Global fit and structure optimization of flexible and rigid macromolecules and nanoparticles from analytical ultracentrifugation and other dilute solution properties

Size-Exclusion Chromatography of Macromolecules: A Brief Tutorial Overview on Fundamentals with Computational Tools for Data Analysis and Determination of Structural Information

Size-exclusion chromatography (SEC) is presently a widely used and very informative technique for the characterization of macromolecules in solution. Beyond the first implementations of SEC-which required cumbersome column calibrations and were mainly intended for the determination of molecular weights-the modern SEC approach involving multiple detectors (md-SEC) is based on solution properties such as intrinsic viscosity and light scattering. Thus, md-SEC enables the direct and more efficient determination of molecular weights, as well as the determination of relationships between property and molecular weight, which can be quite useful in structural studies. Here, we first present a review of the fundamental aspects of the dilute-solution properties of macromolecules-particularly the differential refractive index, intrinsic viscosity, and scattering-related properties-on which the various detectors involved in md-SEC are based. Then, we developed SECtools, a suite of public-domain, open-source computer programs, which allow for the full analysis of md-SEC chromatograms. These analyses range from just the recorded raw signals (mV) of the detectors to a full determination of molecular weight averages and distributions. The use of these programs is illustrated through experimental studies using various samples.

Dynamic light scattering: a practical guide and applications in biomedical sciences

Dynamic light scattering (DLS), also known as photon correlation spectroscopy (PCS), is a very powerful tool for studying the diffusion behaviour of macromolecules in solution. The diffusion coefficient, and hence the hydrodynamic radii calculated from it, depends on the size and shape of macromolecules. In this review, we provide evidence of the usefulness of DLS to study the homogeneity of proteins, nucleic acids, and complexes of protein-protein or protein-nucleic acid preparations, as well as to study protein-small molecule interactions. Further, we provide examples of DLS's application both as a complementary method to analytical ultracentrifugation studies and as a screening tool to validate solution scattering models using determined hydrodynamic radii.

A histogram approach to the quality of fit in sedimentation velocity analyses

The quality of fit of sedimentation velocity data is critical to judge the veracity of the sedimentation model and accuracy of the derived macromolecular parameters. Absolute statistical measures are usually complicated by the presence of characteristic systematic errors and run-to-run variation in the stochastic noise of data acquisition. We present a new graphical approach to visualize systematic deviations between data and model in the form of a histogram of residuals. In comparison with the ideally expected Gaussian distribution, it can provide a robust measure of fit quality and be used to flag poor models.

Comparative study of the immunogenicity in mice and monkeys of an inactivated CA16 vaccine made from a human diploid cell line

The coxsackie A16 virus (CA16), along with enterovirus 71 (EV71), is a primary pathogen that causes hand, foot, and mouth disease (HFMD). To control HFMD, CA16, and EV71 vaccines are needed. In this study, an experimental inactivated CA16 vaccine was prepared using human diploid cells, and the vaccine's immunogenicity was analyzed in mice and rhesus monkeys. The results showed that the neutralizing antibody was developed in a dose-dependent manner, and was sustained for 70 days with an average GMT (geometric mean titer) level of 80 to 90 in immunized mouse and for 56 days with GMT of higher than 300 in monkeys. The neutralizing antibody had a cross-neutralizing activity against different viral strains (genotype A and B), and the specific IFN-γ-secreting cell response was activated by these virus strains in an ELISPOT assay. This study provides evidence for the potential use of inactivated CA16 as a candidate for use in vaccines.

Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO

The last three decades has seen some important advances in our ability to represent the conformation of proteins in solution on the basis of hydrodynamic measurements. Advances in theoretical modeling capabilities have been matched by commensurate advances in the precision of hydrodynamic measurements. We consider the advances in whole-body (simple ellipsoid-based) modeling-still useful for providing an overall idea of molecular shape, particularly for those systems where only a limited amount of data is available-and outline the ELLIPS suite of algorithms which facilitates the use of this approach. We then focus on bead modeling strategies, particularly the surface or shell-bead approaches and the HYDRO suite of algorithms. We demonstrate how these are providing great insights into complex issues such as the conformation of immunoglobulins and other multi-domain complexes.

NMR line shapes and multi-state binding equilibria

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes-NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results show that distinct multi-state models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight.

Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models

Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface.