Protein data processing

Many key protein ET processes have become accessible to theoretical analysis recently because of high-resolution x-ray stmctural data. These proteins include the bacterial photosynthetic reaction centre [18], nitrogenase (responsible for nitrogen fixation), and cytochrome c oxidase (the tenninal ET protein in mammals) [19, 20]. Although much is understood about ET in these molecular machines, considerable debate persists about details of the molecular transfonnations. 

Manually processing each chromatographic peak is not only time and labor intensive but difficult to reproduce. To overcome these problems and to provide a consistent data format that was independent of retention time, a number of data-processing subroutines were automated to produce a single representative cellular protein spectrum. 

These solution NMR and X-ray crystallographic findings have been contradicted by X-ray structures solved by Rypniewski et al.32 The results show a reduced active site unchanged from the oxidized state and let these authors to propose a five-coordinate copper ion that exists throughout the oxidation and reduction process. In 2001 the Protein Data Bank listed 39 X-ray crystallographic and NMR solution structures for CuZnSOD, including oxidized, reduced, genetically modified, and other species with or without attached substrates or substrate mimics such as azide ion. The reader is advised to search the Protein Data Bank for additional and more up-to-date structural depositions and search the literature for further discussion of mechanism. 

In practice, modern data-processing software applications perform these calculations very rapidly [23,24]. These algorithms are capable of deconvolving the relatively simple envelope of peaks generated by ESI of a single protein, or complex spectra produced by protein mixtures. 

During the past 25 years a considerable body of data has been accumulated, often to atomic resolution, on the structure and function of proteins. In contrast we know far less about the life cycle of these proteins—those processes which put a protein in the part of the cell in which it is to function and the cellular movements (if any) of this protein as it carries out its function. We know even less about those processes which eventually single out the protein for degradation. 

Data processing occurs in two stages. Initially, diffraction images are reduced to a tabulation of reflection indices and intensities or, after truncation, structure factors. The second stage involves conversion of the observed structure factors into an experimental electron density map. The choice of how to execute the latter step depends on the method used to determine the phase for each reflection. The software packages enumerated above generally focus on exploitation of anomalous signals to overcome the phase problem for a protein of unknown structure. 

Tsuruta, H., et al. (1998). Imaging RNA and dynamic protein segments with low-resolution virus crystallography experimental design, data processing and imph-cations of electron density maps. /. Mol. Biol. 284, 1439-1452. 

Pelczer and B.G. Carter, Data processing in Multidimensional NMR, in Protein NMR Protocols (series Methods in Molecular Biology, Vol. 60), ed. D.G. Reid (Humana Press, NJ, 1997) Ch. 4. 

Hydrophilicity and hydrophobicity are the most fundamental properties to be controlled for materials whenever they are utilized in biomedical devices. Protein-adsorption behavior on several biomaterials of different hydrophilicity was discussed by comparing available data with two modellings (Ikada and Peppas) for the protein-adsorption process. The adsorptive behavior of poly(HEMA) carrying polyamine functional groups was also discussed. It is well-known that protein adsorption is the first event when any of the body fluids encounters an artificial material. 

Note that the myelin P2 coordinates were not yet available from the Protein Data Bank and were obtained directly from the laboratory in which the P2 structure was determined. Because of the time required for publication of research papers and processing of coordinates by the PDB, coordinates may be available directly from a crystallographic research group several months before they are available from PDB. 

PDB is one of the oldest protein data bases, founded in 1971. It has three locations, Rutgers University in New Jersey, San Diego Supercomputer Center (SDSC) at the University of California, and the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. The PDB is a source for protein characterization and structure as well. The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Approximately 50-100 new structures are deposited each week, which are annotated and released upon the depositor s specifications. PDB data are freely available worldwide. PDB formats, annotates, validates, and releases dozens of complicated structure files each week some of them take only a couple of hours, others take weeks to process. Data processing is the main task of people at the PDB and validation is the most time-consuming part (Smith-Schmidt, 2002). 

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