Protein Purification and Analysis I: Methods and Applications

Chapter 1 is a review of the bioinformatics literature on protein-protein interactions (PPIs). A protein-protein interaction network (PPIN) is a collection of PPIs, often deposited in online databases. PPINs may complement other datasets, such as protein structural information.

Chapter 2 describes the usability and advantages of the micro-patterning technique to study protein-protein interactions in a live cell context. It summarizes results achieved so far, discusses latest technical developments and describes potential future applications.

Chapter 3 describes a strategy for identification of protein peptides cross-linked to radiolabeled RNA derivatives in specific complexes of proteins or ribonucleoproteins with these derivatives. This strategy is alternative to the identification based on mass-spectrometry and can be used for determination of protein sites involved in interactions with specific RNAs when mass-spectrometry is not applicable.

Chapter 4 describes biochemical methods for assessing interaction between distinct ligand-gated channels. This chapter proposes also methods to examine functional impact of these receptor-receptor interactions in the nervous system.

Chapter 5 proposes a statistical approach based on Structural Equation Modeling, in combination with step-wise factor analysis, to infer protein-DNA interactions for gene transcriptional control in the absence of protein information. Such approach only uses gene expression profiles.

Chapter 6 describes procedures for the biochemical analysis of amyloid proteins in transgenic Drosophila, specifically the prion protein. The authors show that protocols from the mammalian literature can be easily adapted and scaled to these small flies and by ensuring robust expression of the prion protein and proper handling of these delicate samples.

Chapter 7 discusses DEAD-box proteins. DEAD-box protein family members participate in many aspects of RNA metabolism, particularly in the ATP-driven disruption of secondary structures of RNA. Genes coding for these types of proteins are recognised in all free living bacteria.

Chapter 8 provides an experimental model of restriction-modification enzyme fusion and proposes a molecular mechanism for appearance of type IIC restriction-modification and M. SsoII-related enzymes, as well as other multifunctional proteins.

Chapter 9 describes the role of branched chain amino acids, leucine, isoleucine and valine, in exercise with respect to performance, muscle kinetics, fatigue and immunity. It also discusses the existing evidence on any superior benefits of branched chain amino acid supplements to exercising individuals and athletes.

Chapter 10 provides an overview of the protein-peptide based research in dermatology and the recent emergence of many new dermatologic therapeutic modalities.

Chapter 11 summarizes the adverse health effects of prenatal or early postnatal exposure to environmental pollutants (lead, arsenic and dioxins are the best known), pharmaceuticals, some food additives, and other chemicals through the mechanism of cell deprogramming or imprinting.

Chapter 12 put forward 2D-PAGE as an important tool, especially for clinical laboratories involved in the determination of protein expression levels and disease biomarker discovery.

Chapter 13 shows how to investigate and characterize an open reading frame, from exploiting the similarity in amino acid sequence, until the cloning, expression, purification and activity of the protein and its biological partners.

Chapter 14 focuses on the cloning, heterologous expression and physicochemical characterization of Als5, one of the GPI-anchored adhesins from Candida albicans.