Proteins integral amino acid sequence

Membranes containing the visual pigment rhodopsin, a G-protein-linked receptor, were chosen as a model system for this work. Rhodopsin was one of the first integral membrane proteins whose amino acid sequence was determined (16-18). More than 40 receptors have been reported to have structural and functional homologies with rhodopsin (19). This chapter describes the use of electrochemical impedance spectroscopy to evaluate lipid bilayer membranes containing rhodopsin formed on electrode surfaces. 

Cytochrome c is a small protein (Mr = 13,000). It is associated with the inner membrane of the mitochondria, but is readily extracted in soluble form. Because it is small and relatively abundant, detailed structural studies have been carried out with this protein. The amino acid sequence of the protein has been highly conserved in evolution, with nearly 50% identity between residues at corresponding positions of cytochromes c in organisms as diverse as yeast and human. The other cytochromes are integral membrane proteins and are exceedingly difficult to dissociate from the membrane. As a result, less is known about their structure. 

Odorants are thought to bind to integral membrane receptors on the cilia of the olfactory sensory neurons. The receptors are thought to he specific different olfactory neuron types recognize different odorants that share certain characteristics (Buck, 1993). The odorant receptors transduce signals via interactions with G-proteins (so-called because guanosine trisphosphate is involved in their activation). These G-protein-coupled exhibit seven hydrophobic domains (Fig. 5.6). Variation in the amino acid sequence of the transmembrane domain may account for specificity and selectivity of odor reception. 

Protein fragmentation, on the other hand, may be needed for functional activity of some proteins, such as chymotrypsin and insulin, which assume active forms after removal of amino-acid sequences in chy-motrypsinogen and proinsuhn. Additional complexity in analytical methodologies to deduce protein function in situ could also arise from a single protein exhibiting more than one function. Conversely, a given function may require integration of multiple proteins, or that many other proteins can perform the same function. 

On the basis of their amino acid sequences and hydropathy plots, many of the transport proteins described in this chapter are believed to have multiple membrane-spanning helical regions—that is, they are type III or type IV integral proteins (Fig. 11-8). When predictions are consistent with chemical studies of protein localization (such as those described above for glycophorin and bacteriorhodopsin), the assumption that hydrophobic regions correspond to membrane-spanning domains is much better justified. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

Much more is known about the interaction of cells with laminin. A high-affinity (Ad = 1 x 10 9 to 4 x 10-9) receptor for laminin has been found on many cells including myoblasts, tumor cells, and macrophages (Lesot et al., 1983 Rao et al., 1983 Malinoff and Wicha, 1983). The laminin receptor (Mr 67K) is solubilized by detergent and has all the characteristics of an integral membrane protein. A partial amino acid sequence of the receptor has been deduced from the nucleotide sequence of cDNA clones. These show a possible transmembrane sequence and suggest that this receptor has substantial cytoplasmic and extracellular domains (Wewer et al., 1986). 

Despite the size of the protein subunits, their integrity does not depend on cross-linking via disulfide bonds (63) and no disulfide bridges have been identified within the partially completed amino acid sequence (41, 6Sa). Nor is there any evidence that association of subunits depends on covalent bonding rather, it appears to involve mainly hydrophobic interactions (50). Of particular interest in this context is the observation that some forms of acatalasemia are attributable to the formation of a catalase variant, of approximately normal specific activity, but with a tendency to dissociate into subunits (64). 

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