The self-association of human interferon-α2b (hIFN-α2b), albinterferon-α2b (a recombinant protein with human serum albumin and hIFN-α2b peptides fused together in a single polypeptide chain), and Pegasys (PEGylated hIFN-α2a) was characterized by analytical ultracentrifugation analyses. By examining the apparent sedimentation coefficient distribution profiles of each protein at different concentrations, it was concluded that the above three proteins are self-associating in albinterferon-α2b formulation buffer. By model fitting of sedimentation data using SEDANAL software, the stoichiometry and equilibrium constants of the self-association of these proteins were characterized. The self-association of hIFN-α2b results in the formation of stable dimers, fast-reversible tetramers, octamers, and hexadecamers. In contrast, although both albinterferon-α2b and Pegasys are self-associated, their self-association stoichiometries are significantly different from that of hIFN-α2b. The self-association of albinterferon-α2b results in the formation of reversible dimers and trimers, whereas the self-association of Pegasys gives only reversible dimers. The self-association behaviors of hIFN-α2b and albinterferon-α2b involves attractive electrostatic forces, which can be suppressed to a negligible level in low pH (pH 4.0-4.5) and high salt concentration (400 mM NaCl) buffer, allowing quantification of their size variant contents by sedimentation velocity analysis. © 2011 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci.

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS.

The ability to obtain a sedimentation coefficient distribution as the run proceeds, and to get an early idea of the quality of a particular sample, has not been made available in real-time during the run in any of the existing software packages. It is desirable on many occasions to be able to see the number of components present in a sample at an early stage of the run. The ability to ascertain the extent of heterogeneity of sample would help enormously to reduce the amount of time that is necessary to obtain that information. Most software packages currently available require that the run be completed before analysis is carried out or at least some of the early scans analyzed off-line to determine if the run should continue. A software package called SEDVIEW has been developed by us to allow early analysis in real-time.

Smooth muscle myosin light chain kinase (smMLCK) is a calcium/calmodulin dependent enzyme that activates contraction of smooth muscle. The polypeptide chain of rabbit uterine smMLCK (Swiss-Prot: P29294) contains the catalytic/regulatory domain, three immunoglobulin related motifs (Ig), one fibronectin related motif (Fn3), a repetitive, proline rich segment (PEVK) and, at the N-terminus, a unique F-actin binding domain. We have evaluated the spatial arrangement of these domains in a recombinant 125 kDa full-length smMLCK and its two catalytically active C-terminal fragments (77 kDa, residues 461-1147 and 61 kDa, residues 461-1002). Electron microscopic images of smMLCK cross-linked to F-actin show particles at variable distance (11-55 nm) from the filament, suggesting that a well-structured C-terminal segment of smMLCK is connected to the actin-binding domain by a long, flexible tether. We have used structural homology and molecular dynamics methods to construct various all-atom representation models of smMLCK and its two fragments. The theoretical sedimentation coefficients computed with the program HYDROPRO were compared with those determined by sedimentation velocity. We found agreement between the predicted and observed sedimentation coefficients for models in which the independently folded catalytic domain, Fn3 and Ig domains are aligned consecutively on the long axis of the molecule. The PEVK segment is modeled as an extensible linker that enables smMLCK to remain bound to F-actin and simultaneously activate the myosin heads of adjacent myosin filaments at a distance of 40 nm or more. The structural properties of smMLCK may contribute to the elasticity of smooth muscle cells.

We have previously presented a tutorial on direct boundary fitting of sedimentation velocity data for kinetically mediated monomer-dimer systems [Correia and Stafford, 2009]. We emphasized the ability of Sedanal to fit for the k(off) values and measure their uncertainty at the 95% confidence interval. We concluded for a monomer-dimer system the range of well-determined k(off) values is limited to 0.005-10(-5)s(-1) corresponding to relaxation times of ~70 to ~33,000s. More complicated reaction schemes introduce the potential complexity of low concentrations of an intermediate that may also influence the kinetic behavior during sedimentation. This can be seen in a cooperative ABCD system (A+B --> C; B+C --> D) where C, the 1:1 complex, is sparsely populated (K(1)=10(4)M(-1), K(2)=10(8)M(-1)). Under these conditions a k(1,off)<0.01s(-1) produces slow kinetic features. The low concentration of species C contributes to this effect while still allowing the accurate estimation of k(1,off)(although k(2,off) can readily compensate and contribute to the kinetics). More complex reactions involving concerted assembly or cooperative ring formation with low concentrations of intermediate species also display kinetic effects due to a slow flux of material through the sparsely populated intermediate states. This produces a kinetically limited reaction boundary that produces partial resolution of individual species during sedimentation. Cooperativity of ring formation drives the reaction and thus separation of these two effects, kinetics and energetics, can be challenging. This situation is experimentally exhibited by systems that form large oligomers or rings and may especially contribute to formation of micelles and various protein aggregation diseases including formation of beta-amyloid and tau aggregates. Simulations, quantitative parameter estimation by direct boundary fitting and diagnostic features for these systems are presented with an emphasis on the features available in Sedanal to simulate and analyze kinetically mediated systems.

