Protein packing

Chofhia, C., Levitt, M., Richardson, D. Structure of proteins packing of a-helices and pleated sheets. 

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

The human caliciviruses, norovirus (NoV) and sapovirus, have also been described as small round structured viruses, for their 27-30 nm capsids. The NoV capsid consists of 180 copies of the VPl major capsid protein packed as an icosahedron (Prasad et ah, 1999) and the VP2 minor capsid protein, which may contribute to stability (Bertolotti-Ciarlet et al., 2002). The S domain of VPl forms the inner shell of the capsid, while the P domain protrudes from the capsid surface and contributes to binding the histoblood group antigen receptor (Cao et ah, 2007) and antigenicity (Donaldson et ah, 2008 Lindesmith et ah, 2010). 

Goren EN, Reeves DC, Akabas MH. 2004. Loose protein packing around the extracellular half of the GABAa receptor pi subunit M2 channel-lining segment. J Biol Chem 279 11198-111205. 

The entire thermodynamic system of the membrane and TM protein must be considered to understand how the protein and bilayer achieve their native state. We have summarized four of the mechanisms, hydrophobic matching, tilt angles, and specific protein/lipid and protein/protein interactions that are important in determining the stability (Fig. 5). Other important factors, such as the stability of lipid/lipid interactions, have been left out of our protein-centric view. We describe a hydrophobic mismatch as an unfavorable interaction that can be relieved by the other three processes, but we would expect all these properties of the system to interact. We could easily describe the same equilibria by saying that a strain in curvature is relieved by a hydrophobic mismatch or that strong protein/protein packing interactions might help relieve the hydrophobic mismatch or curvature stress. The complex interplay between all these interactions is at the heart of what determines membrane protein stability and will no doubt be difficult to quantify. 

A. Tropsha, C. W. Carter Jr., S. Cammer and I. I. Vaisman, Simplicial neighborhood analysis of protein packing (SNAPP) a computational geometry approach to studying proteins.. Methods EnzymoL, 2003, 374, 509-544. 

VIBRATE (normal modes), VOID (protein packing), and mdXvu (visualization of AMBER trajectory files). QCPE has also accepted the responsibility to distribute semicommercial academic software, such as MM2, MM3, MOPAC 93, POLYRATE, PEFF, and COMPARE-CONFORMER. Most programs in library are in FORTRAN and are available as source code. Current catalogs and information are available by anonymous ftp from qcpe6.chem.indiana.edu (129.79.74.206). Many of the programs run on several hardware platforms, including DEC VAX, IBM, Silicon Graphics, Stardent, Sun, Fujitsu, and Cray. 

Axons are surrounded by while matter coating called myelin that consists of a layer of proteins packed betw een two... 

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 ... 

Chothia, C., Levitt, M., and Richardson, D. Structure of proteins packing of a-helices and pleated sheets. Proc. Natl. Acad. Set. USA 74, 4130-4134 (1977). Branden, C.-I., Eklund, H., Nordstrom, B., Boiwe, T., Soderlund, G., Zeppeza-uer, E., Ohlsson, I. and Akeson, A. Structure of liver alcohol dehydrogenase at 2.9-A resolution. Proc. Natl. Acad. Sci. USA 70, 2439-2442 (1973). 

Fernandez A (2005) Incomplete protein packing as a selectivity filter in drug design. Structure 13 1829-1836... 

Although both primary H/T and D/T isotope effects were measured as a function of temperature, the focus of the interpretation was on primary D/T isotope effects, since the smaller commitment for D- than H-transfer leads to a more complete contribution of the chemical step to the measured parameters (see e.g. Section 10.21). The results obtained from this study [92], as well as the earlier work [91], indicate a striking trend in which the value of Ad /At moves from near unity to below unity as the surface of the protein is modified (either by glycosylation or addition of polyethylene glycol). A similar type of pattern has been seen in other enzyme systems, such as the thermophilic ADH [24] (Section 10.5.1.1) and soybean lipoxygenase (SLO) [43] (see Section 10.5.3.1 below) where modification of reaction conditions away from either optimal temperature (ht-ADH) or optimal protein packing (via... 

Secondary structure prediction methods have been complemented by packing analyses of amino acid residues in globular proteins. Packing arrangements have been examined extensively [13, 14] in attempts to identify preferred interaction patterns between non-contiguous amino acid residues. While there is no straightforward way to cast this information into a scheme for prediction of protein structure from sequence, it can certainly be used for plausibility checks on hypothetical protein models or to score protein models obtained by protein folding simulations on lattices [15]. 

Brynda E, Hlady V and Andrade J D 1990 Protein packing in adsorbed layers studied by excitation-energy transfer J. Colloid Interface Sci. 139 374-80... 

Hydrophobic protein-protein or protein-packing interactions can be eliminated In many cases by the addition of detergents to the aqueous buffer. Protein solubilization without denaturatlon can be achieved with mild detergents such as sodium deoxycholate, Triton X-100, or Nonldet P40 (27). 

An effective hair conditioner and softener. Its high concentration and free-flowing form assure a homogeneous and reproducible end product. Well suited for conditioners, protein packs and mousses. 

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