order bond orientational TCF are obtained as a function of the residue number for vnd/NK-2. The stability of the corresponding local dynamics pattern for the fluctuating structure as a function of the length of the MD trajectory is presented. Diffusive dynamics, which is essentially free of model parameters even at first order in the mode-coupling diffusion approach, confirm that local dynamics of proteins can be described in terms of rotational diffusion of a fluctuating quasi-rigid structure. The comparison with the nmr data shows that the first-order mode coupling diffusion approximation accounts for the correct order of magnitude of the results and of important qualitative aspects of the data sensitive to conformational changes. Indications are obtained from this study to efficiently extend the theory to higher order in the mode-coupling expansion. These results demonstrate the promise of the mode-coupling approach, where the local dynamics of proteins is described in terms of rotational diffusion of a fluctuating quasi-rigid structure, to analyze nmr spin-lattice relaxation behavior.

No abstract

Extremely large domains of the genome of resting cells (calf thymus) have been visualized in the electron microscope by combining mild extraction procedures with a non-artifactual method of mounting the sample (the phospholipid monolayer technique). The observed chromatin strands, free from distortion, reach contour lengths up to 60 micrometers. After lysis of the nuclei, four classes of fibres may be identified on the basis of their diameters (30, 24, 18 and 11 nm, respectively). The morphology of giant chromatin strands is strikingly regular; long trains of equally sized, arc-shaped segments are observed, their length being, in many cases, multiples of a fixed value. The inflection points delimiting contiguous segments are often associated with laminar fragments of the nuclear envelope or, less frequently, linked to fibrillar elements. It appears that higher-order structures of chromatin in resting cells conform, to a large extent, to a so called ‘drapery-like’ mode, according to which a continuous strand runs between contiguous anchorage sites placed on the nuclear envelope. Because of the presence of regularly spaced inflection points, this organization is much more ordered than expected. Spontaneous unwinding of the fibres at low ionic strength, limited nuclease digestion, and relaxation in the presence of ethidium bromide, have been used as probes of the conformation. All these experiments rule out its identification with a single-strand helix. The final ordered state is attained by folding the basic 11 nm strand and by winding up this configuration on itself. This leads to a coiled-coil or ‘rope-like’ model. The 11 nm strand is ‘punctuated’ by sharp kinks. Roughly, it may be assimilated to a chain of semirigid, freely joined elements. As a consequence, local flexibility is greatly enhanced, so allowing the assembly mode described.

The molecular structure of Bombyx mori fibroin is still subjected to much controversy; there are discordant reports in the literature on both the value of the molecular weight and the subunit structure of the molecule. The method reported in the present paper allows the molecular weight of Na,CO, extracted fibroin samples to be unambiguously determined, and investigations on the composition and the molecular weight of the peptides arising from the degradation process succeeded in establishing some overall aspects of the structure of the subunits. The main results are: 1) the molecular weight of undegraded fibrion is 4 . 1 6 ; 2) two small subunits are disulfide linked to the main chain; 3) the subunits are located near the terminals of the main chain; 4) in agreement with previous partial literature data, the small subunits are rich in bulky and acid amino acids; our work further shows that they possess a three-block structure, consisting of a central hydrophobic core bearing two strongly acid sequences at the terminals. The mechanism of degradation of the fiber appears to be directed by structural, rather than chemical, factors, and its detailed investigation may represent a valuable method to determine the molecular architecture of the fiber.