Protein-protein and protein-ligand interactions

What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems?

This review covers the analytical applications of protein partitioning in aqueous two-phase systems (ATPSs). We review the advancements in the analytical application of protein partitioning in ATPSs that have been achieved over the last two decades. Multiple examples of different applications, such as the quality control of recombinant proteins, analysis of protein misfolding, characterization of structural changes as small as a single-point mutation, conformational changes upon binding of different ligands, detection of protein-protein interactions, and analysis of structurally different isoforms of a protein are presented. The new approach to discovering new drugs for a known target (e.g., a receptor) is described when one or more previous drugs are already available with well-characterized biological efficacy profiles.

Aqueous Two-Phase Systems and Microfluidics for Microscale Assays and Analytical Measurements

Phase separation is a common occurrence in nature. Synthetic and natural polymers, salts, ionic liquids, surfactants, and biomacromolecules phase separate in water, resulting in an aqueous two-phase system (ATPS). This review discusses the properties, handling, and uses of ATPSs. These systems have been used for protein, nucleic acid, virus, and cell purification and have in recent years found new uses for small organics, polysaccharides, extracellular vesicles, and biopharmaceuticals. Analytical biochemistry applications such as quantifying protein-protein binding, probing for conformational changes, or monitoring enzyme activity have been performed with ATPSs. Not only are ATPSs biocompatible, they also retain their properties at the microscale, enabling miniaturization experiments such as droplet microfluidics, bacterial quorum sensing, multiplexed and point-of-care immunoassays, and cell patterning. ATPSs include coacervates and may find wider interest in the context of intracellular phase separation and origin of life. Recent advances in fundamental understanding and in commercial application are also considered.

Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease

Most biological processes are initiated or mediated by the association of ligands and proteins. This work studies multistep, ligand-protein association processes by Brownian dynamics simulations with coarse-grained models for HIV-1 protease (HIVp) and its neutral ligands. We report the average association times when the ligand concentration is 100 μM. The influence of crowding on the simulated binding time was also studied. HIVp has flexible loops that serve as a gate during the ligand binding processes. It is believed that the flaps are partially closed most of the time in its free state. To accelerate our simulations, we fixed a part of the HIVp and reparameterized our coarse-grained model, using atomistic molecular dynamics simulations, to reproduce the "gating" motions of HIVp. HIVp-ligand interactions changed the gating behavior of HIVp and helped ligands diffuse on HIVp surface to accelerate binding. The structural adjustment of the ligand toward its final stable state was the limiting step in the binding processes, which is highly system dependent. The intermolecular attraction between the ligands and crowder proteins contributes the most to the crowding effects. The results highlight broader implications in recognition pathways under more complex environment that considers molecular dynamics and conformational changes. This work brings insights into ligand-protein associations and is helpful in the design of targeted ligands.

Improved partitioning in aqueous two-phase system of tyrosine-tagged recombinant lactate dehydrogenase

The partitioning of Bacillus stearothermophilus lactate dehydrogenase (LDH) in an aqueous two-phase system was studied. Particularly, the influence of tyrosine tags on the partitioning was evaluated. The hydrophobic effect, caused by the addition of tyrosine residues, was determined in a system based on dextran and the thermoseparating ethylene oxide-propylene oxide random copolymer (EO30PO70). Five different LDH variants were constructed with N-terminal tags containing tyrosines (Y3 and Y6), tyrosines and prolines (Y3P2 and Y6P2), and only prolines (P2). LDH fused with tags containing tyrosines increased the partitioning coefficient, and the more tyrosines added to the protein, the larger improvement in partitioning. When prolines were added between the tyrosine-rich tag and the protein, a further increased partitioning was obtained. The enhanced partitioning was attributed to the rigid structure of the proline, which in turn led to an increase in the exposure of the tag to the surroundings. The best tyrosine tag, Y6P2, increased the partition coefficient four times and additionally, a higher thermostability was observed.

