Protein specific protein

Ulfers AL, McMurry JL, Miller A, Wang L, Kendall DA, Mierke DF (2002b) Cannabinoid receptor-G protein interactions G(alphail )-bound structures of IC3 and a mutant with altered G protein specificity. Protein Sci 11 2526-2531... 

Kim, S., Tuck, M., Kim, M., Campagnoni, A. T., Paik, W. K. (1984). Studies on myelin basic protein-specific protein methylase 1 in various dysmyelinating mutant mice. Biochem. Biophys. Res. Commun. 123, 468 74. 

Membranes surround the individual cells of animals and organelles within the cell. They are composed of lipids and proteins. Specific proteins are responsible for the transport... 

Figure Bl.20.10. Typical force curve for a streptavidin surface interacting with a biotin surface in an aqueous electrolyte of controlled pH. This result demonstrates the power of specific protein interactions. Reproduced with pennission from [81].

Chemiluminescence has been studied extensively (2) for several reasons (/) chemiexcitation relates to fundamental molecular interactions and transformations and its study provides access to basic elements of reaction mechanisms and molecular properties (2) efficient chemiluminescence can provide an emergency or portable light source (J) chemiluminescence provides means to detect and measure trace elements and pollutants for environmental control, or clinically important substances (eg, metaboHtes, specific proteins, cancer markers, hormones, DNA) and (4) classification of the hioluminescent relationship between different organisms defines their biological relationship and pattern of evolution. 

ImmunO lSS iy. Chemiluminescence compounds (eg, acridinium esters and sulfonamides, isoluminol), luciferases (eg, firefly, marine bacterial, Benilla and Varela luciferase), photoproteins (eg, aequorin, Benilld), and components of bioluminescence reactions have been tested as replacements for radioactive labels in both competitive and sandwich-type immunoassays. Acridinium ester labels are used extensively in routine clinical immunoassay analysis designed to detect a wide range of hormones, cancer markers, specific antibodies, specific proteins, and therapeutic dmgs. An acridinium ester label produces a flash of light when it reacts with an alkaline solution of hydrogen peroxide. The detection limit for the label is 0.5 amol. 

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

To conclude, although the models used in lattice simulations are very simplified, the results provide general information on possible protein folding scenarios, albeit not on the detailed behavior of specific proteins, which would require more complex models and more accurate potentials. The contribution made by these simulations is that they enable an analysis of the structures, energetics, and dynamics of folding reactions at a level of detail not accessible to experiment. 

The transparency and refractive power of the lenses of our eyes depend on a smooth gradient of refractive index for visible light. This is achieved partly by a regular packing arrangement of the cells in the lens and partly by a smoothly changing concentration gradient of lens-specific proteins, the crystallins. 

Summers, L., et al. X-ray studies of the lens specific proteins. The crystallins. Pept. Protein Rev. 

The specific protein-DNA interactions described in this book are all with DNA in its regular B-form, or, in some cases with distorted B-DNA. In biological systems DNA appears not to adopt the A conformation, although double-stranded RNA does preferentially adopt this conformation in vivo. Whether or not Z-DNA occurs in nature is a matter of controversy. However, the formation of A-DNA and Z-DNA in vitro does illustrate the large structural changes that DNA can be forced to undergo. 

Only a rather limited number of base pairs is needed to provide unique and discriminatory recognition sites in the major groove. This is illustrated in Figure 7.8, which gives the color codes for the hexanucleotide recognition sites of three different restriction enzymes—Eco Rl, Bal 1, and Sma 1. It is clear that these patterns are quite different, and each can be uniquely recognized by specific protein-DNA interactions. 

Sequence-specific protein-DNA interactions recognize operator regions... 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

The NMR study by Wiithrich and coworkers has shown that there is a cavity between the protein and the DNA in the major groove of the Antennapedia complex. There are several water molecules in this cavity with a residence time with respect to exchange with bulk water in the millisecond to nanosecond range. These observations indicate that at least some of the specific protein-DNA interactions are short-lived and mediated by water molecules. In particular, the interactions between DNA and the highly conserved Gin 50 and the invariant Asn 51 are best rationalized as a fluctuating network of weak-bonding interactions involving interfacial hydration water molecules. 

An a helix in the first zinc motif provides the specific protein-DNA interactions... 

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