P secondary structure

Cuff IA and G J Barton 1999. Evaluation and Improvement of Multiple Sequence Methods for P Secondary Structure Prediction. Proteins Structure, Function and Genetics 34 508-519. 

Fig. 4.12(a). An outline structure of a protein (here the enzyme phospholipase A2), showing a-helical runs of amino acids as cylinders (A-E) and anti-parallel P-sheet runs as heavy black arrows. Disulfide cross-links are shown (the enzyme is extracellular), and runs of no a/p secondary structure appear as thin lines. The structure is relatively immobile, and binds calcium in a constrained loop. (Reproduced with permission from Professor J. Drenth.)... 

Gamulya, G.D., Lebedeva, I.L., Vvedensky, Yu. V. and Yukhno, T.P., Secondary Structure Formation and Wear Mechanisms for Solid Lubricant Coatings Under Friction in Vacuum, Wear, 171, 143, (1994). 

Fig. 3 Schematic view of the human vimentin protein and force-strain curves of coiled-coil intermediate filament under tensile loadings, (a) Schematic representation of vimentin structure, (b) Force-strain behaviors of a coiled-coil a-helical structures revealing the loading rate dependency of the molecular-level stiffness under tensile loading. (Reprinted from [66], with kind permission from Springer Science and Business Media), (c) a-p secondary structural transition of coiled-coil a-helix under tensile loading. (Reprinted from [67])...

Once proteins are divided into domains the domains are then classified hierarchically. At the top of the classification we usually find the class of a protein domain, which is generally determined from its overall composition in secondary structure elements. Three main classes of protein domains exist mainly a domains, mainly (3 domains, and mixed a p domains (the domains in the a — p class are sometimes subdivided into domains with alternating a/p secondary structures and domains with mixed a + p secondary structures). In each class, domains are clustered into folds according to their topology. A fold is determined from the number, arrangement, and connectivity of the domain s secondary structure elements. The folds are subdivided into superfamilies. A superfamily contains protein domains with similar functions, which suggests a common ancestry, often in the absence of detectable sequence similarity. Sequence information defines families, i.e., subclasses of superfamilies that regroup domains whose sequences are similar. 

The C=0 stretching mode, with contributions from in-phase bending of the N-H bond and stretching of the C-N braid, occurs in the region of 1,650 to 1,660 cm in a-helical structures and between 1,620 and 1,640 cm in P-sheets [34, 35]. This band is often called the amide 1 band. Its polarization in a and p secondary structures is the same as that of the N-H stretching mode. 

On one hand, it forms annular p-oligomers with a central channel-like pore that can perforate the plasma membrane of brain cells and affect Ca fluxes. On the other hand, the peptide can form p-rich protofibrils and fibrils. Kallberg et al. studied the propensity of various amyloid proteins to form either a or p secondary structures. They report the interesting observation that all amyloid proteins contain a/p discordant segments. These a/p discordant stretches correspond to a part of the protein that has been shown to adopt an a-helix structure in spite of being composed by amino acids that have a higher propensity... 

Weber P L, Brown S 0 and Mueller L 1987 Sequential NMR assignment and secondary structure identification of human ubiquitin Biochemistry 26 7282-90... 

In order to develop a quantitative interpretation of the effects contributing to heats of atomization, we will introduce other schemes that have been advocated for estimating heats of formation and heats of atomization. We will discuss two schemes and illustrate them with the example of alkanes. Laidler [11] modified a bond additivity scheme by using different bond contributions for C-H bonds, depending on whether hydrogen is bonded to a primary (F(C-H)p), secondary ( (C-H)g), or tertiary ( (C-H)t) carbon atom. Thus, in effect, Laidler also used four different kinds of structure elements to estimate heats of formation of alkanes, in agreement with the four different groups used by Benson. 

Chou P Y and G D Fasman 1978. Prediction of the Secondary Structure of Proteins from Tlieir Amino Acid Sequence. Advances in Enzymology 47 45-148. 

