muramidase and carbene

The knowledge of ligand-protein interactions is essential for understanding fundamental biological processes and for the rational design of drugs that target such processes. Carbene footprinting efficiently labels proteinaceous residues and has been used with mass spectrometry (MS) to map ligand-protein interactions. Nevertheless, previous footprinting studies are typically performed at the residue level, and therefore, the resolution may not be high enough to couple with conventional crystallography techniques. Herein we developed a subresidue footprinting strategy based on the discovery that carbene labeling produces subresidue peptide isomers and the intensity changes of these isomers in response to ligand binding can be exploited to delineate ligand-protein topography at the subresidue level. The established workflow combines carbene footprinting, extended liquid chromatographic separation, and ion mobility (IM)-MS for efficient separation and identification of subresidue isomers. Analysis of representative subresidue isomers located within the binding cleft of lysozyme and those produced from an amyloid-β segment have both uncovered structural information heretofore unavailable by residue-level footprinting. Lastly, a "real-world" application shows that the reactivity changes of subresidue isomers at Phe399 can identify the interactive nuances between estrogen-related receptor α, a potential drug target for cancer and metabolic diseases, with its three ligands. These findings have significant implications for drug design. Taken together, we envision the subresidue-level resolution enabled by IM-MS-coupled carbene footprinting can bridge the gap between structural MS and the more-established biophysical tools and ultimately facilitate diverse applications for fundamental research and pharmaceutical development.

Topics: Amyloid beta-Peptides; Animals; Binding Sites; Chickens; ERRalpha Estrogen-Related Receptor; Humans; Ion Mobility Spectrometry; Ligands; Mass Spectrometry; Methane; Muramidase; Protein Binding; Receptors, Estrogen

While most Rh-N-heterocyclic carbene (NHC) complexes currently investigated in anticancer research contain a Rh(III) metal center, an increasing amount of research is focusing on the cytotoxic activity and mode of action of square-planar [RhCl(COD)(NHC)] (where COD = 1,5-cyclooctadiene) which contains a Rh(I) center. The enzyme thioredoxin reductase (TrxR) and the protein albumin have been proposed as potential targets, but the molecular processes taking place upon protein interaction remain elusive. Herein, we report the preparation of peptide-conjugated and its nonconjugated parent [RhCl(COD)(NHC)] complexes, an in-depth investigation of both their stability in solution, and a crystallographic study of protein interaction. The organorhodium compounds showed a rapid loss of the COD ligand and slow loss of the NHC ligand in aqueous solution. These ligand exchange reactions were reflected in studies on the interaction with hen egg white lysozyme (HEWL) as a model protein in single-crystal X-ray crystallographic investigations. Upon treatment of HEWL with an amino acid functionalized [RhCl(COD)(NHC)] complex, two distinct rhodium adducts were found initially after 7 d of incubation at His15 and after 4 weeks also at Lys33. In both cases, the COD and chlorido ligands had been substituted with aqua and/or hydroxido ligands. While the histidine (His) adduct also indicated a loss of the NHC ligand, the lysine (Lys) adduct retained the NHC core derived from the amino acid l-histidine. In either case, an octahedral coordination environment of the metal center indicates oxidation to Rh(III). This investigation gives the first insight on the interaction of Rh(I)(NHC) complexes and proteins at the molecular level.

Topics: Coordination Complexes; Crystallography, X-Ray; Heterocyclic Compounds; Methane; Models, Molecular; Molecular Structure; Muramidase; Rhodium

Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

Topics: Animals; Binding Sites; Chickens; Glucosides; Horses; Ligands; Methane; Models, Molecular; Molecular Probes; Muramidase; Oligosaccharides; Protein Footprinting; Protein Interaction Mapping; Proteins; Staining and Labeling; Ubiquitin

A new NHC iridium(I) complex (1) showing significant antiproliferative properties in vitro is described here. Its crystal structure, solution behaviour and interactions with the model proteins cytochrome c (cyt c) and lysozyme were investigated. High resolution ESI-MS measurements suggest that this iridium(i) complex acts as a prodrug and binds cyt c tightly through an unusual "oxidative" mechanism. Eventually, an iridium(III)-NHC fragment is found associated to the protein.

