title: Using singular value decomposition to characterize protein-protein interactions by in-cell NMR spectroscopy.
abstract: Distinct differences between how model proteins interact in-cell and in vitro suggest that the cytosol might have a profound effect in modulating protein-protein and/or protein-ligand interactions that are not observed in vitro. Analyses of in-cell NMR spectra of target proteins interacting with physiological partners are further complicated by low signal-to-noise ratios, and the long overexpression times used in protein-protein interaction studies may lead to changes in the in-cell spectra over the course of the experiment. To unambiguously resolve the principal binding mode between two interacting species against the dynamic cellular background, we analyzed in-cell spectral data of a target protein over the time course of overexpression of its interacting partner by using single-value decomposition (SVD). SVD differentiates between concentration-dependent and concentration-independent events and identifies the principal binding mode between the two species. The analysis implicates a set of amino acids involved in the specific interaction that differs from previous NMR analyses but is in good agreement with crystallographic data.
authors.affiliation: Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222 (USA).
authors.forename: Subhabrata
authors.initials: S
authors.lastname: Majumder
authors.forename: Christopher M
authors.initials: CM
authors.lastname: DeMott
authors.forename: David S
authors.initials: DS
authors.lastname: Burz
authors.forename: Alexander
authors.initials: A
authors.lastname: Shekhtman
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D014452:Ubiquitins / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; C533288:Pup protein, Mycobacterium tuberculosis; D014452:Ubiquitins; D000251:Adenosine Triphosphatases; C479920:Mpa protein, Mycobacterium tuberculosis
keywords: NMR spectroscopy; protein-protein interactions; single-cell measurements; single-value decomposition; statistical analysis