Rhodopsin Project

Membrane proteins are coded for by approximately 30% of the human genome.However, the study of them is diffi cult due to their hydrophobic nature.What are the latest techniques to tackle this? ou may be surprised to learn that membrane proteins are coded for by approximately 30% of the human genome [1].That's nearly a third of all genetic information in our cells dedicated to the production of membrane proteins.Although elusive, these proteins are critical for cellular function, especially in cell communication and transport pathways.The cause of their elusiveness can be attributed to their hydrophobic nature, leading to diffi culty in structural studies because they can't be dissolved in water and are prevented from crystallizing -a necessary step in techniques such as x-ray c rystallography.Once extracted from cell membranes, the proteins are made water-soluble only when suspended in detergents that mimic the hydrophobicity of a cell membrane.However, these are expensive and there is no 'one size fi ts all'.Detergents can also disrupt the structure and function of membrane proteins, as they inte r fe re with inter-and intramolecular proteinprotein interactions.Of ~8000 known membrane proteins found in human cells, only ~50 have a determined structure [2].With membrane proteins being implicated in many different diseases [3], including heart disease, Alzheimer's and cystic fi brosis, it is of crucial importance that structures are characterized in order for novel ideas for therapies and treatments to come to light.So, just what new approaches and techniques are being developed to tackle this issue?

2 - Physiological Structure and Function of Proteins

Salmonella typhimurium strain SL1344(S.typhi) is a non typhoidal bacteria which may cause infection in human gastrointestinal tract, may cause abdominal pain, fever, diarrhea, and inflammation some times which may lead to the human death. A comparative study of hypothetical outer membrane proteins of Salmonella typhimurium strain SL1344 (S.typhi) was performed using bioinformatic tools. Bioinformatics is a source to analyse whole genomic sequence of a vast number of uncharacterized genes. Online databases like UniProt, String, Pfam and other tools were used. Thirteen uncharacterized and hypothetical protein present in outer membrane of the bacteria S.typhi were retrieved from UniProt and its structure and function were studied. In this study the cellular function, pathway of enzyme interaction, antibiotic resistance were analyzed. The structure of the protein as well the function of these proteins provides better understanding to perform molecular docking and identification of small molecule inhibitors.

Ultraviolet C (UV-C) radiation induces apoptosis in mammalian cells via the mitochondrion-mediated pathway. The Bcl-2 family of proteins are the regulators of the mitochondrial pathway of apoptosis and appears responsive to UV-C radiation. It is unknown how the structure and, effectively, the function of these proteins are directly impacted by UV-C exposure. Here, we present the effect of UV-C irradiation on the structure and function of pro-apoptotic Bid-FL and anti-apoptotic Bcl-xlΔC proteins. Using a variety of biophysical tools, we show that, following UV-C irradiation, the structures of Bcl-xlΔC and Bid-FL are irreversibly altered. Bcl-xLΔC is found to be more sensitive to UV stress than Bid-FL Interestingly, UV-C exposure shows dramatic chemical shift perturbations in consequence of dramatic structural perturbations (α-helix to β-sheet) in the BH3- binding region, a crucial segment of Bcl-xlΔC. Furter it has been shown that UV-exposed Bcl-xlΔC has reduced efficacy of its interactions with pro-apoptotic tBid.

Chapter 1 The structure and function of blue copper proteins

Protein adsorption at oil-water interfaces interfacial structure and function of proteins in emulsions

Thallapuranam K Suresh Kumar, Ryan Thurman and Srinivas Jayanthi-In-Cell NMR Spectroscopy–<em>In vivo</em> Monitoring of the Structure, Dynamics, Folding, and Interactions of Proteins at Atomic Resolution

The Physiological Structure and Function of Proteins

2 - The Physiological Structure and Function of Proteins

To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.

This review describes and discusses new data about the structure and function of proteins which contain ankyrin-like repeats in their structure. These proteins have been found in cells of different organisms but they are not belonging to the cytoskeletal proteins. Many important functions of such proteins are provided by ankyrin repeats which maintain protein-protein interactions involved in the formation of transcription complexes, initiation of immuno-responses, biogenesis and assembly of cation channels in the membranes, regulation of some cell cycle stages, symbiotic interactions and many other processes. Mutations in genes encoding ankyrin-like proteins can cause defects in gene expression leading to diseases onset and progression in animals and humans. Therefore, the structure, dynamics and function of these proteins is an area of extensive research in modern biology.

Structural and nonstructural proteins of Senecavirus A: Recent research advances, and lessons learned from those of other picornaviruses

Late cornified envelope proteins are predominantly expressed in the skin and other cornified epithelia. On the basis of sequence similarity, this 18-member homologous gene family has been subdivided into six groups. The LCE3 proteins have been the focus of dermatological research because the combined deletion of LCE3B and LCE3C genes (LCE3B/C-del) is a risk factor for psoriasis. We previously reported that LCE3B/C-del increases the expression of the LCE3A gene and that LCE3 proteins exert antibacterial activity. In this study, we analyzed the antimicrobial properties of other family members and the role of LCE3B/C-del in the modulation of microbiota composition of the skin and oral cavity. Differences in killing efficiency and specificity between the late cornified envelope proteins and their target microbes were found, and the amino acid content rather than the order of the well-conserved central domain of the LCE3A protein was found responsible for its antibacterial activity. Invivo, LCE3B/C-del correlated with a higher beta-diversity in the skin and oral microbiota. From these results, we conclude that all late cornified envelope proteins possess antimicrobial activity. Tissue-specific and genotype-dependent antimicrobial protein profiles impact skin and oral microbiota composition, which could direct toward LCE3B/C-del‒associated dysbiosis and a possible role for microbiota in the pathophysiology of psoriasis.

The elucidation of structure and function of proteins and membrane proteins by EPR spectroscopy has become increasingly important in recent years as technological advances have been made in the design of spectrometers and in the chemistry of the nitroxide group. These new developments have increased the demand for tailor-made amino acids carrying a spin label on the one hand and for reliable methods for their incorporation into proteins on the other. Here we describe methods for site-specific spin labelling of proteins. It is shown that a combination of recombinant synthesis of proteins with chemically produced peptides (expressed protein ligation) allows the preparation of site-specifically spin-labelled proteins.

The exquisite specificity of antibody molecules combined with the ease with which they can be labelled makes them valuable in the study of the structure and function of proteins. Historically, the generation of an antibody against a defined protein required the purification to homogeneity of high concentrations of the antigen followed by animal immunization and the production of polyclonal antibodies. The specificity of these antibodies was determined by the major antigenic regions of the immunogen. In general, channel proteins are not easily isolated in the amounts required for polyclonal antibody production. However, the advent of monoclonal antibody technology has circumvented the need for a pure antigen. There was a requirement instead for a rapid, selective screening method for the production of antibodies against those proteins expressed at low abundance. The specificity of these antibodies was again dictated, for the most part, by the antigenic regions of the protein of interest. Today, the availability of cDNAs encoding channel polypeptides means that the natural proteins themselves are no longer required for antibody production, since recombinant or synthetic antigens can be employed instead. In many cases, the specificities of the antibodies thus produced are predetermined, which means that they are even more powerful research tools.