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Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)-Based Strategy for Proteome-Wide Thermodynamic Analysis of Protein-Ligand Binding Interactions
Authors:Duc T. Tran  Jagat Adhikari  Michael C. Fitzgerald
Affiliation:From the ‡Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710; ;§Department of Chemistry, Duke University, Durham, North Carolina 27708
Abstract:Described here is a quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with a Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) approach to compare the equilibrium folding/unfolding properties of proteins in the absence and presence of target ligands. The method, which is general with respect to ligand, measures the ligand-induced changes in protein stability associated with protein-ligand binding. The methodology is demonstrated in a proof-of-principle study in which the well-characterized protein-drug interaction between cyclosporine A (CsA) and cyclophilin A was successfully analyzed in the context of a yeast cell lysate. A control experiment was also performed to assess the method''s false positive rate of ligand discovery, which was found to be on the order of 0.4 - 3.5%. The new method was utilized to characterize the adenosine triphosphate (ATP)-interactome in Saccharomyces cerevisiae using the nonhydrolyzable ATP analog, adenylyl imidodiphosphate (AMP-PNP), and the proteins in a yeast cell lysate. The new methodology enabled the interrogation of 526 yeast proteins for interactions with ATP using 2035 peptide probes. Ultimately, 325 peptide hits from 139 different proteins were identified. Approximately 70% of the hit proteins identified in this work were not previously annotated as ATP binding proteins. However, nearly two-thirds of the newly discovered ATP interacting proteins have known interactions with other nucleotides and co-factors (e.g. NAD and GTP), DNA, and RNA based on GO-term analyses. The current work is the first proteome-wide profile of the yeast ATP-interactome, and it is the largest proteome-wide profile of any ATP-interactome generated, to date, using an energetics-based method. The data is available via ProteomeXchange with identifiers PXD000858, DOI 10.6019/PXD000858, and PXD000860.The characterization of protein-ligand interactions is important in many areas of biochemical research from fundamental studies of biological processes to understanding drug action. Currently, the most widely used methods for proteome-wide analyses of protein-ligand binding interactions are those that combine an affinity purification step with a mass spectrometry-based proteomics analysis. Such methods have provided a wealth of information about protein-protein interaction networks in different proteomes (14), and they have helped identify the protein targets of small molecules (57). However, a significant drawback to their use is the need for specially designed ligands to facilitate the affinity purification. This has prompted the development of more general methods for protein-ligand binding analyses that can be performed directly in solution and do not require derivatization and/or immobilization of the ligand. Several such methods involving the use of chromatography co-elution (8), protease susceptibility (9), and energetics-based approaches (1015) have recently been reported.Energetics-based approaches are especially attractive for protein-ligand binding analyses because they can be both quantitative and general with respect to ligand class. Two energetics-based approaches, the stability of proteins from rates of oxidation (SPROX)1 (10, 16, 17) and pulse proteolysis techniques (13, 18), have shown promise for protein-ligand binding analyses on the proteomic scale, but so far have been limited in their proteomic coverage. Although the pulse proteolysis technique does utilize targeted mass spectrometry-based proteomics analyses for the identification of hit proteins, the technique relies on gel-based strategies for the resolution, detection, and quantitation of potential protein targets (13, 18). This reliance on gel-based strategies for protein resolution, detection, and quantitation, ultimately limits the complexity of protein samples that can be interrogated for ligand binding. In contrast, the SPROX technique has been interfaced with conventional bottom-up shotgun proteomics platforms that exploit the capabilities of modern LC-MS/MS systems to resolve, detect, and quantify the protein components of complex biological mixtures (10, 16, 17).A key limitation to the bottom-up shotgun proteomics protocols developed for SPROX analyses, to date, is that they require the detection and quantitation of methionine-containing peptides to report on the thermodynamic stability of the proteins to which they map. Although the frequency of methionine residues in proteins is relatively low (∼2.5%) (19), the large majority of proteins have at least one methionine. Because one methionine residue can report on the global equilibrium folding/unfolding properties of the protein or protein domain to which it maps, the scope of SPROX is not fundamentally limited by the relatively low frequency of methionine residues in proteins. Rather, the protein coverage in proteome-wide SPROX experiments is limited by the practicalities associated with the comprehensive detection and quantitation of methionine-containing peptides in the bottom-up shotgun proteomics experiment.The SPROX protocol described here utilizes a stable isotope labeling with amino acids in cell culture (SILAC)-based strategy to expand the protein coverage in proteome-wide SPROX experiments by enabling any peptide (i.e. methionine-containing or not) that is identified and quantified in a bottom-up shotgun proteomics experiment to report on the stability of the protein to which it maps. As part of the work described here the capabilities of this new method for protein-ligand binding analysis (referred to hereafter as SILAC-SPROX) are demonstrated and benchmarked in two protein-ligand binding studies. In the first part of this work, the endogenous proteins in a yeast cell lysate are analyzed for binding to cyclosporine A (CsA), an immunosuppressant with well-characterized protein targets (5, 20). In the second part of this work, the endogenous proteins in a yeast cell lysate are analyzed for binding to adenylyl imidodiphosphate (AMP-PNP), a nonhydrolyzable analog of the ubiquitous enzyme co-factor, adenosine triphosphate (ATP), which has less well-characterized protein targets. In the CsA binding study, the already well-characterized tight-binding interaction between CsA and cyclophilin A (2123) was successfully detected and quantified using the methodology. A number of known and unknown protein binding interactions of ATP were identified and quantified in the ATP-binding experiments described here. The SILAC-SPROX approach shows promise for future studies of protein-ligand interactions at the systems level (e.g. in cellular processes and disease states).
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