The shape and solution properties of fibrinogen are affected by the location of the C-terminal portion of the Aalpha chains, which is presently still controversial. We have measured the hydrodynamic properties of a human fibrinogen fraction with these appendages mostly intact, of chicken fibrinogen, where they lack eleven characteristic thirteen-amino acids repeats, and of human fragment X, a plasmin early degradation product in which they have been removed. The human fibrinogen/fragmentX samples were extensively characterized by SDS-PAGE/Western blotting and mass spectrometry, allowing their composition to be precisely determined. The solution properties of all samples were then investigated by analytical ultracentrifugation and size-exclusion HPLC coupled with multi-angle light scattering and differential pressure viscometry detectors. The measured parameters suggest that the extra repeats have little influence on the overall fibrinogen conformation, while a significant change is brought about by the removal of the C-terminal portion of the Aalpha chains beyond residue Aalpha200.

The molecular chaperone Hsp27 exists as a distribution of large oligomers that are disassembled by phosphorylation at Ser15, 78, and 82. It is controversial whether the unphosphorylated Hsp27 or the widely-used triple Ser-to-Asp phospho-mimic mutant is the more active molecular chaperone in vitro. This question was investigated here by correlating chaperone activity, as measured by the aggregation of reduced insulin or alpha-lactalbumin, with Hsp27 self association as monitored by analytical ultracentrifugation. Furthermore, since the phospho-mimic is generally assumed to reproduce the phosphorylated molecule, the size and chaperone activity of phosphorylated Hsp27 was compared to that of the phospho-mimic. Hsp27 was triply-phosphorylated by MAPKAP-2 kinase and phosphorylation was tracked by urea-PAGE. An increasing degree of suppression of insulin or alpha-lactalbumin aggregation correlated with a decreasing Hsp27 self association which was the least for phosphorylated Hsp27 followed by the mimic followed by the unphosphorylated protein. It was also found that Hsp27 added to pre-aggregated insulin did not reverse aggregation but did inhibit these aggregates from assembling into even larger aggregates. This chaperone activity appears to be independent of Hsp27 phosphorylation. In conclusion, the most active chaperone of insulin and alpha-lactalbumin was the Hsp27 (elongated) dimer, the smallest Hsp27 subunit observed under physiological conditions. Second, the Hsp27 phospho-mimic is only a partial mimic of phosphorylated Hsp27, both in self association and in chaperone function. Finally, the efficient inhibition of insulin aggregation by Hsp27 dimer led to the proposal of two models for this chaperone activity.

It has been known for some time that slow kinetics will distort the shape of a reversible reaction boundary. Here we present a tutorial on direct boundary fitting of sedimentation velocity data for a monomer-dimer system that exhibits kinetic effects. Previous analysis of a monomer-dimer system suggested that rapid reaction behavior will persist until the relaxation time of the system exceeds 100 s (reviewed in Kegeles and Cann, 1978). Utilizing a kinetic integrator feature in Sedanal (Stafford and Sherwood, 2004), we can now fit for the k(off) values and measure the uncertainty at the 95% confidence interval. For the monomer-dimer system the range of well determined k(off) values is limited to 0.005 to 10(-5) s(-1) corresponding to relaxation times (at a loading concentration of the Kd) of approximately 70 to approximately 33,000 s. For shorter relaxation times the system is fast and only the equilibrium constant K but not k(off) can be uniquely determined. For longer relaxation times the system is irreversibly slow, and assuming the system was at initial equilibrium before the start of the run, only the equilibrium constant K but not k(off) can be uniquely determined.

E3-19K is a type I membrane glycoprotein expressed by adenoviruses (Ads) to modulate host antiviral immune responses. We have developed an expression system for the endoplasmic reticulum lumenal domain (residues 1 to 100) of Ad type 2 E3-19K tagged with a C-terminal His6 sequence in baculovirus-infected insect cells. In this system, recombinant E3-19K is secreted into the culture medium. A characterization of soluble E3-19K by analytical ultracentrifugation and circular dichroism showed that the protein is monomeric and adopts a stable and correctly folded tertiary structure. Using a gel mobility shift assay and analytical ultracentrifugation, we showed that soluble E3-19K associates with soluble peptide-filled and peptide-deficient HLA-A*1101 molecules. This is the first example of a viral immunomodulatory protein that interacts with conformationally distinct forms of class I major histocompatibility complex molecules. The E3-19K/HLA-A*1101 complexes formed in a 1:1 stoichiometry with equilibrium dissociation constants (Kd) of 50 +/- 10 nM for peptide-filled molecules and of about 10 microM for peptide-deficient molecules. A temperature-dependent proteolysis study revealed that the association of E3-19K with peptide-deficient HLA-A*1101 molecules stabilizes the binding groove. Importantly, our studies showed that peptide-deficient HLA-A*1101 molecules sequestered by E3-19K are capable of binding antigenic peptides and maturing into peptide-filled molecules. This firmly establishes that E3-19K does not block binding of antigenic peptides. Together, our results suggest that Ads have evolved to exploit the late and early stages of the class I antigen presentation pathway.

The class I myosin, Myo1b, is a calmodulin- and actin-associated molecular motor widely expressed in mammalian tissues. Analytical ultracentrifugation studies indicate that Myo1b purified from rat liver has a Stokes radius of 6.7 nm and a sedimentation coefficient, s(20,w), of 7.0 S with a predicted molar mass of 213 kg/mol. These results indicate that Myo1b is monomeric and consists primarily of a splice variant having five associated calmodulins. Molecular modeling based on the analytical ultracentrifugation studies are supported by electron microscopy studies that depict Myo1b as a single-headed, tadpole-shaped molecule with outer dimensions of 27.9 x 4.0 nm. Above a certain Myo1b/actin ratio, Myo1b bundles actin filaments presumably by virtue of a second actin-binding site. These studies provide new information regarding the oligomeric state and morphology of Myo1b and support a model in which Myo1b cross-links actin through a cryptic actin-binding site.