A strategy for efficient characterization of macromolecular heteroassociations via measurement of sedimentation equilibrium

Analytical Ultracentrifugation as a Tool for Studying Protein Interactions

The last two decades have led to significant progress in the field of analytical ultracentrifugation driven by instrumental, theoretical, and computational methods. This review will highlight key developments in sedimentation equilibrium (SE) and sedimentation velocity (SV) analysis. For SE, this includes the analysis of tracer sedimentation equilibrium at high concentrations with strong thermodynamic non-ideality, and for ideally interacting systems the development of strategies for the analysis of heterogeneous interactions towards global multi-signal and multi-speed SE analysis with implicit mass conservation. For SV, this includes the development and applications of numerical solutions of the Lamm equation, noise decomposition techniques enabling direct boundary fitting, diffusion deconvoluted sedimentation coefficient distributions, and multi-signal sedimentation coefficient distributions. Recently, effective particle theory has uncovered simple physical rules for the co-migration of rapidly exchanging systems of interacting components in SV. This has opened new possibilities for the robust interpretation of the boundary patterns of heterogeneous interacting systems. Together, these SE and SV techniques have led to new approaches to study macromolecular interactions across the entire the spectrum of affinities, including both attractive and repulsive interactions, in both dilute and highly concentrated solutions, which can be applied to single-component solutions of self-associating proteins as well as the study of multi-protein complex formation in multi-component solutions.

Sequential assembly of the wedge of the baseplate of phage T4 in the presence and absence of gp11 as monitored by analytical ultracentrifugation

The baseplate wedge of bacteriophage T4 consists of seven gene products, namely, gp11, gp10, gp7, gp8, gp6, gp53, and gp25, which assemble strictly in this order with an exception that gp11 can bind to gp10 at any stage of the assembly. In this study, all the seven corresponding genes are expressed as recombinant proteins and all the possible combinations of the gene products are tested for interactions by analytical ultracentrifugation. No interactions among gene products that violate the strict sequential binding are observed except that gp6, gp53, and gp25 interact with each other weakly, but significantly. However, when gp6 is previously bound to the precursor complex, only gp53 binds to gp6 strongly and then gp25 binds to complete the wedge formation. This result indicates that the strict sequential association is based on the conformational change of the complex upon addition of each gene product. The binding constant between subunits in the intermediate complexes is too high to be measured. In fact, the binding of gp11 to gp10 is so tight that the binding constant could not be determined by trace sedimentation equilibrium. Also, no indication of dissociation of the intermediate complexes is found in sedimentation velocity, which indicates that other subunit interactions in the intermediate complexes are also strong. The 43.7 S complex, which formed upon addition of gp53, is a hexamer of the wedge complex and resembles the star-shaped baseplate. The s-value of the baseplate-like complex decreased to 40.6 S upon association with gp11 in spite of the increased molecular weight, which is reflected in the sharper edges of the baseplate-like structure which would have a higher friction.

Modern applications of analytical ultracentrifugation

Analytical ultracentrifugation is a classical method of biochemistry and molecular biology. Because it is a primary technique, sedimentation can provide first-principle hydrodynamic and first-principle thermodynamic information for nearly any molecule, in a wide range of solvents and over a wide range of solute concentrations. For many questions, it is the technique of choice. This review stresses what information is available from analytical ultracentrifugation and how that information is being extracted and used in contemporary applications.

Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin

The solution structure of bacteriocin AS-48, a 70-residue cyclic polypeptide from Enterococcus faecalis, consists of a globular arrangement of five alpha-helices enclosing a compact hydrophobic core. The head-to-tail union lies in the middle of helix 5, a fact that is shown to have a pronounced effect on the stability of the three-dimensional structure. Positive charges in the side chains of residues in helix 4 and in the turn linking helix 4 to helix 5 form a cluster that most probably determine its antibacterial activity by promoting pore formation in cell membranes. A similar five-helix structural motif has been found in the antimicrobial NK-lysin, an effector polypeptide of T and natural killer (NK) cells. Bacteriocin AS-48 lacks the three disulfide bridges characteristic of the saposin fold present in NK-lysin, and has no sequence homology with it. Nevertheless, the similar molecular architecture and high positive charge strongly suggest a common mechanism of antibacterial action.

Characterization of heterologous protein-protein interactions using analytical ultracentrifugation

Methods for quantitative characterization of heterologous protein-protein interactions by means of analytical ultracentrifugation (AUC) include sedimentation equilibrium, tracer sedimentation equilibrium, sedimentation velocity, and analytical band sedimentation. Fundamental principles governing the behavior of macromolecules in a centrifugal field are summarized, and the application of these principles to the interpretation of data obtained from each type of experiment is reviewed. Instrumentation and software for the acquisition and analysis of data obtained from different types of AUC experiments are described.

