Protein packing contacts

What is the relevance of a structure determined in a crystalline state to its native structure in solution Protein crystals have a solvent content of 40-70% by volume. Thus, there are few direct intermolecular contacts between molecules which affect the structure. Structures of the same protein determined in different crystal forms, and therefore containing different packing contacts, have generally been found to be the same. This is also true of structures determined using both NMR spectroscopy and protein x-ray crystallography. It has also been found that some enzymes are fully active in the crystalline state, implying that crystallization has not altered the native conformation. 

In contrast to the smaller /3-barrels of water-soluble proteins, those of membrane-inserted /3-barrels start at eight strands and run up to 22 (Table II). Presumably, the required tightly packed nonpolar barrel core of the water-soluble proteins limits the radius of circular barrels to small values. In contrast, transmembrane barrels form polar cores the stability of which depends on hydrogen bonds rather than on geometrically exact nonpolar packing contacts. Such polar cores can be constructed much more leisurely and may also include water molecules that increase... 

Carugo, O., Argos, P., Protein-protein crystal-packing contacts. Protein Sci. 

Various Definitions of Protein Surfaces. It is crucial that the size of the probe is small enough so that the small detail of surface irregularities (hills and valleys) can be resolved. Because of different probe sizes, different definitions of protein surface arose. Contact surface would be used if the probe were not small enough to resolve every hills and valleys of the protein surface. It refers to the contact area of the probe with the protein surface. Accessible surface is not preferred for Ds determination because it includes both protein and solvent atoms surfaces. It is more suitable to describe properties of protein packing. Molecular surface is favored to represent protein-solvent interaction because it describes area inaccessible to the solvent.f It is this surface that claimed to best describe self-similarity. Eq. (11) can be employed to obtain after replacing d with the probe diameter. When the molecular surface (Am) is used, Ds can be determined as follows ... 

Detailed structure determinations of GCN4 and other coiled-coil proteins have shown that the a helices pack against each other according to the "knobs in holes" model first suggested by Francis Crick (Figure 3.5). Each side chain in the hydrophobic region of one of the a helices can contact four side chains from the second a helix. The side chain of a residue in position "d"... 

To answer the first question, Lesk and Chothia examined in detail residues at structurally equivalent positions that are involved in helix-heme contacts and in packing the a helices against each other. After comparing the nine globin structures then known, the 59 positions they found that fulfilled these criteria were divided into 31 positions buried in the interior of the protein and 28 in contact with the heme group. These positions are the principal determinants of both the function and the three-dimensional structure of the globin family. 

Tomato bushy stunt virus is a T = 3 plant virus with 180 chemically identical subunits. Each polypeptide chain is divided into several domains. The subunits preserve quasi-equivalent packing in most contact regions by conformational differences of the protein chains, especially a large change in... 

The particle has a head, within which the viral DNA is folded, and a long, fairly complex tail, at the end of which is a series of tail fibers. During the attachment process, the vims particles first attach to the cells by means of the tail fibers. These tail fibers then contract, and the core of the tail makes contact with the cell envelope of the bacterium. The action of a lysozyme-like enzyme results in the formation of a small hole. The tail sheath contracts and the DNA of the vims passes into the cell through a hole in the tip of the tail, the majority of the coat protein remaining outside. The DNA of T4 has a total length of about 50 /xm, whereas the dimensions of the head of the T4 particle are 0.095 Am by 0.065 fim. This means that the DNA must be highly folded and packed very tightly within the head. 

Ribozymes are a class of metallo-enzymes based on RNA rather than proteins. They have potential in clinical medicine, for example, as potential anti-HIV agents (568, 569) and as possible new tools for the treatment of cancer (570). The active structures of ribozymes contain domains of stacked helices which pack together through tertiary contacts. Divalent metal ions such as Mg(II), Zn(II), and Mn(II) can tune the reactivity and shape the structures of ribozymes (571). Manganese(II) and Mg(II) have similar hexacoordinate ionic radii (0.86 and 0.97 A, respectively) (572) and octahedral geometry ( )Ka of hydrates Ca(II), 12.7 Mg(II), 11.4 Mn(II), 10.7 Zn2+, 9.6) (571). There are several potential oxygen donors on the ribose sugar moiety. 

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