Applications Protein Function

Nanoparticle surface modification is of tremendous importance to prevent nanoparticle aggregation prior to injection, decrease the toxicity, and increase the solubility and the biocompatibility in a living system [20]. Imaging studies in mice clearly show that QD surface coatings alter the disposition and pharmacokinetic properties of the nanoparticles. The key factors in surface modifications include the use of proper solvents and chemicals or biomolecules used for the attachment of the drug, targeting ligands, proteins, peptides, nucleic acids etc. for their site-specific biomedical applications. The functionalized or capped nanoparticles should be preferably dispersible in aqueous media. 

Currently, protein microarrays can be divided into various types depending on the strategies to be chosen. For example, according to the array structure and shape, protein microarrays include 3D-surface structure [30, 31], nanowell [32], and plain chips [33-36], Meanwhile, considering the field of application, protein microarrays can be classified into five categories antibody array, antigen or reserve array, functional array, capture array, and solute array. Table 11.6 shows the differences among them. 

Pharmacokinetics Poorly absorbed from the GI tract minimal absorption following topical application. Protein binding 9%-36%. Widely distributed. Partially metabolized in liver. Excreted primarily in urine. Removed by hemodialysis. Half-life 2.5 hr (increased in impaired renal function). 

To date, complex proteins with biological activity (6), for use in X-ray crystal structure analysis (7) and ELISA systems (8), and for the development of animal drugs (9) have successfully been produced by using this system. Therefore, the Kaiko-baculovirus protein production system has broad applicability across the field of reverse chemical genetics for the analysis of protein function on the basis of interactions with chemical compounds. 

The protein phosphatase calcineurin was of particular interest since it mediates the immunosuppressive effect of the pharmaceuticals cyclosporin and FK506, often used in organ and tissue transplantations. The biochemical point of application of both pharmaceuticals was unclear for a long time. In initial experiments, it was found that cyclosporin and FK506 bind specifically to two proteins known as cyclophilin and FK506 binding protein, respectively. Both proteins function as peptidyl prolyl cis/trans isome-rases (review Fischer, 1994). 

Many standardized functional property tests have been published. Standardized methods are available from many organizations, including the American Association of Cereal Chemists, American Oil Chemists Society, and International Dairy Federation. Generally, these methods have been tested in collaborative studies by several laboratories and found to be repeatable. Therefore the use of standardized methods may facilitate comparison of results between laboratories. Even though a method has been standardized, there is no guarantee that the test results will relate to protein functionality in a particular product or product application. Another problem is that most of the standardized tests are empirical. If any step in the procedure is changed or equipment is substituted, comparisons between laboratories may not be possible. 

Model systems tests have played an important role leading to our understanding of protein functionality in food systems. There is no si ngle test that is applicable for all food systems. Careful consideration must be given when designing a model system and selecting a specific protein functionality test for a particular application. Comparison of results from different methods and from other laboratories must be made with caution. Similarly, extrapolation of results from model systems to real food products must also be carefully interpreted. 

Protein microarrays have many potential applications in high-throughput analysis of protein function. However, simple, reproducible, and robust methods for array fabrication are required. Here we discuss the background to different routes to array fabrication and describe in detail one approach in which the purification and immobilization procedures are combined into a single step, dramatically simplifying the array fabrication process. We illustrate this approach by reference to the creation of an array of p53 variants, and discuss methods for assay and data analysis on such arrays. 

The possible applications of synthetic proteins appear to be extensive. In some cases, it may be possible to redesign natural proteins to allow them to function more efficiently than they do in nature. For example, most proteins carry out their normal functions only in rather narrow environmental conditions, often near body temperature of 37°C and a pH close to 7.0. But there may be circumstances under which it would be helpful if those proteins functioned over a broader range of temperature, acidity, and other conditions. The ability to rearrange the primary sequence of the protein may make changes of this kind possible. 

We, the volume editors, hope that this book will prove to be a helpful reference for students as well as the advanced researcher. We have attempted to provide a background to ABPP as well as review some of the more intriguing applications of this emerging technology. At the time of writing, this field is far from being comprehensively explored, and novel innovations and applications of ABPP will undoubtedly provide insight into protein function for many years to come. 

All these approaches have been used to alter protein function, to increase the activity or solubility of proteins, or to adapt enzymes for industrial applications. The goal of artificial man-made proteins with tailor-made activities is, however, still far away and none of the currently existing approaches provides the ultimate solution to the directed evolution of proteins. Nevertheless, numerous examples of successfully altered and improved proteins clearly show the power of directed evolution for protein design. 

Gabaldon T (2005) Origin and evolution of the mitochondrial proteome. Applications for protein function prediction in the eukaryotes. Thesis, Nijmegen Gabaldon T, Huynen MA (2003) Reconstruction of the proto-mitochondrial metabolism. Science 301 609-609... 

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