Structure, secondary

Using the primary sequence, the secondary structure of the proteins has been predicted by the application of four different statistical proce- 

In the last one and one-half decades many studies have been made on the ORD and CD of ribosomal proteins. Early studies (McPhie and Grat-zer, 1966 Sarkar et al., 1967 Cotter and Gratzer, 1969) were made on a mixture of proteins, and the general conclusion was that both in the ribosome and in the isolated state (usually after acetic acid and urea extraction) the protein moiety contained approximately 25% a helix together with some -pleated sheet and random-coil conformation. 

CD studies have recently been made on urea-isolated and renatured individual proteins from the small ribosomal subunit (Venyaminov and Gogia, 1982). In another study (Dijk et al., 1983a), many proteins obtained from both the small and large ribosomal subunits by a gentler salt extraction method were measured with the CD technique. It was found that, in general, the 30 S proteins are rich in a helix and contain a rather small amount of /3 sheet, whereas the 50 S proteins are more diverse, especially in their a helix content, and most are relatively rich in /3 sheet (Dijk et al., 1983a). 

A comparison between the amount of a helix predicted from the primary structure (Wittmann et al, 1980) with that obtained from CD measurements (Dijk et al, 1983a) gives a good agreement for a number of the proteins (e.g., S4, S8, Lll, L27). However, there are discrepancies 

The availability of the purified transporter in large quantity has enabled investigation of its secondary structure by biophysical techniques. Comparison of the circular dichroism (CD) spectrum of the transporter in lipid vesicles with the CD spectra of water-soluble proteins of known structure indicated the presence of approximately 82% a-helix, 10% ) -turns and 8% other random coil structure [97]. No / -sheet structure was detected either in this study or in a study of the protein by the same group using polarized Fourier transform infrared (FTIR) spectroscopy [98]. In our laboratory FTIR spectroscopy of the transporter has similarly revealed that 

The polypeptide backbone exists in different sections of the protein as an a-helix, P-pleated sheet, or random y-coil. The study of the protein secondary structure 

The random coil refers to a section of polypeptide in a protein whose conformation is not recognizable as one of the defined structures of helices and pleated sheets. It is determined by side-chain interactions and, within a given protein, is fixed rather than varying in a random way. 

One good way to measure the protein secondary structure is by x-ray crystallography. In addition, the techniques of neutron diffraction and NMR can be used to measure the protein secondary structure. 

Stretches of a-helix are most often positioned on the protein s surface, with one face of the helix facing the hydrophobic interior and the other facing the surrounding aqueous medium. The amino acid sequence of these helices is such that hydrophobic amino acid residues are positioned on one 

The trans and cis configurations of peptide bonds involving proline. 

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 

and Goldwhite, Harold (1995). Creations of Fire Chemistry s Lively History from Alchemy to the Atomic Age. New York Plenum Press. 

Laidler, Keith J. (1998). To Light Such a Candle Chapters in the History of Science and Technology. New York Oxford University Press. 

Wollaston, George F. (1993). Glenn Seaborg. Nobel Laureates in Chemistry 1901-1992, ed. Laylin K. James. Washington, DC American Chemical Society Chemical Heritage Foundation. 

Seaborg, Glenn. Glenn Seaborg An Autobiographical Account. Available from http //www-ial.lbl/Seaborg/ . 

Creighton, Thomas E. (1993). Proteins Structures and Molecular Properties, 2nd edition. New York W. H. Freeman. 

Have you ever noticed that your hair gets longer when it is wet Why does this happen  

Hair is composed of a protein called keratin. The secondary structure of keratin is a-helix throughout, meaning that the protein has a wound-up helical structure. As we learned earlier, this structure is maintained by hydrogen bonding. 

Individual hair fibers are composed of several strands of keratin coiled around each other. When hair is dry, the keratin protein is tightly coiled, resulting in the normal 

CAN YOU ANSWER THIS Wien curlers are put into wet hair and the wet hair is allowed to dry, the hair tends to retain the shape of the curler. Can you explain why this happens  

The bond between adjacent thienylene units in PT can adopt the trans or c/s configuration by virtue of adjacent units being syn or anti. X-ray diffraction reveals an anti conformation (planar) leading to straight chains with an orthorhombic unit cell in the solid state [71,97,114,115]. The syn conformation which can occur in alkyl substituted oligo- and poly(thiophene)s represents a deviation from the ideal all-anti conformation and introduces rotational defects into the polymer which interrupt or weaken the extent of conjugation [115]. Theoretical information on the gas-phase conformations in PMT in the neutral state can be obtained by the ab initio quantum-chemical calculations on bithiophene and methyl substituted bithiophenes [116]. 

