Amino acid partial sequence

Partial amino acid (aa) sequences of the most prevalent extract proteins were determined using an Applied Biosystems 470A Gas Phase Peptide/Protein Sequencer coupled to a 120A HPLC and DEC computer in the Protein Chemistry Core Facility (PCCF) of the University of Louisville. The aa compositions of major protein isoforms were determined using a Waters Pico-Tag System in the PCCF. 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

The most common location for an a helix in a protein structure is along the outside of the protein, with one side of the helix facing the solution and the other side facing the hydrophobic interior of the protein. Therefore, with 3.6 residues per turn, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues. Although this trend can sometimes be seen in the amino acid sequence, it is not strong enough for reliable stmctural prediction by itself, because residues that face the solution can be hydrophobic and, furthermore, a helices can be either completely buried within the protein or completely exposed. Table 2.1 shows examples of the amino acid sequences of a totally buried, a partially buried, and a completely exposed a helix. 

Implicit in the presumption of folding pathways is the existence of intermediate, partially folded conformational states. The notion of intermediate states on the pathway to a tertiary structure raises the possibility that segments of a protein might independently adopt local and well-defined secondary structures (a-helices and /3-sheets). The tendency of a peptide segment to prefer a particular secondary structure depends in turn on its amino acid composition and sequence. 

Give the amino acid sequence of hexapeptides that produce the following sets of fragments on partial acid hydrolysis ... 

On complete hydrolysis, a polypeptide gives two alanine, one leucine, one methionine, one phenylalanine, and one valine residue. Partial hydrolysis gives the following fragments Ala-Phe, Leu-Met, Val-Ala, Phe-Leu. It is known that the first amino acid in the sequence is valine and the last one is methionine. What is the complete sequence of amino acids ... 

It Is hoped that current work being carried out on the amino acid sequence of human PTH (1-4) will be successful, so that synthetic preparations of Important regions of the hormone can become commercially available. This would partially... 

From purified receptor protein, obtain partial amino-acid sequence information which will allow molecular biologists to isolate the gene (or genes) coding for the receptor. 

It was determined that the minimal peptide sequence required to stimulate pheromone biosynthesis was the C-terminal 5 amino acids, FXPRLamide, and that the carboxy terminus needs to be amidated [148,149]. This sequence was also established as the minimal sequence required for myotropic activity in cockroaches [ 150] and induction of embryonic diapause in B. mori [ 151 ]. Crossreactivity of peptides containing the FXPRLamide motif was also established for myotropic, diapause induction, and pheromone biosynthesis [152-154]. Therefore, the common C-terminal FXPRLamide defines this family of peptides. A partial listing of peptides identified to date is shown in Table 1. 

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