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Current  Proteomics, Vol. 2, No. 2, 2005

 

Contents

 

Minireview

 

Toxicoproteomics: Applications in Drug Development Pp. 97-101

Nitin Gupta, Amanda Law, Richa Poddar, Melissa Louie, Animesh Ray and Deb N. Chakravarti

[Abstract]

 

Functional Proteomics Using Direct Protein Inactivation Pp. 103-107

Brenda K. Eustace and Daniel G. Jay

[Abstract]

 

Functional and Structural Analysis of Bacillus Proteome Pp. 109-145

Supachok Sinchaikul, Boonyaras Sookkheo, Supachai Topanurak, Fu-Ming Pan, Suree Phutrakul and Shui-Tein Chen

[Abstract]

 

Identification and Characterization of Plant Allergens Using Proteomic Approaches Pp. 147-164

Amanda Law, Nitin Gupta, Melissa Louie, Richa Poddar, Animesh Ray and Deb N. Chakravarti

[Abstract]

 

Functional RNAs as Tools in Proteomics Pp. 165-178

Narendra K. Vaish and Shawn Zinnen

[Abstract]

Abstracts

 

[Back to top] Toxicoproteomics: Applications in Drug Development

Nitin Gupta, Amanda Law, Richa Poddar, Melissa Louie, Animesh Ray and Deb N. Chakravarti

 

Toxicoproteomics is the study of the effects of chemical exposure on tissues through identification and quantitative evaluation of changes occurring in the proteome profile. This approach has been and continues to be applied in the preclinical testing of drugs for precise as well as high-throughput determination of toxic effects. Several investigations have indicated that use of proteomics can lead to successful identification of potentially toxic compounds earlier in the drug development process. This review covers recent studies that have used simultaneous measurement of multiple protein markers for prediction of tissue toxicities. In addition, conventional and newer proteomic techniques have been evaluated for applicability to drug toxicology studies. The potential of toxicoproteomics to predict adverse drug reactions in clinical use have also been explored.

 

[Back to top] Functional Proteomics Using Direct Protein Inactivation

Brenda K. Eustace and Daniel G. Jay

 

There is a great need for high-throughput methods to help assign function to the proteins in the cell. In humans, there are ~30,000 genes that may be expressed in any particular cell type resulting in >1 million distinct proteins. However, there are few functional proteomic methods to comprehensively study these proteins. One such method to address the cellular function of proteins is CALI (Chromophore-Assisted Laser Inactivation). CALI uses the specificity of antibodies (or other protein binding reagents) and the energy generated from excited dye molecules to specifically damage proteins. FALI (Fluorophore-Assisted Light Inactivation) is a modification of CALI that allows high-throughput protein disruption with a diffuse light source to inactivate samples simultaneously in multiwell plates. FALI is currently being used with large libraries of monoclonal or recombinant antibodies to identify proteins involved in tumor cell invasion, dispersal, and apoptosis. However, new innovations in light-mediated protein inactivation continue to be developed, and provide novel strategies for proteomics. GFP-CALI (Green Fluorescent Protein) and FlAsH-FALI (Fluorescein-Arsenical Helix) are two examples of such innovations. These methods use genetically encoded fusion proteins to direct light-induced damage to the protein. So far these methods have been used in hypothesis-driven experiments, but they are readily adaptable to high-throughput proteomic screens. In this review, we will describe the current applications of CALI and FALI, and speculate on the future of direct light-induced protein inactivation for functional proteomics.

 

[Back to top]  Functional and Structural Analysis of Bacillus Proteome

Supachok Sinchaikul, Boonyaras Sookkheo, Supachai Topanurak, Fu-Ming Pan, Suree Phutrakul and Shui-Tein Chen

 

This review summarizes the current status of application of functional and structural proteomic strategies for bacteria belonging to the species Bacillus and their applications in life science research. Structural proteomics plays a crucial role for studying the relationship between structures and functions of proteins. In addition, bioinformatics is very useful for rapid search of unknown proteins including their functions, and interpretation of data in both genomics and proteomics. Expression proteome analysis based on advanced and high throughput technologyis available now is important for quantifying and analyzing protein or gene expression and understanding their biological functions. Such analysis is currently possible by the application of various multidimensional techniques, such as two-dimensional (2-D) gel electrophoresis, mass spectrometry (MS), capillary electrophoresis (CE) and other related techniques. Proteome analysis has been extensively used to study the physiology as well as molecular mechanisms of responses of Bacillus under various stress condition such as heat, cold, acid, alkali, osmotic pressure and starvation to obtain important information for comprehensive study of protein and gene functions. The applications of proteomic analysis for biomarkers and drug discovery for Bacillus sp. and the future applications of proteomics for Bacillus have been discussed.

 

[Back to top] Identification and Characterization of Plant Allergens Using Proteomic Approaches

Amanda Law, Nitin Gupta, Melissa Louie, Richa Poddar, Animesh Ray and Deb N. Chakravarti

 

Rapid identification of protein allergens is important for understanding the mechanisms of pathogenesis of allergen induced diseases, and for improving diagnostic and therapeutic strategies. The most frequently used methods for characterizing protein allergens are two dimensional gel electrophoresis and immunoblot analysis. The amino acid sequences of allergens have usually been determined by Edman degradation as well as by mass spectrometry. Recent investigations have revealed a complex heterogeneity of allergen types that have varying reactivities to immunoglobulin E antibodies. This information is extremely important for the design of relevant diagnostic assays and therapeutic products. This review article attempts to evaluate the various proteomic techniques that have been used to identify and characterize protein allergens.

 

[Back to top] Functional RNAs as Tools in Proteomics

Narendra K. Vaish and Shawn Zinnen

 

Ribozymes and small interfering RNAs (siRNAs) as well as non-natural RNA molecules, such as aptamers, can be used for detection and modulation of gene function at RNA and protein levels. These technologies provide overlapping and complementary methods to antibody-based protein detection. Functional RNAs offer easy to design and simple tools for understanding the function of genes and their products and have potential as therapeutic agents. We review here the advances made with functional RNAs, and illustrate their promise as tools for both in vitro and in vivo proteomic studies.