A new method for analysis of components in a mixture without preseparation: evaluation of the concentration ratio and protein-protein interaction

A new method for evaluating the ratio of two structurally different proteins or other compounds in a mixture that does not require any preseparation steps and is based on using the aqueous two-phase partition technique is described. Mathematical analysis of the partitioning of a mixture of two solutes demonstrates its ability to quantitatively evaluate the ratio of the concentrations of the solutes in the initial mixture. It also provides the means for detecting interactions between the two solutes. Experimental results confirm the analysis to be correct for mixtures of low-molecular-weight compounds as well as for mixtures of structurally different proteins. An example of analysis of a clinically relevant mixture of two proteins-transferrin and carbohydrate-deficient transferrin-is provided. An analysis of interactions between two proteins and/or peptides is also illustrated using two examples.

Purification of recombinant cutinase by extraction in an aqueous two-phase system facilitated by a fatty acid substrate

Purification of recombinant wild-type cutinase from the culture supernatant of Saccharomyces cerevisiae by extraction in aqueous two-phase system was investigated. The partition of the enzyme in a polyethylene glycol (PEG)-potassium phosphate system to the top phase was increased with lower molecular weight PEG. Enzyme partition in a 20% PEG/15% phosphate two-phase system was studied in the presence of detergents, fatty acids, and alcohols, respectively. Addition of 0.5% (w/w) butyrate increased the partition coefficient from 17 to 135 and the purification factor from 10 to 23. The effect of butyrate was also confirmed by using the countercurrent mode of extraction. Recovery of cutinase from the top phase was achieved by a secondary extraction into a new salt phase at a lower pH or a lower temperature. A specific interaction of butyrate to the active site of the enzyme was demonstrated by fluorescence spectroscopy. Size exclusion chromatography showed the cutinase-butyrate complex to be over two times the size of the free enzyme.

Calcium-binding mechanism of human nonerythroid alpha-spectrin EF-structures

We have used circular dichroism and 1H- and 15N-NMR spectroscopy to investigate calcium binding to the two EF-hands of human nonerythroid or alphaII-spectrin. Comparison of the 1H-NMR spectra from the peptide containing both EF-hands to the peptides containing the single EF-I and EF-II structures showed that both the structural and calcium-binding properties are significantly different. Further studies of the 121 amino acid peptide containing both EF-hands using circular dichroism and NMR showed that the binding of calcium ions induces conformational changes. To investigate the calcium-binding mechanism, the chemical shifts changes were recorded using multidimensional NMR spectroscopy during calcium titration. A total of 25 titration curves were obtained, each corresponding to the chemical shift changes of individual amino acid residues. The shapes of these titration curves were either hyperbolic or sigmoidal. Using factor analysis, two functions were extracted, one hyperbolic and one sigmoidal, which accounted for nearly all information present in the titration curves. By fitting the two functions to binding curves based on different binding models, we found that the binding mechanism is best described as sequential. Since the sigmoidal type was more pronounced in the titration curves corresponding to residues from the first EF-hand, we suggest that calcium binding to the first EF-hand is described by the sigmoidal function, and that the hyperbolic function describes calcium binding to the second EF-hand. Therefore, is seems likely that the second EF-hand must contain bound calcium before the first EF-hand can bind.

Cloning, expression and characterization of two putative calcium-binding sites in human non-erythroid alpha-spectrin

The C-terminus of alpha-spectrins contains two putative calcium-binding sites or EF-hands. To characterize the binding, we have isolated clones from a human fetal liver cDNA library and expressed several fragments comprising either one or both of these sites. When the isolated clones were sequenced, we found that three consecutive nucleotides differed compared to the published sequence. The discrepancy affected two codons in the first of the two putative calcium sites. These codons translated into glutamate and phenylalanine, which are identical to the residues present at the same position in other alpha-spectrins. In the presence of magnesium, only recombinant peptides comprising the second putative site bound calcium as determined by a calcium overlay assay. Although the first putative EF-hand appeared to bind some calcium in the absence of magnesium, no binding could be detected under stringent conditions. Therefore, it is likely that the second EF-hand constitutes the only functional calcium-binding site in the C-terminus of human non-erythroid alpha-spectrin. Since peptides comprising the second EF-hand bound calcium nearly as well as intact spectrin, it is also apparent that the second EF-hand constitutes the major binding site for calcium in spectrin. The relative change in negative ellipticity, induced by the binding of calcium, indicates a dissociation constant of approximately 120 microM.