Primary structure amino acid sequence determining

Ans. The primary structure (amino acid sequence) of a polypeptide chain determines the conformation. Interactions among R groups on a-carbons of different amino acid residues result in one conformation being favored over other conformations. 

Sequence analysis, the determination of the primary structure (amino acid sequence) of a peptide or protein. Prior to sequence analysis the determination of the amino acid composition amino acid analysis) and the number of different... 

DETERMINATION OF PRIMARY STRUCTURE AMINO ACID SEQUENCING... 

Amino Acid Sequence Determines Primary Structure... 

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

Chemists have long appreciated that a protein s primary amino acid sequence determines its three-dimensional structure. It has also been known for some time that proteins are able to carry out their diversified functions only when they have folded up into compact three-dimensional structures. The protein-folding problem first gained prominence in the 1950s and 1960s, when Christian Anfinsen demonstrated that ribonuclease could be denatured (unfolded) and renatured reversibly. 

The major paradigm of structural biology is that the amino acid sequence determines protein structure and function. Recent advances in understanding protein dynamics calls for an extension of this picture by including that protein dynamics, essentially coupled to function, is also encoded in the primary... 

The technology used to determine protein structure has changed significantly since the 1950s. For example, the determination of insulin s structure required the efforts of many scientists over 10 years. Currently, a well-funded research team can determine the primary structure of a newly discovered protein in less than a year. Much of this time is devoted to devising efficient methods for the protein s extraction and purification. Because of automated technology, the amino acid sequence determination may require only a few days of work. 

Primary structures of several CSFs have been reported, based on partial protein sequencing and on sequence prediction from cloned cDNA murine GM-CSF [M, 23,000 N. M. Gough et al. Nature 309 (1984) 763-767] murine multi-CSF [M, 23,000-28,000 M. C. Fung et al. Nature 307 (1984) 233-237 T. Yokata et al. Proc. Nall Acad. Scl USA 81 (1984) 1070-1074] human GM-CSF [M, 22,000 G.G. Wong el al. Science 228 (1985) 810-815] human M-CSF M, 45,000 of the homodimer also called CSF-1 E.S. Kawasaki Science 230 (1985) 291-296]. The CSF amino acid sequences determined so far show no homologies, and they display considerable differences in predicted secondary and tertiary structures, which is surprising in view of their extensive functional overlap and the similar response of progenitor cells to different CSFs. 

The chemical reactions discussed above are not by themselves sufficient to develop a mechanistic scheme for underwater glue formation unless they are reviewed in the context of the three-dimensional structure of the mussel adhesive protein. The structure of this protein however is not available. We therefore decided to derive its three-dimensional structure from the consensus decapeptide sequence in an incremental fashion using computer modeling and chemical intuition. It is well-known that the primary amino acid sequence determines the structure of a protein. However, predicting three-dimensional structures from an amino acid sequence is a risky venture unless there are experimental guide posts that support or reject the predicted structures. 

The conformation of a protein molecule is thought to be dictated first by the genetic code that determines the primary stnicture (amino acid sequence) and then by parameters that produce the transition from a linear polypeptide to a three-dimensional folded structure. Proteins in their folded state usually are sufficiently stable against small changes of external conditions. But if the deviation exceeds some critical values the protein denatures within a relatively narrow range of temperature, pressure, pH, denaturant concentration, etc. [146-148]. Denaturation produces changes in many properties of the protein molecule that are sensitive to its three-dimensional structure, suggesting that this process... 

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Different techniques give different and complementary information about protein structure. The primary structure is obtained by biochemical methods, either by direct determination of the amino acid sequence from the protein or indirectly, but more rapidly, from the nucleotide sequence of the... 

There are several levels of peptide structure. The primary structure is the amino acid sequence plus any disulfide links. With the 20 anino acids of Table 27.1 as building blocks, 20 dipeptides, 20 tripeptides, 20" tetrapeptides, and so on, are possible. Given a peptide of unknown structure, how do we determine its anino acid sequence ... 

Somatostatin is a tetradecapeptide of the hypothalamus that inhibits the release of pituitary growth hormone. Its amino acid sequence has been determined by a combination of Edman degradations and enzymic hydrolysis experiments. On the basis of the following data, deduce the primary structure of somatostatin ... 

The Primary Structure of a Protein Determining the Amino Acid Sequence... 

Proteins start out life as a bunch of amino acids linked together in a head-to-tail fashion—the primary sequence. The one-dimensional information contained in the primary amino acid sequence of cellular proteins is enough to guide a protein into its three-dimensional structure, to determine its specificity for interaction with other molecules, to determine its ability to function as an enzyme, and to set its stability and lifetime. 

Currently, there exists an enormous and growing deficit between the number of polypeptides whose amino acid sequence has been determined and the numbers of polypeptides whose three-dimensional structure has been resolved. Given the complexities of resolving three-dimensional structure experimentally, it is not surprising that scientists are continually attempting to develop methods by which they could predict higher order structure from amino acid sequence data. Although modestly successful secondary structure predictive approaches have been developed, no method by which tertiary structure may be predicted from primary data has thus far been developed. 

---