Macromolecular Bioscience

Front Cover: The image features recent results in analytical ultracentrifugation research with a photograph of Theodor Svedberg, who invented the technique; last year marked the 125^th anniversary of his birth. The upper panel highlights advanced hydrodynamic modeling with the UltraScan SOlution MOdeler (US-SOMO) program; direct correspondence (top structures) and grid (bottom) bead models are built from atomic-level 3D protein structures (middle). Additional details can be found in the full paper by by E. Brookes, B. Demeler, and M. Rocco^*on page 746. The lower panel features the sedimentation- and frictional coefficient distribution of nanoparticles reflecting spherical and nonspherical morphologies. Further details can be found in the full paper by V. Mittal, A. Völkel,^* and H. Cölfen on page 754. Photograph is courtesy of Curt Ekström, The Svedberg Laboratory.

The oil-Turbine ultracentrifuge invented by Svedberg allowed high centrifugal fields to be applied to solutions of proteins and other types of macromolecule. Refined optical recording methods allow the different sedimentation rates to be observed and essential macromolecular characteristics to be determined.

The antiviral kinase PKR contains an N-terminal dsRNA binding domain and a C-terminal kinase domain. Analytical ultracentrifugation has been used to define PKR self-association and the assembly of PKR on dsRNA lattices and complex natural RNAs.

The advances that have been made using the analytical ultracentrifuge for characterising polydisperse polymer systems with a quasi-continuous distribution of molecular weight are explored here. We focus on polysaccharides, mucins and other glycoconjugates, systems that benefit from the availability of long optical path length cells for the minimisation of complications through thermodynamic non-ideality.

We have developed procedures to carry out Monte Carlo and Brownian dynamics simulations of flexible molecules, which have been implemented in public domain programs. As an application to the computation of solution properties of macromolecules, we show the rotor-speed-dependence of the sedimentation coefficient of large DNA molecules.

A software package called SEDVIEW has been developed to allow real-time analysis of sedimentation velocity runs. Sedimentation coefficient distribution patterns can be displayed allowing one to observe development of boundary details as the run proceeds. Time derivative methods are used to eliminate systematic time independent noise. The figure shows distribution curves for the wild type and three mutants of HSP27.

Sedimentation velocity analytical ultracentrifugation has re-emerged as an important tool for macromolecular characterization in solution, including their size-distribution and their hydrodynamic and thermodynamic parameters. It is shown how the data analysis model can be extended to account for signal contributions from small molecular weight co-solutes, thereby improving the flexibility and reliability of the method.

The UltraScan US-SOMO suite is a powerful collection of algorithms for computing macromolecular hydrodynamics from 3D atomic structures through bead modeling procedures. The accuracy of the results and their dependence on various settings, like overlap removal procedures and hydration schemes, are thoroughly investigated in this paper.

Model nanoparticles representing biological as well as synthetic systems are analysed in the analytical ultracentrifuge for their size distributions using different analysis programs and methods. The figure demonstrates the size distribution analysis of silica particles with ≈5 nm peak diameter with the chosen methods.

Maintaining productive folding of membrane proteins is crucial to all cells. Proteins known to be “good” in vitro folders (OmpA) show monomeric unfolded states, whereas other OMPs self-associate to different extents, with OmpT displaying sedimentation coefficients as large as ribosomal subunits. The judicious choice of buffer conditions can minimize aggregation and facilitate folding studies.

The investigation of the suppression of protein aggregation by GroEL is of considerable importance in elucidating the mechanism of GroEL-assisted protein folding. The study of the effect of GroEL on the thermal aggregation of muscle glycogen phosphorylase b shows that the suppression of the aggregation is due to a transition of the aggregation process from the diffusion-controlled regime to a regime wherein the sticking probability for the colliding particles becomes lower than one.

A new genetic algorithm optimization method implemented in UltraScan for the analysis of reversible systems by sedimentation velocity (SV) is presented. It is shown that SV is better suited for the analysis of reversible systems since it provides additional and more reliable information about equilibrium constants, slow kinetics, and shape than can be obtained from sedimentation equilibrium.

Interaction of the wild type Hsp27 and its 3D phosphomimic mutant with rabbit muscle phosphorylase kinase (PhK) has been studied under crowding conditions induced by 1 M trimethylamine N-oxide. Under crowding conditions PhK interacts with small oligomers of Hsp27 to form stable complexes and by this means induces dissociation of large Hsp27 oligomers. It is speculated that by these means native PhK might regulate the chaperone-like activity of small heat shock proteins.

New water-soluble synthetic polymers which can be used as potential carriers of biologically active substances are studied by hydrodynamic methods in a 150-fold range of molecular masses. The conformational parameters of poly-N-methyl-N-vinylamide chain are estimated through the comparison of hydrodynamic characteristics with the molecular masses.

Weak interactions are determinative for many cellular processes. Simulation and experimentation are used to show that by sedimentation equilibrium analysis such weak interaction (Kd > mM) can be accurately characterized in terms of both ‘virial’ (2nd and 3rd) and K_a coefficients through ‘INVEQ’ analysis of data from a single experiment.

The assembly of the baseplate wedge of bacteriophage T4 was studied by analytical ultracentrifugation, gel permeation chromatography, and electron microscopy in order to elucidate the molecular mechanism of the ‘strictly ordered’ or ‘legitimate’ assembly pathway. Observations of the assembly strongly suggest that the ‘strictly ordered’ assembly is materialized by successive conformational changes of the subunit protein upon incorporation. The strong binding of subunits at each step of incorporation allows isolation of all the assembly intermediates.

Back Cover: The image displays Svedberg's analytical centrifuge along with a recent development in analytical ultracentrifugation (AUC), a new computational model for the analysis of macromolecules in sedimentation velocity. The plot shows macromolecular concentration profiles superimposed by solvent signals, such as those arising from optically mismatched small co-solutes. The macromolecular boundaries appear obscure and twisted due to the buffer signal and are not interpretable using traditional analysis. The new model accounts simultaneously for macromolecular and small co-solvent concentration distributions. Further details can be found in the full paper by H. Zhao,^* P. H. Brown, A. Balbo, M. d. C. F. Alonso, N. Polishchuck, C. Chaudhry, M. L. Mayer, R. Ghirlando, and P. Schuck on page 736. Photograph is courtesy of Curt Ekström, The Svedberg Laboratory.