Secondary structure a-helix

A representative sampling of non-heme iron proteins is presented in Fig. 3. Evident from this atlas is the diversity of structural folds exhibited by non-heme iron proteins it may be safely concluded that there is no unique structural motif associated with non-heme iron proteins in general, or even for specific types of non-heme iron centers. Protein folds may be generally classified into several categories (i.e., all a, parallel a/)3, or antiparallel /8) on the basis of the types and interactions of secondary structures (a helix and sheet) present (Richardson, 1981). Non-heme iron proteins are found in all three classes (all a myohemerythrin, ribonucleotide reductase, and photosynthetic reaction center parallel a/)8 iron superoxide dismutase, lactoferrin, and aconitase antiparallel )3 protocatechuate dioxygenase, rubredoxins, and ferredoxins). This structural diversity is another reflection of the wide variety of functional roles exhibited by non-heme iron centers. 

CD Spectrum Circular Dichroism Secondary structure, a-helix, p-sheet,.. . 

The coiled-coil motif is an ideal model system for the following reasons there is only one type of secondary structure present (the a-helix) the a-helical structure can be easily monitored by circular dichroism spectroscopy the two-stranded coiled coil contains two subunits stabilized by both intrachain and interchain interactions and, lastly, its small size reduces the potential complexity in the analysis and interpretation of results encountered in the analysis of globular proteins, which have multiple elements of secondary structure (a-helix, (3-sheet, (3-turns, loops, and regions of undefined structure). 

Fig. 8. The four levels of structure in proteins, (a) Primary structure (amino acid sequence), (b) secondary structure (a-helix), (c) tertiary structure, (d) quaternary structure.

Protein has a secondary structure a-helix, -structure or random chain. The contents of these components in the protein structure can be calculated on the basis of circular dichroism spectrum in the region of far-ultraviolet wavelength (around 220 nm),46 or amino acid sequences.47 Although these methods do not always reflect a secondary structure of protein, they are applicable to research on the structure of proteins, especially homologous proteins whose three-dimensional structures have not been shown. 

As is clear from the Figure, all the adjacent distributions have sufficient overlaps with the neighboring ones, suggesting that this REMD simulation was successful. We indeed observed a random walk in the potential energy space. This random walk in potential energy space induced a random walk in the conformational space, and we indeed observed many occasions of the formation of native-like secondary structures (a-helix and /1-strands) during the REMD simulation. 

Alternatively, one tries to extrapolate the correct rotamer from examples of residues in a similar environment in the database of known structures. The main problem here is how to define similar environments. In practice, similar environments for residues have most often been defined as having the same secondary structure (a-helix, P-strand, or loop). Until recently, side chains were normally placed using standard rotamer libraries [28-30]. A variety of procedures have been used to get rid of van der Waals clashes. These range from manual... 

Tertiary structure is the level above secondary structure in the hierarchy of structures. For example, in the zinc-finger motif mentioned above, there are regions of secondary structure, a-helix, and b-sheet. These interact to form a specific higher-order structure, the tertiary structure. 

Most fibrous proteins, such as silk, collagen, and the a-keratins, are almost completely insoluble in water. (Our skin would do us very little good if it dissolved in the rain.) The majority of cellular proteins, however, are soluble in the cell cytoplasm. Soluble proteins are usually globular proteins. Globular proteins have three-dimensional structures called the tertiary structure of the protein, which are distinct from their secondary structure. The pol)cpeptide chain with its regions of secondary structure, a-helix and fj-pleated sheet, further folds on itself to achieve the tertiary structure. 

Describe the forces that maintain the two types of secondary structure a-helix and (3-pleated sheet. 

There is a natural hierarchy in proteins (see Figure 15.1) which allows the complex three-dimensional structure to be simplified and categorized as combinations of smaller motifs. At the atom level there are patterns of side-chain interactions at the backbone level we see formation of secondary structure (a helix, P sheet and yS turn) and loop families these combine to give supersecondary structures (e.g. P hairpins) and motifs (e.g. Greek key) and ultimately the whole tertiary and quaternary structure. In this chapter we present an overview of current patterns which are observed... 

The minimum number of amino acids required to form a P-sheet is usually 6-7 and around 12-13 for an a-helix. For such small peptides it is possible to predict the specific secondary structure (a-helix, P-sheet, P-tum) as well as the orientation of side chains (Fig. 9.2.12), thereby allowing an efficient design. For shorter peptides the conformational equilibrium is displaced towards the unordered coil, and for large peptides predictions are still impossible. 

Fig. 1. CD spectra of three types of protein secondary structure a helix (—), poly(Glu), pH 4.5 /3 sheet poly(Lys-Leu), 0.5 M NaF, pH 7 unordered (—), poly(Lys-Leu) in salt-free aqueous solution. ...

Protein Secondary structure (%) a Helix jS Sheet Turn Random Method... 

More distantly related structures can be modeled by the use of the process of threading. This is a computational technique by which the sequence of the protein of an unknown structure is threaded through a nom-edun-dant library of well-determined structures to determine which are compatible with the sequence. Basic statistical methods for predicting secondary structure, a helix and p sheet, have 80% veracity. 

The quality of the separation depends, among other things, on the steepness of the gradient and the temperature. The temperature is in play because peptides can maintain a secondary structure (a-helix, P-fold) imder the conditions of the reversed-phase HPLC, which influences the adsorption. High temperatures prevent secondary structures. Because it is more comfortable, people predominantly work at RT. Regarding the column dimensions the separation of peptides and smaller proteins improves with longer columns. For tryptic digestion, people... 

Adler et al 2000). These studies show that a considerable amount of protein is inactivated or denatured due to thermal as well as air interface-related stresses. These stresses cause irreversible damage of the secondary structure (a-helix, j0-sheet, and random coil) (Ameri and Maa, 2006). 

The key feature that allows IR spectroscopy to be used to study proteins is the dependence of the amide band on the protein secondary structure (a-helix, parallel and antiparallel j6-sheets, /S-tums, and random). The frequency-structure correlations have been most reliably established for the amide I band (Table 7.9), althongh a nnmber of exceptions to these correlations have already been reported [748, 803], and the assignment for parallel and antiparallel j0-sheets is still debatable [751, 804]. Similar data for amide II bands are less well understood and hence less nseful [803]. Being of lower intensity but free from interference with water (see below), the amide III band is particularly attractive for structural studies [805-812]. A number of comprehensive recent reviews contain more detailed information on the amide band assigmnent [748, 749, 802, 803, 811, 813-817]. 

There are even higher structural orders for these molecules. It might have been that polypeptides were best described as ordered regions of secondary structure (a-helix or P-pleated sheets) connected by sections of random coil. In such a case,... 

The information on local secondary structures (a helix and /3 sheet) is usually obtained by using spectroscopic methods such as NMR, ORD, and/or CD. However, secondary structures can be best derived from the tertiary structural information. 

---