Determination of dissociation constants between polyelectrolytes and proteins by affinity capillary electrophoresis

Advances in Studying Glycosaminoglycan-Protein Interactions Using Capillary Electrophoresis

Methods for studying interactions between glycosaminoglycans (GAGs) and proteins have assumed considerable significance as their biological importance increases. Capillary electrophoresis (CE) is a powerful method to study these interactions due to its speed, high efficiency, and low sample/reagent consumption. In addition, CE works effectively under a wide range of physiologically relevant conditions. This chapter presents the state of the art on CE methods for studying GAG-protein interactions including affinity capillary electrophoresis (ACE), capillary zone electrophoresis (CZE), frontal analysis (FA)/frontal analysis continuous capillary electrophoresis (FACCE), and capillary electrokinetic chromatography (CEC) with detailed experimental protocols for ACE and CZE methods.

Modelling and predicting the interactions between oppositely and variously charged polyelectrolytes by frontal analysis continuous capillary electrophoresis

In this work, a systematic study of the interactions between poly(l-lysine) and variously charged statistical copolymers of acrylamide and 2-acrylamido-2-methyl-1-propanesulfonate (PAMAMPS) has been carried out by frontal analysis continuous capillary electrophoresis (FACCE). FACCE was successfully implemented to obtain the interaction parameters (binding constant and stoichiometry) at different ionic strengths and for different PAMAMPS charge densities varying between 15% and 100%. The range of investigated ionic strengths was carefully adjusted according to the PAMAMPS charge density to obtain measurable binding constants by FACCE (i.e. formation binding constant typically comprised between 10⁴ and 10⁶ M^-1). The number of released counter-ions during the polyelectrolyte complex formation was systematically quantified via the ionic strength dependence of the binding constant and was compared to the total condensed counter-ion reservoir according to Manning theory on counter-ion condensation. A descriptive and predictive model relating the physico-chemical properties of the two partners, the binding constant and the ionic strength is proposed in the framework of multiple independent interaction sites of equal energy.

Exploring the glycosaminoglycan-protein interaction network by glycan-mediated pull-down proteomics

Glycosaminoglycans (GAGs) are linear, highly sulfated polysaccharides expressed by almost all animal cells. They occur as soluble molecules, or form proteoglycans by being O-linked to different core proteins on the cell surface and in the extracellular matrix. Due to their ability to interact with diverse proteins and to modulate their biologic functions, GAGs are main drivers of mammalian biology. However, to the present day, the human GAG binding proteome has only been insufficiently explored. The aim of this study was therefore to investigate the human GAG binding proteome of different sources by using the major GAG classes as ligands, and to explore the GAG-binding selectivity of the human plasma proteome. For this purpose, proteins were pulled down from immobilized low molecular weight heparin, heparan sulfate, and dermatan sulfate under different conditions and were identified by nano-LC/MS². Four hundred and fifty eight human GAG binding proteins have been identified, whereas plasma proteins showed clear differences in their GAG-binding specificity/selectivity and affinity. We were able to differentiate between proteins that bound to all three glycan ligands and proteins that showed selective binding to one or two glycan ligands. Moreover, step-gradient salt elution revealed different binding affinities toward different GAG ligands. On top of proteins with well-known GAG-binding properties we have identified formerly unknown GAG binders. Functional annotation of the identified GAG-binding proteins showed clusters of proteins that are involved in a variety of biological processes. The method described here is well suited for identifying GAG-binding proteins and for comparing human subproteomes with respect to binding to different GAG classes.

Studying glycosaminoglycan-protein interactions using capillary electrophoresis

Methods for studying interactions between glycosaminoglycans (GAGs) and proteins have assumed considerable significance as their biological importance increases. Capillary electrophoresis (CE) is a powerful method to study these interactions due to its speed, high efficiency, and low sample/reagent consumption. In addition, CE works effectively under a wide range of physiologically relevant conditions. This chapter presents state-of-the-art on CE methods for studying GAG-protein interactions including affinity capillary electrophoresis (ACE), capillary zone electrophoresis (CZE), frontal analysis (FA)/frontal analysis continuous capillary electrophoresis (FACCE), and capillary electrokinetic chromatography (CEC) with detailed experimental protocols for ACE and CZE methods.

Effect of dendrimer generation on the interactions between human serum albumin and dendrigraft polylysines

This work aims at studying the interaction between human serum albumin and different generations of dendrigraft poly-L-lysine (DGL) in physiological conditions. The binding constants and stoichiometry of the interaction were successfully determined using frontal analysis continuous capillary electrophoresis. The effect of generation on the interaction was evaluated for the five first generations of DGL. An increase of the binding constant accompanied with a decrease of the HSA:DGL (1:n) stoichiometry and a decrease of the cooperativity with dendrimer generation was observed. These findings were in good agreement with the increase of ligand (DGL) size, the increase of electrostatic ligand-ligand repulsion, and the localization of two negatively charged interaction sites on the HSA. The effect of the ligand topology (linear vs dendrigraft) on the HSA interaction revealed that linear poly(L-lysine) leads to much lower stoichiometry compared to DGL of similar molar mass due to much higher flexibility and contour length.

