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1.1 The potential of bioinformatics for the study of protein structure and function Proteins are macromolecules formed by amino acid polymers that regulate cellular functions. Each protein is composed by the repetition and combination of 20 different amino acids, whose order is determined by the genetic code. To perform their biological functions, proteins fold into one or more specific spatial conformations, determined by non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces and hydrophobic packing, and covalent interactions, such as disulfide bonds (Chiang et al., 2007). Determining the structure and function of a protein is a milestone of many aspects of modern biology to understand its role in cell physiology. Bioinformatics is the research, development or application of computational approaches for expanding the use of biological, medical, behavioral or health-related data. It also includes those tools to acquire, store, organize, archive, analyze or visualize infomation. Over the past years, bioinformatical tools have been widely used for the prediction and study of protein biology. Moreover, bioinformatical tools have revealed the existence of protein “interactomes”, demonstrating the interaction among distinct biomolecules (protein-protein, protein-lipids, protein-carbohydrates, etc.) to perform cellular processes (Kuchaiev & Przulj, 2011). During the last decades, genome sequencing projects together with bioinformatics programs and algorithms have enormously contributed to understand protein structure, protein interactions and protein functions. At present, over six million unique protein sequences have been deposited in public databases, and this number is increasing rapidly. Meanwhile, despite the progress of high-throughput structural genomics initiatives, just over 50,000 protein structures have been experimentally determined (Kelley & Sterberg, 2009). The greatest challenge the molecular biology community is facing today is to analyze the wealth of data that has been produced by the genome sequencing projects, where bioinformatics

Phenol contamination of soil and water has raised concerns among people living near phenol-producing factories and hazardous waste sites containing the chemical. Phenol, particularly in high concentrations, is an irritating and corrosive substance, making mucosal membranes targets of toxicity in humans. However, few data on the effects of phenol after oral exposure exist. We used an in vitro model employing human intestinal epithelial cells (SK-CO15) cultured on permeable supports to examine effects of phenol on epithelial barrier function. We hypothesized that phenol disrupts epithelial barrier by altering tight junction (TJ) protein expression. The dose-response effect of phenol on epithelial barrier function was determined using transepithelial electrical resistance (TER) and FITC-dextran permeability measurements. We studied phenol-induced changes in cell morphology and expression of several tight junction proteins by immunofluorescence and Western blot analysis. Effects on cell viability were assessed by MTT, Trypan blue, propidium iodide and TUNEL staining. Exposure to phenol resulted in decreased TER and increased paracellular flux of FITC-dextran in a dose-dependent manner. Delocalization of claudin-1 and ZO-1 from TJs to cytosol correlated with the observed increase in permeability after phenol treatment. Additionally, the decrease in TER correlated with changes in the distribution of a membrane raft marker, suggesting phenol-mediated effects on membrane fluidity. Such observations were independent of effects of phenol on cell viability as enhanced permeability occurred at doses of phenol that did not cause cell death. Overall, these findings suggest that phenol may affect transiently the lipid bilayer of the cell membrane, thus destabilizing TJ-containing microdomains.

Guanylate-binding protein-1 (GBP-1) is an interferon inducible large GTPase involved in endothelial cell proliferation and invasion. In this report, expression and function of GBP-1 were investigated in vitro in intestinal epithelia after exposure to interferon-gamma and in human colonic mucosa from individuals with inflammatory bowel disease (IBD). Interestingly, in contrast to other epithelia, GBP-1 distributed to the plasma membrane in intestinal epithelial cells where it colocalized with the tight junction protein coxsackie- and adenovirus receptor. In addition, expression of GBP-1 was upregulated in colonic epithelia of individuals with IBD. Downregulation of GBP-1 by siRNA resulted in enhanced permeability that correlated with increased apoptosis. Indeed, inhibition of caspase activity prevented the inhibition of barrier formation induced by the loss of GBP-1. These data suggest that GBP-1 is a novel marker of intestinal mucosal inflammation that may protect against epithelial apoptosis induced by inflammatory cytokines and subsequent loss of barrier function.

The tight junction (TJ) located at the limit between the apical and basolateral plasma membranes, is a multiprotein complex integrated by both integral and cortical proteins. Through TJ epithelial cells establish a link with their neighbors that seals the paracellular pathway. Lately some TJ proteins like the MAGUK ZO-1 and ZO-2, MAGI 1c, as well as the unrelated proteins symplekin and ubinuclein, have been found to concentrate at the nucleus. In this chapter we describe such proteins and how their arrival to the nucleus is connected to the degree of cell-cell contact. We analyze the signals present in these TJ proteins that may be responsible for their movement from the membrane to the nucleus and vice-versa. We then detail, the interaction of these proteins to nuclear molecules involved in gene transcription, chromatin remodeling, RNA processing and polyadenylation.

A fundamental function of epithelia and endothelia is to separate different compartments within the organism and to regulate the exchange of substances between them. The tight junction (TJ) constitutes the barrier both to the passage of ions and molecules through the paracellular pathway and to the movement of proteins and lipids between the apical and the basolateral domains of the plasma membrane. In recent years more than 40 different proteins have been discovered to be located at the TJs of epithelia, endothelia and myelinated cells. This unprecedented expansion of information has changed our view of TJs from merely a paracellular barrier to a complex structure involved in signaling cascades that control cell growth and differentiation. Both cortical and transmembrane proteins integrate TJs. Among the former are scaffolding proteins containing PDZ domains, tumor suppressors, transcription factors and proteins involved in vesicle transport. To date two components of the TJ filaments have been identified: occludin and claudin. The latter is a protein family with more than 20 members. Both occludin and claudins are integral proteins capable of interacting adhesively with complementary molecules on adjacent cells and of co-polymerizing laterally. These advancements in the knowledge of the molecular structure of TJ support previous physiological models that exhibited TJ as dynamic structures that present distinct permeability and morphological characteristics in different tissues and in response to changing natural, pathological or experimental conditions.

Most of the information on the structure and function of the tight junction (TJ) has been obtained in MDCK cells. Accordingly, we have sequenced ZO-1 in this cell type, because this protein is involved in the response of the TJ to changes in Ca 21 , phosphorylation, and the cytoskeleton. ZO-1 of MDCK cells comprises 6805 bp with a predicted open reading frame of 1769 amino acids. This sequence is 92 and 87% homologous to human and mouse ZO-1, respectively. Two nuclear sorting signals located at the PDZ1 and GK domains and 17 SH3 putative binding sites at the proline-rich domain were detected. We found two new splicing regions at the proline-rich region: b had not been reported in human and mouse counterparts, and g, which was previously sequenced in human and mouse ZO-1, is now identified as a splicing region. The expression of different b and g isoforms varies according to the tissue tested. With the information provided by the sequence, Southern blot, and PCR experiments we can predict a single genomic copy of MDCK-ZO-1 that is at least 13.16 kb long. MDCK-ZO-1 mRNA is 7.4 kb long. Its expression is regulated by calcium, while the expression of MDCK-ZO-1 protein is not. © 1999 Academic Press