Compact globular structures

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

Inspection of protein structures can show which regions of a protein form compact globular structure and hence the domains of the protein. Several methods can be used to automatically extract domain definitions from three-dimensional structures (Holm and Sander, 1995 Islam et al.,... 

Studies of the properties of the isolated fragments emphasized the question, Can F2 and F2 acquire their native conformations independently A combination of sedimentation velocity and sedimentation equilibrium studies showed frictional ratios f/f0 of 1.3 and 1.4 for F, and F2, respectively, implying compact globular structures in... 

Since an increased number of disulfide bridges in relatively short polypeptide chains leads to compact globular structures with the disulfides mainly buried in the nonpolar core, such excised protein fragments should represent, even in the precursor molecules, stable subdomains. Therefore, sufficient structural information can be retained for a correct refolding at least to some extent, if appropriate experimental conditions are applied in terms of peptide concentration, redox reagents, temperature and/or reaction buffers. A great deal of... 

Many scorpion toxins, insect defensins, and enzyme inhibitors are cystine-rich polypeptides containing three to four disulfide bonds. In a large number of these toxins, two cystines are involved in the consensus Cys-(Xaa)1-Cys/Cys-(Xaa)3-Cys framework which is responsible for the common characteristic fold consisting of an a-helix and a two- or three-stranded antiparallel (3-sheet (a 3 3-fold or 3a 3 3-fold). For a review see ref[69]. The overall compact globular structures of these cystine-rich peptides contain the cystine stabilized a-helix motif (Section 6.1.5.1.2) which is further stabilized by a third disulfide bond between the N-terminus and the (3-strand adjacent to the helix and in some cases by an additional fourth disulfide bridge. Due to the presence of the cystine stabilized a-helix motif, a preferred initial formation of this motif followed by its stabilization via the additional disulfides was expected. However, in contrast to what was observed for the cystine peptides containing only the cystine stabilized a-helix motif, simple air oxidation is not successful. 

Transition occurs between two conformational states of the chain the coil structure in the expanded state and the compact globular structure in the collapsed state. The negative value of the optical anizotropy of the statistical segment indicates the existence of interactions between the side PA Am chains in the collapsed state. 

The decisive role of cholesterol groups in the process of compact globular structure formation is confirmed by the temperature dependence of xw for solutions of PCMA-11... 

The secondary structures are combined with specific geometric arrangement to form compact globular structure known as tertiary structure. The fundamental unit of tertiary structure is the domain, which is defined as a polypeptide chain or a part of a polypeptide chain that can independently fold into a stable tertiary structure (Murphy, 2001). Domains are also units of function, and often the different domains of a protein are associated with different functions. Polypeptide chains, especially of regulatory proteins, often aggregate by specific interactions to form oligomeric structures. These oligomeric proteins are said to exhibit quarternary structure. The association of proteins with other biomacromolecules to form complexes of cellular components is referred to as quinternary structure. 

Dendritic macromolecules exhibit compact globular structures which lead to their low viscosity in the melt or in solution. Furthermore, dendritic macromolecules are characterized by a very large number of available functional groups, which lead to unprecedented freedom for changing/tuning/tailoring the properties of these multivalent scaffolds via complete or partial derivatization with other chemical moieties. All these features have contributed to multidisciplinary applications of these unique macromolecular structures in recent years 6, 7). The development of efficient synthetic routes in recent years has given rise to a virtually unlimited supply of commercially available dendritic polymers, at very affordable price. The transport properties of hyperbranched and dendritic polymers have recently attracted attention as potentially new barrier and membrane materials 8-9). 

Using the phase diagramms the data on the formation of poly(methacrylic acid) (matrix)-poly(ethylene ycol) (oligomer) complexes were interpreted - and it was shown that the prcxluction of compact globular structures of the complexes is possible only for the cxxupkd matrix PMAA and when the critical length of oli mer is reached. 

It is not quite as sufficient to think of proteins as straight sequences of aminoacids, because understanding their function requires some understanding of how they are folded up into compact globular structures, but it will do for now. 

D. Atkinson, 1994) that is formed by the compact globular structure of the lipovitellin-like N-terminal domain. The flexible a-helical domains, and elastic and irreversibly bound P-sheet regions discussed in Section 4.1, are also apparent in this model. 

The tertiary structure is the complete three-dimensional structure of a polypeptide chain. Many polypeptides fold into compact, globular structures in which amino acid residues that are distant from each other in primary structure come into close proximity in the folded structure. Because of efficient packing, most water molecules are excluded from the protein s interior. It is the different interactions between the side chains of the amino acids that stabiUze the tertiary structure. A major force stabiUzing the tertiary strucmre is the hydrophobic interaction among nonpolar side chains in the core of the protein. 

The tertiary structure of jS-lg has been studied in considerable detail using X-ray crystallography. It has a very compact globular structure in which the j8-sheets occur in a )S-barrel-type structure or calyx (Figure 4.23). Each monomer exists almost as a sphere with a diameter of about 3.6 nm. 

Quantitatively, tertiary interactions fold polypeptide chains into one or several domains to form compact globular structure. Their compactness, which characterizes domains, can be expressed as the ratio of their surface area to the surface area of a sphere versus the same volume with an observed values of 1.64 0.08. Thus the domain concerns a polypeptide chain or a part of a polypeptide chain that can independently fold into compact, stable tertiary structure. 

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