Structure, primary amino terminus

Figure 1. The organization of catalytic and non-catalytic domains in cellulases from C. fimi and other bacteria. CfCenA, B and C, and CfCex are the endo- and exo-p- 1, 4-glucanases of C. fimi, ClfX is a translated open reading frame from Cellulomonas flavigena (29), CtEGD and PfEndA are endo-p-1, 4-glucanases from Clostridium thermocellum and Pseudomonas fluorescens, respectively (30,31), The primary structures are drawn approximately to scale and are numbered from the amino terminus of the mature protein ClfX is numbered from the start of the open reading frame. Unshaded areas represent catalytic domains, cross-hatched areas indicate cellulose-binding domains, repeated blocks of amino acids are stippled, and black areas represent linker regions.

The primary structure (i.e., the amino acid sequence) of a protein can be determined by stepwise chemical degradation of the purified protein. By far the most powerful and commonly used technique for doing this is the automated Edman degradation. The amino terminal amino acid residue of the polypeptide is reacted with Edman s reagent (phenylisothiocyanate) to form the phenylthiocar-bamyl derivative, which is removed without hydrolysis of the other peptide bonds by cyclization in anhydrous acid. The amino acid derivative is converted to the more stable phenylthiohydantoin and identified by HPLC. The process can be repeated many times, removing the amino acids from the amino terminus of the polypeptide one residue at a time and identifying them until the entire sequence... 

In addition to the use of NOESY spectra for the assignment of individual resonances, they can also be used for the determination of the three-dimensional structure of the protein in solution. Up to now we have only dealt with the connectivities along the backbone between protons that are close to each other because of chemical bonding. There are also correlations between amino acids that are far apart in the primary structure but are in close proximity because of the folding found in the tertiary structure. For example, a portion of the chain near the amino terminus can be near the carboxy termi-... 

Fig. 12. Primary and tertiary structures of the Newcastle disease virus F protein. Cleavage of the precursor F protein yields the F2 (amino-terminal) and FI (carboxy-terminal) fragments. In the top schematic, F2 is white, the fusion-peptide and transmembrane segments of FI are black, and the remainder of FI is cross-hatched. In the X-ray crystallographic structure of NDV-F (Chen et at, 2001a), electron density for the fusion peptides was not visible, but the fusion peptide is at the amino terminus of FI and would therefore be expected to extend from the bottom of the...

The complete primary structure of the SRP receptor has been determined (Lauffer et al., 1985). It appears that the protein has an uncleaved signal sequence near its amino terminus. Its membrane-bound region is... 

Stable structures such as the naturally occurring ferric porphyrin complexes or porphyrins substituted with copper, cobalt, silver or vanadyl probe the active site of heme-containing enzyme [227]. Complexes of copper not associated with heme are also common. They are frequently formed at an amino terminus because the amino group provides a good primary amine donor atom. Two or three amino acid residues beginning at the N-terminus are often flexible until a more rigid portion of the polypeptide, such as the a helix, is encountered. A peptide nitrogen is available to... 

The linear peptide as observed in its primary structure starts folding on itself because of the interactions among the side chains of the adjacent amino acids. This leads to the formation of different structures, which include (a) helical structure called an alpha helix, (b) stranded folds called beta sheets or beta strands, and (c) random coils. Now, certain criteria can be used to predict the occurrence of these structures in the secondary structure of the protein. This was first established by Chow and Fasman (1978) based on the propensity of certain amino acids associated with these structures, i.e., helix and beta sheet. For example, the amino acids glu, met, ala, and lys are predominantly associated with the helix structure whereas the amino acids val, ile, and tyr are strongly associated with the beta sheet structure. The amino acid leucine is associated with both the helix and the beta sheet. The amino acids glycine and proline occur as breakers of the helix proline usually occurs as the first residue in the helix. Also, asp and glu occurs at the N-terminus, whereas arg and lys occur at the C-terminus. 

The overall domain organization of smooth muscle myosin is similar to that of skeletal muscle myosin when viewed by rotary shadowing in high salt in the electron microscope (Trybus etal, 1982). There are two slightly elongated heads connected to a long tail. Analysis of the primary sequence of the smooth and skeletal muscle and nonmuscle HCs confirms this gross structural similarity (Fig. 3). Each of the molecules has conserved motor domains at the amino terminus fol-... 

A protein or a polypeptide is composed of amino acids linked together by peptide bonds, with amino acids as the monomeric units of the polypeptide. The order of amino acids in a protein is known as the primary structure of that protein. The specific sequence of amino acids in the protein determines its three-dimensional structure and ultimately its function. The amino acids are numbered sequentially, beginning at the amino terminus of the polypeptide. For example, the 45th amino acid in the sequence would be identified as residue 45. Most often, scientists refer to an individual residue using both the name of the amino acid and its position. Therefore, if residue 45 in a particular polypeptide sequence is serine, that residue would be referred to as serine-45, see also Peptide Bond Primary Structure Proteins. 

Primary structure of mouse epidermal growth factor, and schematic representation of its large protein precursor (pre-pro-EFC). The signal sequence is uncertain, but the amino terminus of pro-EGF is probably residue 23 (lie), 26 (Val) or 29 (Trp). The Indicated sequences of basic residues represent potential sites of proteolytic cleavage. 

Lichenysin are cyclic lipopeptides produced by Bacillus licheniformis. The structure of lichenysin varies with the species, which make them categorized into A, B, C, D, and G. Lichenysin is structurally similar to surfactin, whereas surfactin has a cyclic peptide of seven amino acids including both d- and L-amino acids, Glu-Leu-D-Leu-Val-Asp-D-Leu-Leu, linked from the N-terminus to the C-terminus to form a cyclic moiety by a C12-C17 P-hydroxy fatty acid, Hchenysin has a structure with the primary amino acid sequence L-Gln-L-Leu-D-Leu-L-Val-L-Asp-D-Leu-L-Ile, with minor Leu and Val substitutions at the seventh position (Figure 14.12). 

Closer examination of 124 shows that there is one carboxyl group on one end (the carboxyl terminus, or C-terminus) of the peptide and there is an amino group at the other end (the amino terminus, or N-terminus). In the case of 124, an alanine residue occupies the N-terminus and a histidine residue occupies the C-terminus. By convention, the N-terminus is always drawn on the left and the C-terminus is drawn on the right. This is an important convention because when ala-val-ser-leu-ala-phe-glu-met-his is read for 124, it indicates that alanine is the N-terminus and histidine is the C-terminus. The order in which the amino acids are connected together is called the primary structure of a peptide. 

His residues in the peptide sequence are fundamental for Ni11 ion interactions with peptides. When the His residue is relatively distant from the N terminus, it may compete as a primary ligation site with the N-terminal amino nitrogen. However, even the higher number of His residues inserted inside the peptide sequence may be not able to compete with the albumin-like N terminus, unless the specific peptide structure is established. 

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