Hierarchic patterning: architectures beyond 'giant molecular wheels'.

Based on symmetry breaking steps under one-pot conditions, simple molybdenum oxide-based building blocks initially assemble to 'giant molecular wheels' in a fast process followed by further slower assembly processes leading stepwise to more complex mesoscopic architectures including spherical ones and finally to those with a size larger than 500 nm.

Size, shape and secondary structure of calponin.

The overall size and shape of the chicken gizzard calponin (CaP) h1 molecule was investigated by dynamic light scattering (DLS) measurements. From the DLS experiments, a z-averaged translational diffusion coefficient is derived (5.75 +/- 0.3) x 10(-7) cm(2) s(-1), which corresponds to a hydrodynamic radius of 3.72 nm for calponin. The frictional ratio (1.8 for the unhydrated molecule and 1.5 for the hydrated one) suggests a pronounced anisotropic structure for the molecule. An ellipsoidal model in length 19.4 nm and with a diameter of 2.6 nm used for hydrodynamic calculations was found to reproduce the DLS experimental data. The evaluation of the secondary structure of CaP h1 from the CD spectra by two independent methods has revealed that it contains, on average, 23% helix, 19% beta-strand, 18% beta-turns and loops, and 40% of remainder structures. These values are in good agreement with those predicted from the amino-acid sequence. Predictions used for CaP h1 were applied to other isoforms of known sequences and revealed that all calponins share a common secondary structure. Moreover, the predicted structure of the calponin CH domain is identical to that found by X-ray studies of the spectrin, fimbrin and utrophin CH domains.

Structural analysis of G-DNA in solution: A combination of polarized and depolarized dynamic light scattering with hydrodynamic model calculations.

Specific intra- and intermolecular quadruplex conformations of model G-DNA oligonucleotides have been identified from their translational and rotational diffusion coefficients in aqueous solution. The transport properties were determined by polarized and depolarized dynamic light scattering. A comparison with hydrodynamic model calculations provides detailed information about the size and shape of the molecules and allows one to distinguish between alternative intra- and intermolecular association. The potential of this combination of methods to elucidate biomolecular structures in solution, to characterize conformational changes, and follow intermolecular interaction processes due to a response to external stimuli has been discussed.

The size and shape of caldesmon and its fragments in solution studied by dynamic light scattering and hydrodynamic model calculations.

The size and the shape of caldesmon as well as its 50-kDa central and 19-kDa C-terminal fragments were investigated by photon correlation spectroscopy. The hydrodynamic radii, which have been calculated from the experimentally obtained translational diffusion coefficients, are 9.8 nm, 6.0 nm, and 2.9 nm, respectively. Moreover, the experimental values for the translational diffusion coefficients are compared with results obtained from hydrodynamic model calculations. Detailed models for the structure of caldesmon in solution are derived. The contour length is about 64 nm for all of the models used for caldesmon.

Hydrodynamic properties of nitrogenase--the MoFe protein from Azotobacter vinelandii studied by dynamic light scattering and hydrodynamic modelling.

Experimental results for the nitrogenase MoFe protein from Azotobacter vinelandii obtained by dynamic light scattering (DLS) are presented. The translational diffusion coefficient was determined to D = (4.0 +/- 0.2) x 10(-7) cm2/s. Complementary, we have performed hydrodynamic model calculations based on the X-ray crystallographic data of the MoFe protein. The calculated transport coefficient suggests that the size and shape of the protein in solution is consistent with that in the crystal structure.

Interaction of a G-DNA quadruplex with mono- and divalent cations. A force field calculation.

The formation and stability of four-stranded DNA in solution is specifically dependent on the type of cations present. The interaction potential of a model quadruplex structure with different mono- and divalent ions was determined by force field calculations. Though the electrostatic contribution to the total energy is mainly responsible for the stabilisation of the cations within the quadruplex channel, it is the van der Waals interaction at short distances that determines the specific characteristics of the different cations. An explicit consideration of the solvent indicates that the position of water molecules in close proximity to the DNA channel have a strong influence on the form of the potential, and hence on the capability of the cations for leaving and re-entering the cavity. The effect of cation size, as expressed through their Lennard-Jones parameters, is discussed.