Secondary Structure. The silkworm cocoon and spider dragline silks are characterized as an antiparaHel P-pleated sheet wherein the polymer chain axis is parallel to the fiber axis. Other silks are known to form a-hehcal (bees, wasps, ants) or cross- P-sheet (many insects) stmctures. The cross-P-sheets are characterized by a polymer chain axis perpendicular to the fiber axis and a higher serine content. Most silks assume a range of different secondary stmctures during processing from soluble protein in the glands to insoluble spun fibers. 

There is some confusion in using Bayes rule on what are sometimes called explanatory variables. As an example, we can try to use Bayesian statistics to derive the probabilities of each secondary structure type for each amino acid type, that is p( x r), where J. is a, P, or Y (for coil) secondary strucmres and r is one of the 20 amino acids. It is tempting to writep( x r) = p(r x)p( x)lp(r) using Bayes rule. This expression is, of course, correct and can be used on PDB data to relate these probabilities. But this is not Bayesian statistics, which relate parameters that represent underlying properties with (limited) data that are manifestations of those parameters in some way. In this case, the parameters we are after are 0 i(r) = p( x r). The data from the PDB are in the form of counts for y i(r), the number of amino acids of type r in the PDB that have secondary structure J.. There are 60 such numbers (20 amino acid types X 3 secondary structure types). We then have for each amino acid type a Bayesian expression for the posterior distribution for the values of xiiry. 

For example, Stolorz et al. [88] derived a Bayesian formalism for secondary structure prediction, although their method does not use Bayesian statistics. They attempt to find an expression for / ( j. seq) = / (seq j.)/7( j.)//7(seq), where J. is the secondary structure at the middle position of seq, a sequence window of prescribed length. As described earlier in Section II, this is a use of Bayes rule but is not Bayesian statistics, which depends on the equation p(Q y) = p(y Q)p(Q)lp(y), where y is data that connect the parameters in some way to observables. The data are not sequences alone but the combination of sequence and secondary structure that can be culled from the PDB. The parameters we are after are the probabilities of each secondary structure type as a function of the sequence in the sequence window, based on PDB data. The sequence can be thought of as an explanatory variable. That is, we are looking for... 

A similar formalism is used by Thompson and Goldstein [90] to predict residue accessibilities. What they derive would be a very useful prior distribution based on multiplying out independent probabilities to which data could be added to form a Bayesian posterior distribution. The work of Arnold et al. [87] is also not Bayesian statistics but rather the calculation of conditional distributions based on the simple counting argument that p(G r) = p(a, r)lp(r), where a is some property of interest (secondary structure, accessibility) and r is the amino acid type or some property of the amino acid type (hydro-phobicity) or of an amino acid segment (helical moment, etc). 

P Stolorz, A Lapedes, Y Xia. Predicting protein secondary structure using neural net and statistical methods. J Mol Biol 225 363-377, 1992. 

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.

Different side chains have been found to have weak but definite preferences either for or against being in a helices. Thus Ala (A), Glu (E), Leu (L), and Met (M) are good a-helix formers, while Pro (P), Gly (G), Tyr (Y), and Ser (S) are very poor. Such preferences were central to all early attempts to predict secondary structure from amino acid sequence, but they are not strong enough to give accurate predictions. 

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Figure 2.8 Adjacent antiparallel P strands are joined by hairpin loops. Such loops are frequently short and do not have regular secondary structure. Nevertheless, many loop regions in different proteins have similar structures, (a) Histogram showing the frequency of hairpin loops of different lengths in 62 different proteins, (b) The two most frequently occurring two-residue hairpin loops Type I turn to the left and Type II turn to the right. Bonds within the hairpin loop are green, [(a) Adapted from B.L. Sibanda and J.M. Thornton, Nature 316 170-174, 1985.]...

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. 

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

Argos, P., Rossmann, M.G., Johnsson, J.E. A four-helical super-secondary structure. Biochem. Biophys. Res. Comm. 75 83-86, 1977. 

Fibrous proteins can serve as structural materials for the same reason that other polymers do they are long-chain molecules. By cross-linking, interleaving and intertwining the proper combination of individual long-chain molecules, bulk properties are obtained that can serve many different functions. Fibrous proteins are usually divided in three different groups dependent on the secondary structure of the individual molecules coiled-coil a helices present in keratin and myosin, the triple helix in collagen, and P sheets in amyloid fibers and silks. 

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