The main chain of a vacuum-deposited and vapor-deposited PT film is preferably oriented perpendicular to the substrate surface [128-130]. The chain tilt angle to the normal to the surface decreases with increasing substrate temperature during vacuum deposition [128]. In general, PT films deposited on oriented graphite or gold surfaces have helical structures which assemble to form a crystalline array [131]. 

The shift of the absorption maximum upon heating (thermochromism) and by changing of solvents (solvatochromism) is caused the generation of twists (disruption of planarity) and subsequently results in a decrease of the conjugation length [139,140]. It is possible to distinguish three types of twist [140]  

Various thermal analyses, spectroscopic methods, and conductivity measurements show that PATs consist of an ordered and a disordered phase. In unoriented PAT films with long side chains (n 10, e.g. PDDT, PTDT), PAT forms are separated ordered phase resulting in hexagonal packing of the alkyl side chains between the main chain layers [140-142]. The effective distance of the side chain overlap is estimated to be 6.7 A for PTDT for POT having no 

1 (x-Helix and Sheet Segments of the peptide chains are likely to be held in their coiled form because of intramolecular forces. The two best-known cods are the a-helix and p-sheet. 

The hehces do not have to have an integral number of residues per turn. In many proteins, the a-helix repeats after exactly 18 residues, which amounts to five turns. It has, therefore, 3.6 residues per turn. Also, each carbonyl oxygen is hydrogen bonded to the amide proton on the fourth residue up the helix. 

FIGURE 18.1 Dimensions and bond angles of a fully extended trans polypeptide chain. 

FIGURE 18.2 Drawings of the left- and right-handed a-helices. 

---

Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

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

Tjandra N and Bax A 1997 Large variations in C-13(alpha) chemical shift anisotropy in proteins correlate with secondary structured. Am. Chem. Soc. 119 9576-7... 

Nogales E and Downing K C 1997 Visualizing the secondary structure of tubulin three-dimensional map at 4A J. Struct. Biol. 118 119-27... 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Protein dynamics occurs on very different time scales ([McCammon and Harvey 1987, Jardetzky 1996]). Here, we are most interested in long time scale motions such as relative motion between secondary structure elements, and inter-domain motion. 

To facilitate conformational transitions in the before-mentioned adenylate kinase, Elamrani and co-workers scaled all atomic masses by a large factor thus allowing the use of a high effective simulation temperature of 2000K ([Elamrani et al. 1996]). To prevent protein unfolding, elements of secondary structure had to be constrained. 

Sccondaiy structure description of secondary structure HELIX, SHELL, J URN... 

A completely new method of determining siufaces arises from the enormous developments in electron microscopy. In contrast to the above-mentioned methods where the surfaces were calculated, molecular surfaces can be determined experimentally through new technologies such as electron cryomicroscopy [188]. Here, the molecular surface is limited by the resolution of the experimental instruments. Current methods can reach resolutions down to about 10 A, which allows the visualization of protein structures and secondary structure elements [189]. The advantage of this method is that it can be apphed to derive molecular structures of maaomolecules in the native state. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

The comparison of both data sources qualitatively shows a similar picture. Regions of high mobflity are located especially between the secondary structure elements, which are marked on the abscissa of the plot in Figure 7-17. Please remember that the fluctuations plotted in this example also include the amino acid side chains, not only the protein backbone. This is the reason why the side chains of large and flexible amino acids like lysine or arginine can increase the fluctuations dramatically, although the corresponding backbone remains almost immobile. In these cases, it is useful to analyze the fluctuations of the protein backbone and side chains individually. 

Rule-based Approaches Using Secondary Structure Prediction... 

Ihe rule-based approach to protein structure prediction is obviously very reliant on th quality of the initial secondary structure prediction, which may not be particularly accurate The method tends to work best if it is known to which structural class the protein belongs this can sometimes be deduced from experimental techniques such as circular dichroism... 

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. 

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. 

Gamier J, D Osguthorpe and B Robson 1978. Analysis of the Accuracy and ImpUcatiotrs of Simple Mel for Predicting the Secondary Structure of Globular Proteins. Journal of Mokadar Biology 120 97-i... 

Nlng Q and T J Sejnowsld 1988. Predicting the Secondary Structure of Globular Proteins Using Neural Network Models. Journal of Molecular Biology 202 865-888. 

Rost B and C Sander 1993. Prediction of Protein Secondary Structure at Better than 70% Accurt journal of Molecular Biology 232 584-599. 

Rule-based systems try to identify certain subsequences of amino acids that tend to have a particular secondary structure, such as sheets, a-helices, (I-strands,... 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

---