The Ca(2+)-induced conformational change of gelsolin is located in the carboxyl-terminal half of the molecule.

We have purified the two functionally distinct domains of gelsolin, a Ca(2+)-dependent actin binding protein, by proteolytic cleavage and characterized their size and shape in solution by dynamic light scattering. In the absence of calcium we obtained the same translational diffusion coefficient for both fragments which are of approximately equal molecular mass. The frictional ratio fo/fexp (1.33-1.39) is similar to the value as obtained for intact gelsolin (1.37) in aqueous solution (Patkowski, A., J. Seils, H. Hinssen, and T. Dorfmüller. 1990. Biopolymers. 30:427-435), indicating a similar molecular shape for the native protein as well as for the two subdomains. Upon addition of Ca2+ the translational diffusion coefficient of the carboxyl-terminal half decreased by almost 10%, while there was no change observed for the amino terminus. This result indicates that the ligand-induced conformational change as seen for intact gelsolin is probably located on the carboxyl-terminal domain of the protein. Since gelsolin has binding sites in both domains, and the isolated amino terminus binds and severs actin in a calcium-independent manner, our results suggests that the structural transition in the carboxyl-terminal part of intact gelsolin also affects the actin binding properties of the amino-terminal half.

Molecular shape of vinculin in aqueous solution.

We have investigated the molecular structure of chicken gizzard vinculin in solution. The translational diffusion coefficient of the intact protein and its amino-terminal head fragment, as obtained by proteolytic digestion, was determined by photon correlation spectroscopy. The experimental data are compared with hydrodynamic calculations, where the anisotropic shape of the macromolecule is modeled by spherical subunits. Our results are in agreement with the concept of a "balloon on a string" for the molecular shape of native vinculin. The existence of dimer and oligomer structures in low ionic strength buffer can be excluded. The calculated dimensions of the head fragment were estimated to r = 3.3 nm for a spherical particle, but the diffusion coefficient suggests a slightly anisotropic shape. In solution, the rod-like tail exhibits some flexibility, which is probably located in the "neck region" of the protein, considering the known sequence data.

Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements.

The dynamics of three synthetic oligonucleotides d(CG)4, d(CG)6, and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The hydrodynamic diameter of the octamer and dodecamer is 20.5 +/- 1.0 A, assuming a rise per base of 3.4 A. The tridecamer, d(CGCGTTGTTCGCG), adopts a hairpin structure with nearly spherical dimensions and a diameter of 23.0 +/- 2.0 A. The DDLS relaxation measurements provide a powerful method for distinguishing between different conformations of the oligonucleotides (e.g., DNA double-helix versus hairpin structure). Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The NMR results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from NMR is determined by the rotation of both the short and long axes of the oligonucleotide.(ABSTRACT TRUNCATED AT 250 WORDS)

Internal dynamics of tRNA(Phe) studied by depolarized dynamic light scattering.

The collective internal dynamics of transfer RNA(Phe) from brewer's yeast in solution was studied by depolarized dynamic light scattering (DDLS). Within the melting region of tRNA the depolarized spectra consist of two Lorentzian, where the narrow (slow) component describes the overall rotation of the macromolecule. The broad component is attributed to the collective reorientation of the bases within the biopolymer. At high temperature only this relaxation process is observed in the spectrum. The viscosity dependence of the collective internal relaxation process is described by the Stokes-Einstein-Debye equation for rotational diffusion. Estimates of the internal orientational pair correlation factor from the integral depolarized intensities of tRNA(Phe) solutions indicates that the observed dynamics correspond to the collective reorientation of approximately 5 bases. A comparison of the results presented with DDLS studies on the aggregation of the mononucleotide guanosine-5'-monophosphate confirms this result. For a further characterization of the relaxation process we studied the effect of hydrostatic pressure (1-1000 bar) on the depolarized spectra of tRNA. While other spectroscopic methods like nmr, fluorescence polarization anisotropy decay, or ESR give information about the very local motion of a single base within the DNA or RNA, this study shows that by DDLS one can characterize collective internal motions of macromolecules.