Peptides sequences

The CA Registry of CAS also comprises 1.6 million protein and peptide sequences and over 21.6 milhon nudeic acid sequences from literature sources and from GenBank. 

Modem methods of peptide sequencing follow a strategy similar to that used to sequence insulin but are automated and can be carried out on a small scale A key feature is repetitive N terminal identification using the Edman degradation... 

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

Mass spectral fragmentation patterns of alkyl and phenyl hydantoins have been investigated by means of labeling techniques (28—30), and similar studies have also been carried out for thiohydantoins (31,32). In all cases, breakdown of the hydantoin ring occurs by a-ftssion at C-4 with concomitant loss of carbon monoxide and an isocyanate molecule. In the case of aryl derivatives, the ease of formation of Ar—NCO is related to the electronic properties of the aryl ring substituents (33). Mass spectrometry has been used for identification of the phenylthiohydantoin derivatives formed from amino acids during peptide sequence determination by the Edman method (34). 

The dimethoxybenzyl group was used for backbone protection of the pseudopeptides of the form Xaai/r(CH2N)Gly (Xaa = amino acid). It is introduced by reductive alkylation with the aldehyde and NaCNBH3. Acidolysis with TFMSA in TFA/thioanisole is used to remove it from the amine, but the efficiency is dependent upon the peptide sequence. ... 

Petir Victor Edman (1916-1977) was born in Stockholm, Sweden, and received an M.D. in 1946 at the Karolinska Institute. After a year in the United States at the Rockefeller Institute, he returned to Sweden as professor at the University of Lund. In 1957, he moved to St. Vincent s School of Medical Research in Melbourne, Australia, where he developed and automated the method of peptide sequencing that bears his name. A reclusive man, he never received the prizes or recognition merited by the importance or his work. 

With the identities and amounts of amino acids known, the peptide is sequenced to find out in what order the amino acids are linked together. Much peptide sequencing is now done by mass spectrometry, using either electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) linked to a time-of-flight (TOF) mass analyzer, as described in Section 12.4. Also in common use is a chemical method of peptide sequencing called the Edman degradation. 

The general idea of peptide sequencing by Edman degradation is to cleave one amino acid at a time from an end of the peptide chain. That terminal amino acid is then separated and identified, and the cleavage reactions are repeated on the chain-shortened peptide until the entire peptide sequence is known. Automated protein sequencers are available that allow as many as 50 repetitive sequencing cycles to be carried out before a buildup of unwanted by products interferes with the results. So efficient are these instruments that sequence information can be obtained from as little as 1 to 5 picomoles of sample—less than 0.1 /xg. 

Melanocortins. Figure 1 Shows the melanocortin receptors, function and naturally occurring peptide sequences that activate them. 

The Src-homology 2 (SH2) domain is a protein domain of roughly 100 amino acids found in many signaling molecules. It binds to phosphorylated tyrosines, in particular peptide sequences on activated receptor tyrosine kinases or docking proteins. By recognizing specific phosphorylated tyrosines, these small domains serve as modules that enable the proteins that contain them to bind to activated receptor tyrosine kinases or other intracellular signaling proteins that have been transiently phosphorylated on tyrosines. 

Tachykinins and their Receptors. Table 2 Peptide sequences of mammalian tachykinins... 

A modified 1,4 diketone 17 was employed for the microwave-assisted preparation of amino acids containing the pyrrole ring (Scheme 6). The products were further employed for the introduction of this original moiety into a peptide sequence [33]. 

Crystallographic studies imply that although little sequence homology exists between the different protease cleavage sites, what is conserved is the shape that they adopt within the active site of the enzyme (Prabu-Jeyabalan et al. 2002). This shape has been termed the substrate envelope and represents the consensus volume overlapping the majority of the substrates. Most likely, HIV-1 protease recognizes a particular peptide sequence as being a substrate by a combination of accessibility and the shape the sequence can adopt. 

Gallaher WR (1987) Detection of a fusion peptide sequence in the transmembrane protein of human immunodeficiency virus. Cell 50 327-328... 

There are 17 human type I IFN genes, all clustering on chromosome 9. They are intronless and encode secretory signal peptide sequences that are proteolytically cleaved prior to secretion from the cell. Type I IFNs are genetically and structurally closely related. They range in length from 161 to 208 amino acids and have apparent molecular weights of 15-24 kDa (Table 1) (Chen et al. 2004). The different subtypes of human IFN-a have approximately 50% amino acid sequence identity, whereas IFN-a shares approximately 22% amino acid identity with human IFN-p and 37% with human IFN-m (Chen et al. 2004). 

Translate Bioactive Peptide Sequences into Bioactive Peptoid Sequences... 

Since our backbone 2 aPNA incorporates six Lys residues in its peptide sequence and is cationic at a physiological pH, we were optimistic that this aPNA would be taken up into cells without the need for any external carrier system. To answer the simple question of whether b2 aPNAs are intemahzed, a standard fluorescence microscopy experiment was performed to see if whole cells that were incubated with a fluorescent-labeled aPNA would internahze labeled material [70]. Chinese Hamster Ovary (CHO) cells in culture were incubated with BODIPY-la-beled TCCCT(b2) at 37 °C for various periods of time. Following incubation, the cells were rinsed in phosphate-buffered sahne (PBS), fixed with 4% formaldehyde at ambient temperature for 20 min, then washed with PBS and stored in a refrigerator until examined by fluorescence microscopy. 

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