Folding stability of the kinetoplastid membrane protein-11 (KMP-11) from Leishmania infantum

Kinetoplastid membrane protein-11 (KMP-11) is a major component of the cell surface of kinetoplastids, and acts as a potent B- and T-cell immunogen during Leishmania infection. Here we report that the Leishmania infantum KMP-11 secondary structure adopts mainly an alpha-helical conformation at pH 7.5 and that its urea- and thermally-induced unfolding constitute a fully reversible two-step process. This allows estimation of a half-denaturation temperature of approximately 65 degrees C, a delta GDH2O at 20 degrees C of approximately 14.63 kJ.mol-1, and an increment of the reaction heat of approximately 183.92 kJ.mol-1 and an entropy of approximately 543.4 J.mol-1.deg-1, respectively, for the native-denatured equilibrium of the KMP-11 in solution. We also report that the KPM-11 protein is induced to adopt a molten globule state at a pH range between pH 4 and pH 6. As a whole, the stability and the specific features of the denaturing effect induced by changes in pH are similar in KMP-11 to various other lipoproteins.

Negative cooperativity in tryptophan synthase alpha subunit dissociation is caused by the bound coenzyme: pyridoxal 5'-phosphate

Sedimentation equilibrium studies of dilute solutions of tryptophan synthase reveal dissociation from the holoenzyme form, alpha 2 beta 2, into mixtures of alpha beta 2, small amounts of beta 2, and alpha as well as the original alpha 2 beta 2 holoenzyme. The holoenzyme form is stabilized by pyridoxal 5'-phosphate. A new sedimentation equilibrium analytical procedure shows the dissociation of the second alpha subunit to be negatively cooperative. The analytical procedure calculates theoretical error profiles with assumed values of the dissociation constant, k, and a cooperativity parameter until a match is made between one of the theoretical profiles and that computed from experimental data. The latter profile is calculated with an experimentally determined k and assumed values of the cooperativity parameter.

Dissociation equilibria of the tryptophan synthase alpha 2 beta 2 complex in saline buffer and guanidine isothiocyanate, as studied by sedimentation equilibrium

The dissociation equilibria of Salmonella typhimurium tryptophan synthase alpha 2 beta 2 complex were studied via centrifugation of the complex to sedimentation equilibrium in neutral saline buffers containing 0 to 137 mM guanidine isothiocyanate (GuSCN). The resulting concentration gradients were analyzed in the context of an equilibrium model for sequential dissociation of two alpha subunits from a stable beta 2 subunit. Under the conditions of these experiments, the first dissociation constant alone could be evaluated at GuSCN concentrations < or = 100 mM, and the second dissociation constant alone could be evaluated at GuSCN = 137 mM. At intermediate GuSCN, both dissociation constants were sufficiently well defined to rule out the presence of a large equilibrium cooperative effect in the stepwise dissociation of the alpha subunits.

Binding of fibrinogen to platelet integrin alpha IIb beta 3 in solution as monitored by tracer sedimentation equilibrium

Fibrinogen showed essentially no binding (KD > 1 mM) to platelet alpha IIb beta 3 integrin in solution in the presence of Triton or octylglucoside above critical micellar concentrations. Under these conditions the integrin was an alpha beta monomer. After removal of the detergent from the Triton containing buffer (25 mM Tris/HCl;, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, pH 7.4) the integrin formed aggregates with hexamers as the most prominent species, as demonstrated by analytical ultracentrifugation and electron microscopy. Tracer sedimentation equilibrium experiments indicate that fibrinogen binds to the integrin aggregates, but with a surprisingly large KD (at least 3 microM). This value is 10- to 100-fold higher than values determined by solid phase assays or with integrins reconstituted onto lipid bilayers.

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

The conformational properties of a 16 residue peptide, corresponding to the second beta-hairpin of the B1 domain of protein G, have been studied by nuclear magnetic resonance spectroscopy (NMR). This fragment is monomeric under our experimental conditions and in pure water adopts a population containing up to 40% native-like beta-hairpin structure. The detection by NMR of a native-like beta-hairpin in aqueous solution, reported here for the first time, indicates that these structural elements may have an important role in the early steps of protein folding. It also provides a good model to study in detail the sequence determinants of beta-hairpin structure stability, as has been done with alpha-helices.

New developments in the study of biomolecular associations via sedimentation equilibrium

The measurement and analysis of sedimentation equilibrium provide one of the most powerful techniques for quantitative characterization of reversible and irreversible macromolecular associations in solution. The use of this technique by nonspecialists has been greatly helped in recent years by the development of new instrumentation, new types of experiments and new PC-based software for computer-aided analysis of experimental results.