Information informed cellular systems 117

Membrane-integrated proteins were always hard to express in cell-based systems in sufficient quantity for structural analysis. In cell-free systems, they can be produced on a milligrams per milliliter scale, which, combined with labeling with stable isotopes, is also very amenable forNMR spectroscopy [157-161]. Possible applications of in vitro expression systems also include incorporation of selenomethionine (Se-Met) into proteins for multiwavelength anomalous diffraction phasing of protein crystal structures [162], Se-Met-containing proteins are usually toxic for cellular systems [163]. Consequently, rational design of more efficient biocatalysts is facilitated by quick access to structural information about the enzyme. 

From an industrial perspective, quantitative knowledge of the existence of different transporters within the cellular system used in screening procedures is of major importance as it can influence both the predictive value of the permeability coefficients and interpretation of the results. In addition, information on species differences or similarities or discrepancies between cell culture models and animals now provide an important basis for the scaling of data during the early phases of drug discovery for animals or humans [48]. 

Fluorescence excitation spectroscopy is thus a powerful technique for obtaining molecular information about systems of cellular size. At present, the technique is restricted to single small objects because of the requirement of angular integration of the emitted fluorescence. As work progresses, similiar information will be obtainable from spectra taken at a particular angle with respect to the exciting beam. This will allow extension of the photoselection concept to suspensions of particles and perhaps to individual cells. 

Looking at the literature in the field of biomineralization, one notices, that the majority of articles is descriptive in nature. On the basis of electron micrographs or thin section studies, the intricate relationships between mineral phase and organic matrix are investigated. Other papers deal with the chemical composition of the mineralized tissue and the minerals. Only a few authors address themselves to the question of metal ion transport mechanisms in cellular systems and the solid state principles involved in mineral deposition on organic substrates. All three sets of information, however, are essential to understand calcification processes. It appears, therefore, that information on the functionality of metal ions in living systems and their role in mineral deposition are particularly desired in this area of research. 

An answer to this apparent riddle is provided by RNA. Ribonucleic acid is actually a DNA equivalent, since it can store and replicate genetic information. Importantly, it is also a protein equivalent, since it can catalyze critical chemical reactions. Indeed, the first life-forms were probably entirely RNA based, and RNA has remained part of our cellular systems (Watson, 2004). Thus, RNA translates the genetic information coded for in our DNA into information that proteins can understand and act upon and does so in a remarkable manner. 

Fluorescence microscopy has long been a powerful tool for cell biology as well as drug discovery research. It can measure both the contents and locations of multiple biomolecules or probes in cells simultaneously. Thus it provides unparalleled levels of detailed information about cellular responses to drug treatment or other perturbations. It has been particularly useful for rapidly validating drug leads in multiple cellular systems relevant to their efficacy and toxicity profiles. 

Toxicokinetics describe Absorption, Distribution, Metabolism and Elimination (ADME) of a chemical in humans, experimental animals or cellular systems. Of specific importance for interpretation of animal studies and for extrapolation of hazards between species is the comparative information on the exposure and the dose that reaches the critical target. 

Similarly, we have described how information related to protein-splicing variants, amino acid peptide variants (polymorphisms), and PTMs is being introduced in data analysis pipelines in order to increase the rate of identifiable peptides. The introduction of genomics and transcriptomics information, often neglected in routine proteomics analyses, will enable the characterization of myriad splicing variants and amino acid polymorphisms, as well as the development of robust proteomics analysis pipelines, which will contribute to elucidate their role in health and disease states. These tools will make it possible to uncover a new layer of the proteome complexity and to expand the information available from cellular systems and the potential implication of these protein variants in different physiological processes. Finally, several bioinformatics tools that perform unbiased PTM analysis have also been reviewed. The tools that are currently being developed and refined tackle... 

Whereas detailed dynamic models can precisely answer questions on cellular behavior, the widespread application of such approaches has been hampered by the lack of kinetic information. In the absence of kinetic information, a method known as flux balance analysis (FBA) has been developed to analyze the metabolic capabilities of a cellular system based on mass balance constraints [Varma and Palsson 1994 Edwards et al. 1999 Edwards and Palsson 2000],... 

One of the concerns alx)ut studies on the function of particular residues in site-directed mutagenesis is that expressions in some cellular systems lead to competition between P450s 1 lAl and 1 IBl for (adrenodoxin) reducing equivalents in cellular systems". Another issue is that human P450s llBl and 11B2 have been difficult to express in bacteria, so that most experiments have relied on mammalian cells Schizosaccharomyces pombe has provided some success ). Nevertheless, much information about function has been obtained from patients samples . ... 

The pre-genomic era was characterized in some measure by a race to acquire information. The post-genomic era saw a secondary race to identify the transcriptional outputs of mammalian genomes, and the impact of proteomic, and ultimately a metabolomic, revolution is probably still to come. However, at this point in time we do have many of the tools needed to create predictive network models of a cellular system like macrophage activation and transcription control. 

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