Linear polyalkylamines as fingerprinting agents in capillary electrophoresis of low-molecular-weight heparins and glycosaminoglycans

Glycosaminoglycan (GAG) analysis represents a challenging frontier despite the advent of many high-resolution technologies because of their unparalleled structural complexity. We previously developed a resolving agent-aided capillary electrophoretic approach for fingerprinting low-molecular-weight heparins (LMWHs) to profile their microscopic differences and assess batch-to-batch variability. In this report, we study the application of this approach for fingerprinting other GAGs and analyze the basis for the fingerprints observed in CE. Although the resolving agents, linear polyalkylamines, could resolve the broad featureless electropherogram of LMWH into a large number of distinct, highly reproducible peaks, longer GAGs such as chondroitin sulfate, dermatan sulfate, and heparin responded in a highly individualistic manner. Full-length heparin interacted with linear polyalkylamines very strongly followed by dermatan sulfate, whereas chondroitin sulfate remained essentially unaffected. Oversulfated chondroitin sulfate could be easily identified from full-length heparin. Scatchard analysis of the binding profile of enoxaparin with three linear polyalkylamines displayed a biphasic binding profile suggesting two distinctly different types of interactions. Some LMWH chains were found to interact with linear polyalkylamines with affinities as high as 10 nM, whereas others displayed nearly 5000-fold weaker affinities. These observations provide fundamental insight into the basis for fingerprinting of LMWHs by linear polyalkylamine-based resolving agents, which could be utilized in the design of advanced resolving agents for compositional profiling, direct sequencing, and chemoinformatics studies.

Hindered diffusion in polymeric solutions studied by fluorescence correlation spectroscopy

Diffusion of molecules in the crowded and charged interior of the cell has long been of interest for understanding cellular processes. Here, we introduce a model system of hindered diffusion that includes both crowding and binding. In particular, we obtained the diffusivity of the positively charged protein, ribonuclease A (RNase), in solutions of dextrans of various charges (binding) and concentrations (crowding), as well as combinations of both, in a buffer of physiological ionic strength. Using fluorescence correlation spectroscopy, we observed that the diffusivity of RNase was unaffected by the presence of positively charged or neutral dextrans in the dilute regime but was affected by crowding at higher polymer concentrations. Conversely, protein diffusivity was significantly reduced by negatively charged dextrans, even at 0.4 μM (0.02% w/v) dextran. The diffusivity of RNase decreased with increasing concentrations of negative dextran, and the amount of bound RNase increased until it reached a plateau of ∼80% bound RNase. High salt concentrations were used to establish the electrostatic nature of the binding. Binding of RNase to the negatively charged dextrans was further confirmed by ultrafiltration.

Neutral coatings for the study of polycation/multicharged anion interactions by capillary electrophoresis: application to dendrigraft poly-L-lysines with negatively multicharged molecules

The study of interactions between oppositely multicharged (macro)molecules remains a challenging issue. In frontal analysis capillary electrophoresis (FACE), it is difficult to avoid the adsorption of one of the interacting partners onto the capillary wall. In this work, we demonstrate the possibility to use FACE and affinity capillary electrophoresis (ACE) on a neutrally coated capillary for the study of interactions between a polycationic dendrigraft (or linear) poly-l-lysines, on one hand, and a multicharged anionic biomolecule (adenosine monophosphate, AMP, or adenosine triphosphate, ATP), on the other hand. A systematic comparison of four different neutral coatings (hydroxypropyl cellulose, polydimethylacrylamide, polyacrylamide, polyethylene glycol) has been performed based on the repeatability of the electrophoretic migration of the dendrigraft poly-l-lysines at pH close to neutrality. Both FACE and ACE methodogies were then used to study the interactions and to get the association constants and the stoichiometry of the complex. Multisite interactions, with two classes of independent sites, were determined. The specificity of the dendritic polylysine structure compared with linear polylysine in the interaction with ATP or AMP is also emphasized.

Glycosaminoglycans as polyelectrolytes

One of the barriers to understanding structure-property relations for glycosaminoglycans has been the lack of constructive interplay between the principles and methodologies of the life sciences (molecular biology, biochemistry and cell biology) and the physical sciences, particularly in the field of polyelectrolytes. To address this, we first review the similarities and differences between the physicochemical properties of GAGs and other statistical chain polyelectrolytes of both natural and abioitic origin. Since the biofunctionality and regulation of the structures of GAGs is intimately connected with interactions with their cognate proteins, we particularly compare and contrast aspects of protein binding, i.e. effects of both GAGs and other polyelectrolytes on protein stability, protein aggregation and phase behavior. The protein binding affinities and their dependences on pH and ionic strength for the two groups are discussed not only in terms of observable differences, but also with regard to contrasting descriptions of the bound state and the role of electrostatics. We conclude that early studies of the heparin-Antithromin system, proceeding to a large extent through the methods and models of protein chemistry and drug discovery, established not only many enabling precedents but also constraining paradigms. Current studies on heparan sulfate and chondroitin sulfate seem to reflect a more ecumenical view likely to be more compatible with concepts from physical and polymer chemistry.