Topics: Cell Proliferation; Cell Survival; Coordination Complexes; Cytochromes c; HEK293 Cells; Heterocyclic Compounds; HT29 Cells; Humans; Iridium; MCF-7 Cells; Methane; Muramidase; Oxidation-Reduction

Recent work has shown that engineered variants of cytochrome P450BM3 (CYP102A1) efficiently catalyze non-natural reactions, including carbene and nitrene transfer reactions. Given the broad substrate range of natural P450 enzymes, we set out to explore if this diversity could be leveraged to generate a broad panel of new catalysts for olefin cyclopropanation (i.e., carbene transfer). Here, we took a step towards this goal by characterizing the carbene transfer activities of four new wild-type P450s that have different native substrates. All four were active and exhibited a range of product selectivities in the model reaction: cyclopropanation of styrene by using ethyl diazoacetate (EDA). Previous work on P450BM3 demonstrated that mutation of the axial coordinating cysteine, universally conserved among P450 enzymes, to a serine residue, increased activity for this non-natural reaction. The equivalent mutation in the selected P450s was found to activate carbene transfer chemistry both in vitro and in vivo. Furthermore, serum albumins complexed with hemin were also found to be efficient in vitro cyclopropanation catalysts.

Topics: Alkenes; Animals; Biocatalysis; Cattle; Cyclopropanes; Cytochrome P-450 Enzyme System; Hemin; Humans; Methane; Muramidase; Serum Albumin; Styrene; Substrate Specificity

A cross-metathesis reaction between an alkene terminated self-assembled monolayer (SAM) on glass/Si wafer and an alkene tethered Fischer carbene complex yielded a functionalized surface. Rapid aminolysis of the Fischer carbene moieties permit efficient anchoring of amine containing molecules on such a surface. Attachment of 1-pyrenemethylamine was thus monitored by ATR-IR spectroscopy and fluorescence microscopy. Similarly, BSA and lysozyme were individually grafted to such Fischer carbene modified surfaces using their pendant lysine residues. It has been demonstrated that the anchored lysozyme retains its bactericidal property.

Topics: Alkenes; Enzymes, Immobilized; Glass; Membranes, Artificial; Methane; Molecular Structure; Muramidase; Organosilicon Compounds; Serum Albumin, Bovine; Surface Properties

The introduction of heavy atoms into protein crystals is sometimes rendered difficult and tedious because of the poor specificity of the available reagents for particular target residues. On the other hand, transition organometallic chemistry offers an almost untouched field for this purpose. In particular, Fischer-type metallocarbene complexes of the general formula (CO)5W=C(OR1)R2 may be attractive reagents because they contain the heavy element tungsten and specifically target amino groups to form stable, covalent aminocarbene adducts. With a small protein such as hen egg white lysozyme (HEWL) with a limited number of potential binding sites, it was possible to form protein-aminocarbene conjugates that have an average of one aminocarbene moiety per protein molecule. RP-HPLC combined with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS analysis of the conjugates revealed that they were mixtures of the native protein, monoaminocarbenes and diaminocarbenes. Tryptic proteolysis experiments performed on the protein conjugates combined with MALDI-TOF-MS analysis of the aminocarbenic peptides allowed us to determine that lysines 13, 33, 97 and 116 were involved in the reaction of HEWL with (CO)5W=C(OMe)Me.

Topics: Animals; Binding Sites; Chickens; Chromatography, High Pressure Liquid; Egg Proteins; Female; Hydrocarbons; Methane; Muramidase; Organometallic Compounds; Peptide Mapping; Protein Binding; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Trypsin

Methylene is one of, if not the, most reactive organic chemical known. It has a very low specificity, which makes it essentially useless for synthesis, but suggests a possible role in protein footprinting with special importance in labeling solvent accessible nonpolar areas, identifying ligand binding sites, and outlining interaction areas on protomers that form homo or hetero oligomers in cellular assemblies. The singlet species is easily and conveniently formed by photolysis of diazirine. The reactions of interest are insertion into C-H bonds and addition to multiple bonds, both forming strong covalent bonds and stable compounds. Reaction with proteins and peptides is reported even in aqueous solutions where the vast majority of the reagent is used up in forming methanol. Species containing up to 5 to 10 extra :CH2 groups are easily detected by electrospray mass spectroscopy. In a mixture of a 14 Kd protein and a noninteracting 1.7 Kd peptide, the distribution of mass peaks in the electrospray spectra was close to that expected from random modification of the estimated solvent accessible area for the two molecules. For analysis at the single residue level, quantitation at labeling levels of one 13CH2 group per 10 to 20 kDa of protein appears to be possible with isotope ratio mass spectroscopy. In the absence of reactive solvents, photolysis of diazirine produces oily polymeric species that contain one or two nitrogen atoms, but not more, and are water soluble.

Topics: Animals; Chickens; Diazomethane; Hydrocarbons; Indicators and Reagents; Methane; Muramidase; Photolysis; Polymers; Protein Conformation; Proteins; Solvents; Spectrometry, Mass, Electrospray Ionization