Protein structure coils

Coils ISREC Protein structure (coiled coil regions)... 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

I The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape. 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Protein structures are so diverse that it is sometimes difficult to assign them unambiguously to particular structural classes. Such borderline cases are, in fact, useful in that they mandate precise definition of the structural classes. In the present context, several proteins have been called //-helical although, in a strict sense, they do not fit the definitions of //-helices or //-solenoids. For example, Perutz et al. (2002) proposed a water-filled nanotube model for amyloid fibrils formed as polymers of the Asp2Glni5Lys2 peptide. This model has been called //-helical (Kishimoto et al., 2004 Merlino et al., 2006), but it differs from known //-helices in that (i) it has circular coils formed by uniform deformation of the peptide //-conformation with no turns or linear //-strands, as are usually observed in //-solenoids and (ii) it envisages a tubular structure with a water-filled axial lumen instead of the water-excluding core with tightly packed side chains that is characteristic of //-solenoids. 

Kobe, B., and Kajava, A. V. (2000). When protein folding is simplified to protein coiling The continuum of solenoid protein structures. Trends Biochem. Sci. 25, 509-515. 

Figure 2. Three-dimensional structure of human cytochrome c created by Protein Adviser, ver 3.0 (FQS, Hakata, Japan) with PDB file of human cytochrome c down-loaded from protein structure database of NCBI. a-Helices are shown as purple ribbons, random coils as white strands, and P-tums are blue (see separate colour tip). Heme c is depicted in white straight lines inside the protein.

The dimensions of protein random coils are calculated for a variety of proteins of known amino acid sequence. Glycine and proline contribute to reducing the dimensions of random coil proteins. Branched side chains expand the chain only slightly more than unbranched side chains. Side chains represented as structured to the y position are compared with structureless representations. It is demonstrated that the two approaches give comparable chain dimensions. The effect of sequence is investigated. 

An individual polypeptide in the a-keratin coiled coil has a relatively simple tertiary structure, dominated by an a-helical secondary structure with its helical axis twisted in a left-handed superhelix. The intertwining of the two a-helical polypeptides is an example of quaternary structure. Coiled coils of this type are common structural elements in filamentous proteins and in the muscle protein myosin (see Fig. 5-29). The quaternary structure of a-keratin can be quite complex. Many coiled coils can be assembled into large supramolecular complexes, such as the arrangement of a-keratin to form the intermediate filament of hair (Fig. 4-1 lb). 

The first high-resolution X-ray structure of a two-stranded a-helical coiled coil was reported by O Shea et al.127 and represented the dimerization domain of the DNA-binding protein GCN4. Since then, over 20 other proteins containing coiled-coil domains have been solved to high resolution.12 1 The X-ray crystallographic data indicate that the side chains of residues at positions a and d are almost totally buried in the dimer. 

Advances in NMR instrumentation and methodology have now made it possible to determine site-specific proton chemical shift assignments for a large number of proteins and nucleic acids (1,2). It has been known for some time that in proteins the "structural" chemical shifts (the differences between the resonance positions in a protein and in a "random coil" polypeptide (3-5),) carry useful structural information. We have previously used a database of protein structures to compare shifts calculated from simple empirical models to those observed in solution (6). Here we demonstrate that a similar analysis appears promising for nucleic acids as well. Our conclusions are similar to those recently reported by Wijmenga et al (7),... 

Walshaw, J., and Woolfson, D. N. (2001). SOCKET A program for identifying and analyzing coiled-coil motifs within protein structures. J. Mol. Biol. 307, 1427-1450. 

Cohen, C., and Parry, D. A. D. (1990). Alpha-helical coiled-coils and bundles How to design an alpha-helical protein. Proteins Structure, Function and Genetics 7, 1-15. 

To summarize, the model used in this paper captures many important features of protein structure and dynamics and is indeed seen to reproduce many of the general trends observed in SM-FRET experiments. At the same time, we have also observed several intriguing discrepancies between the model predictions and the experimental results. One possibility is that these discrepancies originate from shortcomings of the model. For example, the SM-FRET measurements reported in Refs. [30, 33] were performed on a coiled-coil that was immobilized on a positively charged amino-silanized glass surface and involved charged dye molecules. This implies that the protein-surface and donor-acceptor interactions may be dominated by electrostatic forces. Our... 

Secondary structure The protein structure characterized by folding of the peptide chain into a helix, sheet, or random coil. 

The four protein conformations that provide mechanical stability to cells, tissues, and organs include the random coil or amorphous structure that characterizes a part of the structure of elastin, the a helix, which is represented by the keratin molecule, the collagen triple helix, and the p structure of silk. In humans the P structure is found only in short sequences connecting parts of other structures such as the a helix, but serves as an example of the relationship between protein structure and properties. The ultimate tensile strength and modulus of each structure differs as discussed below. 

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