Protein! s sequences

Swiss-Prot and TrEMBL are the initial databases one would use to find information regarding the protein s sequence. Depending on the level of refinement and information provided for each sequence, data are deposited into either Swiss-Prot or TrEMBL. Because of the large number of sequences that are now determined from genomics alone, all sequences are first deposited into TrEMBL. Once the correct nomenclature, links to relevant databases, and significant comments are added, and after unnecessary information has been removed, the sequence is added to the Swiss-Prot database. The initial search for a sequence is typically performed on the information contained in these two databases. 

These and odier solutions to die problem of eorreedy folding peptides illustrate not only that the location by epitope mapping of antigenic epitopes within a protein s sequence is a prerequisite for the design of synthetic peptide-based vaccines but also that some knowledge of the three dimensional structure of the antigen may be required. In many cases, unless individual epitopes are identified and appropriate structural features incorporated into them, antibody of the correct specificity will not be induced. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Sickle-cell anemia is the classic example of an inherited disease that is caused by a change in a protein s amino acid sequence. Linus Pauling proposed in 1949 that it was caused by a defect in the hemoglobin molecule he thus coined the term molecular disease. Seven years later Vernon Ingram showed that the disease was caused by a single mutation, a change in residue 6 of the P chain of hemoglobin from Glu to Val. 

Figure S.S Amino acid sequence of p strands 2 3 4 in human plasma retinol-binding protein. The sequences are listed in such a way that residues which point into the barrel are aligned. These hydrophobic residues are arrowed and colored green. The remaining residues are exposed to the solvent.

Bacteriophage repressor proteins provide excellent examples of sequence-specific interactions between the side chains of a protein and bases lining the floor of the major groove of B-DNA. As we shall see, to fit the protein s recognition module into this groove it has to be made even wider in other words, the B-DNA has to be distorted. 

Frequency of occurrence of each amino acid re.sidue in the polypeptide chain.s of 207 unrelated protein.s of known. sequence. 

Role of the Amino Acid Sequence in Protein Structure Secondary Structure in Protein.s Protein Folding and Tertiary Structure Subunit Interaction.s and Quaternary Structure... 

The long, repetitive sequence of —N—CH-CO- atoms that make up a continuous chain is called the protein s backbone. By convention, peptides are written with the N-terminal amino acid (the one with the free -NH3 1 group) on the left and the C-terminal amino acid (the one with the free -C02 group) on the right. The name of the peptide is indicated by using the abbreviations listed in Table 26.1 for each amino add. Thus, alanylserine is abbreviated Ala-Ser or A-S, and serylalanine is abbreviated Ser-Ala or S-A. Needless to say, the one-letter abbreviations are more convenient than the older three-letter abbreviations. 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Goedert, M., Spillantini, M.G., Jakes, R., Rutherford, D., Crowther, R.A. (1989). Multiple isoforms of human microtubule-associated protein tau Sequences and localization in neurofibrillary tangles of Alzheimer s disease. Neuron 3, 519-526. 

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