Structure, primary amino acids

In studies with a sulfonyl-resistant biotype of redroot pigweed, the first weed in Israel to exhibit ALS resistance, Sibony et al. (2001) found it was cross-resistant to all other classes of ALS herbicides. From nucleotide sequencing, they concluded that a proline to leucine change in Domain A at position 248 is the only difference in the amino acid primary structure of the regions sequenced, indicating that it is responsible for all ALS inhibitor resistance observed. 

A prerequisite for the catalytic function of an enzyme is its native tertiary structure which is determined by the number and sequence of amino acids (primary structure) forming the molecule. Favoured by hydrogen bonds, parts of the polypeptide chain exist in an a-helical or a (3-sheet structure (secondary structure). Most enzymes are globular proteins, the tertiary structure of which may be fixed by disulfide bonds between cysteine residues. A famous example is lysozyme (Fig. 20), consisting of 129 amino acids. A defined three-dimensional structure is... 

In addition to the primary structure, proteins also exhibit secondary, tertiary, and quaternary structure. The overall structure of proteins is related to several factors. Primary among these factors is the electrostatic nature of amino acids. The structures displayed in Figure 16.10 do not show the charge distribution displayed by amino acids. In neutral solutions, the carboxyl group tends to donate a proton (hydrogen ion) to the amino group. The transfer of a proton means the amino end of the molecule... 

The primary structure of the ADH from L. brevis contains several structures which are typical for short-chain ADHs. The N-terminus, with a length of approximately 30 amino acids, is widely regarded as the coenzyme binding site with the conserved motif G-X-X-X-G-X-G, which is G-G-T-L-G-I-G for Lactobacillus brevis. A second conserved domain found in the L. brems-ADH sequence is a hydrophobic region comprising 10 or 11 residues, respectively. It contains two highly conserved glycines (G82 and G92), separated by nine amino acids. Such structures seem to be located inside the protein and determine the conformation of the enzyme. 

The first basic tenet of protein-structure prediction is that the amino acid sequence, the primary structure, contains all of the information required for the correct folding of the polymer chain. This is a first approximation which clearly ignores the role of environment on the induction of structure or the action of chaperone proteins which assist the in vivo folding process. The wide variety of structural motifs that have been observed for proteins is derived from only twenty different monomers (amino acids), many of which are structurally quite similar (i.e., isoleucine and leucine vary only in branching of the butyl side chain). However, there are many cases in which the substitution of amino acids with structurally similar residues (so-called conservative substitution) will lead to a protein that will not properly fold. Studies involving deletion of even small portions of the termini of the protein sequence provide similar results. On the other hand there are proteins related through evolution with as little as 20% sequence identity which adopt similar three-dimensional structures. Therefore the information encoded in the primary sequence is specific for one protein fold, however, there are numerous other sequences, only remotely related at first glance, which will produce the same fold. 

Somatrein, the flrsi recombinant preparation, introduced in 1985. contains the natural 191-amino acid primary sequence plus one ntethionyl residue on the N-lerminal end. Hie sontatnipin products all contain the 191 -amino acid sequence and are identical with the hGH produced by the piiui-luiy gland. The thiee-dimen.sional cry.stal structure shows ihjl the protein is oblate, with most of its nonpolar amino acid side chains projecting toward the interior of the molecule. This rhGH is pharmacologically identical with natural hGH. 

Figure 15.22 The structural hierarchy of proteins. A typical protein s structure can be viewed at different levels. Primary structure (shown as a long string of balls leaving and returning to the picture frame) is the sequence of amino acids. Secondary structure consists of highly ordered regions that occur as an a-helix or a p-sheet. Tertiary structure combines these ordered regions with more random sections. In many proteins, several tertiary units interact to give the quaternary structure.

In other words, the sum of functional properties depends on the physicochemical characteristics of the whole system containing the working protein. The determinant properties of the protein itself are the amino acid composition, structure (primary, secondary, tertiary, quaternary), and conformational stability the charge of the molecule and its dimensions, shape, and topography the extent of polarity and hydrophobicity, and the nature of protein-protein interactions. 

Primary structure is the order of the amino acids. Secondary structure is characterized by a repetitive organization of the peptide backbone. Tertiary structure refers to the complete three-dimensional structure of the protein. Quaternary structure describes a protein that has multiple polypeptide chains. 

Side-by-Side Images of Amino Acids Primary through Quaternary Structure of Proteins How Does DNA Work ... 

Basic Research. One major area of proteomic research is to understand how the amino acid primary sequence specifies the stability and dynamics of protein conformation. This research would provide information on how to design novel functionalities of proteins and on disorders that work by changing a protein s three-dimensional structure, such as amyloidosis and prion diseases. Studying the folding and unfolding of proteins will help scientists understand the three-dimensional structures of proteins. 

Peptides are formed by the condensation of carboxyl and amino groups in amino acids. Their primary structure is the sequence of amino acids. Secondary structure is determined by the required planarity of the amide group and interactions between side chains. a-Helices and p-pleated sheets are common motifs. Tertiary structure is the full three-dimensional structure of the peptide. 

Primary structure refers to the sequence of amino acids in the polyamide chain. 

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.

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. 

Domains are formed by different combinations of secondary structure elements and motifs. The a helices and p strands of the motifs are adjacent to each other in the three-dimensional structure and connected by loop regions. Sequentially adjacent motifs, or motifs that are formed from consecutive regions of the primary structure of a polypeptide chain, are usually close together in the three-dimensional structure (Figure 2.20). Thus to a first approximation a polypeptide chain can be considered as a sequential arrangement of these simple motifs. The number of such combinations found in proteins is limited, and some combinations seem to be structurally favored. Thus similar domain structures frequently occur in different proteins with different functions and with completely different amino acid sequences. 

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... 

Although more than 700 different amino acids are known to occur naturally, a group of 20 of them commands special attention. These 20 are the anino acids that are normally present in proteins and are listed in Table 27.1. All the amino acids from which proteins are derived are a-anino acids, and all but one of these contain a primary anino function and conform to the general structure... 

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 ... 

The primary structure of a peptide is given by its amino acid sequence plus any disulfide bonds between two cysteine residues. The primary structure is detemnined by a systematic approach in which the protein is cleaved to smaller fragments, even individual amino acids. The smaller fragments are sequenced and the main sequence deduced by finding regions of overlap among the smaller peptides. 

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 ... 

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