Amino acid sequences dictating

The primary structure of protein (i.e. amino acid sequence) dictates high-level protein structures (secondary, tertiary and quaternary structures) and determines their chemical... 

The cell must possess the machinery necessary to translate information accurately and efficiently from the nucleotide sequence of an mRNA into the sequence of amino acids of the corresponding specific protein. Clarification of our understanding of this process, which is termed translation, awaited deciphering of the genetic code. It was realized early that mRNA molecules themselves have no affinity for amino acids and, therefore, that the translation of the information in the mRNA nucleotide sequence into the amino acid sequence of a protein requires an intermediate adapter molecule. This adapter molecule must recognize a specific nucleotide sequence on the one hand as well as a specific amino acid on the other. With such an adapter molecule, the cell can direct a specific amino acid into the proper sequential position of a protein during its synthesis as dictated by the nucleotide sequence of the specific mRNA. In fact, the functional groups of the amino acids do not themselves actually come into contact with the mRNA template. 

A small number of proteins, and again insulin is an example, are synthesized as pro-proteins with an additional amino acid sequence which dictates the final three-dimensional structure. In the case of proinsulin, proteolytic attack cleaves out a stretch of 35 amino acids in the middle of the molecule to generate insulin. The peptide that is removed is known as the C chain. The other chains, A and B, remain crosslinked and thus locked in a stable tertiary stiucture by the disulphide bridges formed when the molecule originally folded as proinsulin. Bacteria have no mechanism for specifically cutting out the folding sequences from pro-hormones and the way of solving this problem is described in a later section. 

The major structural factors that influence the reactivity of aspartic acid residues are i) conformational aspects of the peptide, particularly the local flexibility of the peptide chain as dictated by primary, secondary, and tertiary structure, and ii) the amino acid sequence (i.e., the nature of the adjacent residues). Most of the available evidence concerns the influence of adjacent residues, as discussed in this section. 

There is one separate tRNA for each amino acid and one separate specific synthetase. The enzyme must bind not only the correct amino acid but also the correct tRNA, so that each synthetase has specific recognition sites for both. Transfer RNAs contain a three-base sequence that is an anticodon, which binds to its complementary codon on messenger RNA. The importance of the synthetase in relation to fidelity of translating the information in messenger RNA is indicated by the fact that, once an amino acid is bound to tRNA, its identity as an amino acid is dictated by the anticodon site on the transfer RNA and not by the amino acid itself. (The enzyme can be considered as a dictionary, since it provides a cross-reference between the nucleic acid and amino acid languages.)... 

When the number of amino acids in a polypeptide chain reaches more than fifty, a protein exists. The structure of both polypeptides and proteins dictate how these biomolecules function. There are several levels of structure associated with polypeptides and proteins. The sequence of the amino acids forming the backbone of the protein is referred to as the primary structure. A different order or even a minor change in an amino acid sequence creates an entirely different molecule. Just reversing the order of amino acids in a dipeptide changes how the dipeptide functions. An example of this is sickle-cell anemia. Sickle-cell anemia is a genetic disorder that occurs when the amino acid valine replaces... 

Specific domains of proteins (for example, those mentioned in the section Organic Phase ) adsorbed to biomaterial surfaces interact with select cell membrane receptors (Fig. 8) accessibility of adhesive domains (such as specific amino acid sequences) of select adsorbed proteins may either enhance or inhibit subsequent cell (such as osteoblast) attachment (Schakenraad, 1996). Several studies have provided evidence that properties (such as chemistry, charge, and topography) of biomaterial surfaces dictate select interactions (such as type, concentration, and conformation or bioactivity) of plasma proteins (Sinha and Tuan, 1996 Horbett, 1993 Horbett, 1996 Brunette, 1988 Davies, 1988 Luck et al., 1998 Curtis and Wilkinson, 1997). Albumin has been the protein of choice in protein-adsorption investigations because of availability, low cost (compared to other proteins contained in serum), and, most importantly, well-documented conformation or bioactive structure (Horbett, 1993) recently, however, a number of research groups have started to examine protein (such as fibronectin and vitronectin) interactions with material surfaces that are more pertinent to subsequent cell adhesion (Luck et al., 1998 Degasne et al., 1999 Dalton et al., 1995 Lopes et al., 1999). 

Protein Structure is Dictated by Amino Acid Sequence... 

The crystal structure of subtilisin BPN dispelled this uncertainty. As already mentioned, the subtilisins and the pancreatic enzymes are dissimilar in amino acid sequence, and they proved to be dissimilar in their gross three-dimensional structure. However, the components of their catalytic site do not differ. Both enzyme groups have the same catalytic triad with hydrogen bonds linking serine to N-3 of histidine and N-1 of histidine to a buried side chain of aspartic acid (29). Since the two enzyme groups are products of different evolutionary pathways, it follows almost inescapably that this striking homology is dictated by necessity and that the buried aspartic acid is essential for catalysis. 

Figure 1.6. Folding of a Protein. The three-dimensional structure of a protein, a linear polymer of amino acids, is dictated hy its amino acid sequence.

Polypeptides would have played only a limited role early in the evolution of life because their structures are not suited to self-replication in the way that nucleic acid structures are. However, polypeptides could have been included in evolutionary processes indirectly. For example, if the properties of a particular polypeptide favored the survival and replication of a class of RNA molecules, then these RNA molecules could have evolved ribozyme activities that promoted the synthesis of that polypeptide. This method of producing polypeptides with specific amino acid sequences has several limitations. First, it seems likely that only relatively short specific polypeptides could have been produced in this manner. Second, it would have been difficult to accurately link the particular amino acids in the polypeptide in a reproducible manner. Finally, a different ribozyme would have been required for each polypeptide. A critical point in evolution was reached when an apparatus for polypeptide synthesis developed that allowed the sequence of bases in an RNA molecule to directly dictate the sequence of amino acids in a polypeptide. A code evolved that established a relation between a specific sequence of three bases in RNA and an amino acid. We now call this set of three-base combinations, each encoding an amino acid, the genetic code. A decoding, or translation, system exists today as the ribosome and associated factors that are responsible for essentially all polypeptide synthesis from RNA templates in modem organisms. The essence of this mode of polypeptide synthesis is illustrated in Figure 2.8. 

DNA carries the genetic code that dictates the amino acid sequence during the synthesis of proteins, which in turn dictates the form of life and the details of structure and action. RNA was until recently thought to be primarily a messenger, carrying information... 

Mass spectrometry has been applied to the structure elucidation of peptides and proteins for some time. Depending on the problem, it is used as both a primary and a complementary technique and although many difficulties still remain it is now an established means of determining amino acid sequences. As instrumental methods and new derivatives have developed, the different approaches employed, with particular combinations of chemical pretreatment and sample introduction to the MS, have been dictated by the size and type of the peptide and the information required. 

Proteins are synthesized on ribosomes as nascent polypeptides in the lumen of the endoplasmic reticulum (ER). The amino acid sequence of proteins that determines the secondary and tertiary structures is dictated by the nucleotide sequence of mRNA. In turn, mRNA sequences are determined by DNA sequences (Chapters 23-25). As discussed earlier, the classic experiments of Pauling and Anfinsen led to the concepts that certain key amino acids at the proper positions are essential for the folding of proteins into a three-dimensional, functional, unique conformation. It is amazing that, of hundreds of millions of conformational possibilities, only a single conformational form is... 

The amino acid sequence of a protein dictates its folding into a specific three-dimensional conformation, the native state. 

---