Proteins repetitive secondary

Approximately one half of an average globular protein is organized into repetitive structures, such as the a-helix and/or 3-sheet. The remainder of the polypeptide chain is described as having a loop or coil conformation. These nonrepetitive secondary structures are not... 

The secondary structure of a protein is generally defined as regular arrangements of amino acids that are located near to each other in the linear sequence. Examples of such elements are the a-helix, p-sheet, and P-bend. Some secondary structure is not regular, but rather is considered non-repetitive (loop and coil). 

Secondary structure. In a protein or a nucleic acid, any repetitive folded pattern that results from the interaction of the corresponding polymeric chains. 

It has been found out that the structure of proteins is flexible and there are many differences between the static spatial image of a protein and a dynamic view of its structure. This divergence is caused by the fact that the repetitive part of a-helices and [3-strands of protein folds, often described as a succession of secondary structures, can assume different local spatial orientation. Two experimental methods can be used to measure the flexibility in precise regions of protein structures (the anatomic mean square displacement, B-factor, measured during crystallographic experiments, and indirectly by NMR experiments which show different local conformation that could correspond directly to different stages of protein structures) (Bornot et al., 2007). 

Despite different sequences and repetitive motives, all gliadins have the same secondary structure of loose spirals which are a balanced compromise between the p-spiral and poly-L-proline structure (polyproline helix II) (Parrot et al., 2002), the balance is dependent on temperature, type of solvent, and hydration level (Miles et al., 1991). Similar sequences can be found in other proteins, mainly animal proteins such as elastin and collagen, and they are responsible for particular biomechanical properties connected to reverse P-spirals or p-sheet structures (Tatham and Shewry, 2000). 

To some extent, the properties of the protein are mainly determined by its primary structure (i.e., the amino acid sequence). The two kinds of structural protein, fibroin and spidroin have a distinct and highly repetitive primary structure, which results in specific secondary and tertiary... 

These assays resemble a hybrid of an immunohistochemistry assay and ELISA. Whole cells are fixed, for example with 3.7% formaldehyde, to MTPs permeabilized by repetitive washing with 0.1% Triton X-100, blocked with a protein solution, probed with primary antibodies (phospho-spe-cific, and non-phospho-specific), washed, and subsequently the secondary antibodies labeled with infrared fluorescent tags are added. After washing, these assays are read in a reader (such as the Odyssey or Aerius) designed for high sensitivity detection of two colors. The two colors are useful because one color can be used to accommodate a stain assigned as a total protein or cell number control or as an antibody to total protein, which allows for normalization. These assays may only require a single antibody versus the dual antibody sandwich required for ELISA. 

Much of our understanding of the secondary structure of proteins is the result of x-ray analysis. For many proteins the x-ray diffraction pattern indicates a regular repetition of certain structural units. For example, there are repeat distances of 7.0 A in silk fibroin, and of 1.5 A and 5.1 A in -keratin of unstretched wool. 

The common feature of these protein polymers is the presence of repetitive sequence motifs which form defined secondary structures. These repetitive amino acid sequences offer the possibihty to construct artificial genes by mul-timerization of small synthetic oligonucleotide sequences and thus the build up of high molecular weight proteins. The constructed artificial genes can be incorporated into an expression plasmid, which can subsequently be transferred to a bacterial host for production of the desired polypeptide (Fig. 19). The most commonly used host is E. coli. 

The folding of polypeptide chains into ordered structures maintained by repetitive hydrogen bonding is called secondary structure. The chemical nature and structures of proteins were first described by Linus Pauling and Robert Corey who used both fundamental chemical principles and experimental observations to elucidate the secondary structures. The most common types of secondary structure are the right-handed cx-helix, parallel and antiparallel /3-pleated sheets, and (3-turns. The absence of repetitive hydrogen-bonded regions (sometimes erroneously called random coil ) may also be part of secondary structure. A protein may possess predominantly one kind of secondary structure (a-keratin of hair and fibroin of silk contain... 

This Chapter focuses on analyses that can be performed based solely on the primary sequence of a protein. Several rationales can be applied. Physico-chemical characteristics of individual amino acids are one basis for predictions of gross structural features. For example, particular repetitive patterns may suggest a coiled-coil structure while in general secondary structure can be predicted based on an a statistical analysis of the primary sequence. The definition of signals recognized by the cellular transport machinery allow the prediction of subcellular location. Although somewhat unsystematic such observations can provide valuable hints as to the structure and/or function of a protein. 

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. 

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