Protein chemistry identification

Zinc is a constituent of over 300 enzymes with much research into the coordination of zinc to the protein backbone, and how its chemistry is modulated by the donor set and environment.2 As well as the Lewis acid catalysis properties in enzymes, the structural role in zinc finger proteins has been a major area of research since the late 1990s. A number of reviews on zinc physiology, enzymology, and proteins in general have been published.978-981 There is extensive analysis available to classify the mononuclear sites in zinc proteins and identification of structural relationships of the extended environment.982,983... 

Methods based on liquid chromatography-mass spectrometry (LC-MS) and universally accepted search algorithms permit reliable identifications of low levels of proteins at high sensitivity [6]. Even semispecialized protein chemistry labs can readily identify proteins at the level of a few picomoles (10 pmol of a 50-kDa protein is 500 ng). Specialized groups with access to the latest advances in HPLC and mass spectrometry routinely work with subpicomolar quantities. Chemical proteomics as discussed here requires the more advanced equipment. 

Mass spectrometry provides a wealth of information for proteomics research, enzymology, and protein chemistry in general. The techniques require only miniscule amounts of sample, so they can be readily applied to the small amounts of protein that can be extracted from a two-dimensional electrophoretic gel. The accurately measured molecular mass of a protein is one of the critical parameters in its identification. Once the mass of a protein is accurately known, mass spectrometry is a convenient and accurate method for detecting changes in mass due to the presence of bound cofactors, bound metal ions, covalent modifications, and so on. 

Seraphin, B. (2002) Identification of transiently interacting proteins and of stable protein complexes. In Advances in Protein Chemistry. J. Janin and S.J. Wodak, eds. (U S A. Elsevier Science), vol. 61, pp. 99-117. 

Proteomics is the study of the proteome, the expression of the genome in cellular and extracellular proteins, i.e., involving the entire complement of proteins expressed by a particular cell, organism, or tissue. It comprises a transformation of protein chemistry and structure biology, where the structure and function of individual proteins are studied, into systems biology, where partial peptide sequencing is performed in combination with database matching to identify proteins in complex mixtures. The focus has moved to understand the cellular function of proteins. This means that next to identification of which proteins are present, other... 

Gradually, over the past twenty years, mass spectrometers were interfaced with a number of protein chemistry assays to generate detectors providing superior information. With the increased performance and versatility of the instrumentation dedicated to the life sciences, new analytical strategies for peptide and protein identification and characterization have emerged in which MS and bioinformatic tools are key players. MS has an enormous impact on the capability for structural analysis of bio-molecules, thanks to the ability to create gas phase ions of the peptides and proteins to be analyzed. Peptides and proteins are often charged and polar, making... 

D.B. Wall, M.T. Kachman, S.Y Gong, R. Hinderer, S. Parus, D.E. Misek, S.M. Hanash and D.M. Lubman, Isoelectric focusing nonporous RP HPLC a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDI-TOF mass spectrometry. Analytical Chemistry, 72, 1099-1111 (2000). 

Shimokawa, J., Ishiwata, T., Shirai, K. et al. (2005) Total synthesis of (+)-batzelladine A and (—)-batzelladine D, and identification of their target protein. Chemistry -A European Journal, 11, 6878-6888. 

Liang S, Li X, Cao M, etal. (2000) Identification of venom proteins of spider S. Huwena on two-dimensional electrophoresis gel by N-terminal microsequencing and mass spectrometric peptide mapping. Journal of Protein Chemistry 19 225-229. 

Schegg, K.M. Denslow, N.D. Andersen, T.T. Bao, Y. Cohen, S.A. Mahrenholz, A.M. Mann, K. Quantitation and identification of proteins by amino acid analysis ABRF-96AAA collaborative trial. In Techniques in Protein Chemistry, 8th Ed. Marshak, D.R., Ed. Academic Press San Diego, CA, 1997, 207-216. Fountoulakis, M. Lahm, H.-W. Hydrolysis and amino acid composition analysis of proteins. J. Chromatogr. A, 1998, 826, 109-134. 

Thin-layer chromatography (TLC) and the more modem technique—high-performance thin-layer chromatography (HPTLC)— have numerous applications in proteins chemistry. These techniques are used for the quantitative determinations of peptides (nanograms), identification of peptides in partially hydrolyzed proteins, correlation of chromatographic properties for peptides and their constituent amino acids, as well as identification and characterization of proteins present in small quantities. 

Because of the advances in the gas-phase ionization of biomacromolecules, such as electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), mass spectrometry (MS) has become a powerful tool for detection, identification, and structural analysis of proteins, peptides, and polynucleotides. The molecules ionized in a gas phase by these methods are subsequently analyzed by sector, quadrupole, ion-trap, or time-of-flight mass spectrometers. In particular, the MS systems consisting of ESI and triple-stage quadrupole (ESI/TSQ) or ion-trap (IT) mass spectrometry and MALDI time-of-flight (MALDl/TOF) mass spectrometry have been most widely applied to the field of protein chemistry for the accurate determination of molecular mass of proteins and peptides, determination of amino acid sequence, identification of proteins by peptide mass databases, and analysis of posttranslational modifications such as phosphorylation and glycosylation. In general, current techniques allow detenni-... 

Proteomics is a multidisciplinary study that includes protein chemistry, MS, chromatography, bioinformatics, etc. The basic proteomics techniques are grouped into two types protein separation and protein identification. 2DGE and LC are the main protein- and peptide-separation techniques, respectively. MS coupled with bioinformatics analysis identifies proteins. Two types of proteomics systems (LC, gel) are used to analyze human pituitary tissues to obtain tumor-related proteins and PTMs. 

---