Globular proteins structure

Efimov, A.E. Favoured structural motifs in globular proteins. Structure 2 999-1002, 1995. 

In globular protein structures, it is common for one face of an a-helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. The outward face of such an amphiphilic helix consists mainly of polar and charged residues, whereas the inward face contains mostly nonpolar, hydrophobic residues. A good example of such a surface helix is that of residues 153 to 166 of flavodoxin from Anabaena (Figure 6.24). Note that the helical wheel presentation of this helix readily shows that one face contains four hydrophobic residues and that the other is almost entirely polar and charged. 

Kuwajima K. The molten globule state as a clue for understanding the folding and coop-erativity of globular-protein structure. Proteins (1989) 6 87-103. 

The only other principal helical species besides the a-helix which occurs to any great extent in globular protein structure is the 310-helix... 

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber et al., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended e helix has been described as occurring in chymotrypsin (Srinivasan et al., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix. 

Privalov, P.L. and N.N. Khechinashvili. 1974. A thermodynamic approach to the problem of stabilization of globular protein structure a calorimetric study. J Mol Biol 86 665-684. 

A vital component of globular protein structure, yet one that is very hard to characterize, is the (3-turn. These have importance in folding the protein and are often recognition sites for interactions, but have many detailed structural variations that lead to a variety of spectral signatures. Several researchers have attempted to categorize turns by detection of bands at... 

Our discussion of globular protein structure begins with the principles gleaned from the earliest protein structures to be elucidated. This is followed by a detailed description of protein substructure and comparative categorization. Such discussions are possible only because of the vast amount of information available over the Internet from resources such as the Protein Data Bank (PDB www.rcsb.org/pdb), an archive of experimentally determined three-dimensional structures of biological macromolecules. 

Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure... 

Globular proteins have more complicated tertiary structures, often containing several types of secondary structure in the same polypeptide chain. The first globular protein structure to be determined, using x-ray diffraction methods, was that of myoglobin. 

The Structure of the a-Keratins Was Determined with the Help of Molecular Models The fi-Keratins Form Sheetlike Structures with Extended Polypeptide Chains Collagen Forms a Unique Triple-Stranded Structure Globular Protein Structures Are Extremely Varied and Require a More Sophisticated Form of Analysis Folding of Globular Proteins Reveals a Hierarchy of Structural Organization... 

Globular Protein Structures Are Extremely Varied and Require a More Sophisticated Form of Analysis... 

Milik et al. (1995) developed a neural network system to evaluate side-chain packing in protein structures. Instead of using protein sequence as input to the neural network as in most other studies, protein structure represented by a side-chain-side-chain contact map was used. Contact maps of globular protein structures in the Protein Data Bank were scanned using 7x7 windows, and converted to 49 binary numbers for the neural network input. One output unit was used to determine whether the contact pattern is popular in... 

It is common in globular protein structures for one face of an a-helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. 

R. Sowdhamini, S. D. Rufino, T. L. Blundell. A database of globular protein structural domains clustering of representative family members into similar folds. Fold. Des. 1996, 1, 209-220. 

The relative success of these crude simulations indicate that simple models using empirical parameters may be able to correctly represent globular protein structure. A correctly parameterized simplified force field should make reasonable, physically appropriate assumptions and should have a global energy minimum corresponding to the native structures of proteins. Initial parameters could be taken from Brookhaven Protein Data Bank averages and be further refined using, e.g., consistent force field (CFF) methods." " ... 

FIGURE 4-15 Globular protein structures are compact and varied. Human serum albumin (M, 64,500) has 585 residues in a single chain. Given here are the approximate dimensions its single polypeptide chain would have if it occurred entirely in extended fi conformation or as an a helix. Also shown is the size of the protein in its native globular form, as determined by X-ray crystallography the polypeptide chain must be very compactly folded to fit into these dimensions. 

Clearly hydrogen bonding is critical in stabilising a globular protein structure. Also of importance are electrostatic and van der Waals interactions, of respective bond strengths 5kcalmole-1 and lkcalmole-1. 

Varieties of Globular Protein Structure Patterns of Folding (Figure 6.16, Figure 6.17, Figure 6.18, Figure 6.19)... 

Structural peculiarities of the different proteins should be therefore taken into account when a relationship between the degree of succinylation and emulsification is derived. These include conformational changes and the contribution of hydrophobic regions exposed by the unfolding of the globular protein structure. Moreover, the technological treatment of the raw material or even the protein, which can induce denaturation or interaction with nonprotein compounds, is to be considered for understanding the possibly different behavior of proteins from the same source. 

For evaluation of 6 we have assumed that the virus would be hexagonally closest-packed in a two-dimensional array on the adsorbent surface where 6 equals unity. The quantity x was estimated to be 50 from space filling models where approximately 3% of a 27-nm diameter icosahedral virion face is estimated, on the basis of globular protein structure (12), to approach the surface of the solid close enough to displace interfacial water molecules. If our estimate is changed to 10 or 250, instead of a most probable value of about 50, Equation 2 predicts that the AGads will be shifted by only zb 4 kj mol, which is comparable to the uncertainty given by experimental data scatter. 

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