Protein association

Actin is a protein which is present in almost all eukaryotic cells and is Important in the cytoskeleton and cell motility. Muscle cdls are filled with arrays of actin and myosin filaments, adiich produce motion by AIT hydrolysis and sliding of the filaments. Polymerization of actin (C actin) to F actin is widely studied In cell biology. 

Fatty acids are a significant source of energy. In blood, fatty acids are usually transported bound to serum albumin. In cells, fafty acids are transported by fatty acid binding proteins (FABPs), which are a family of small proteins 

BtOCHEMtCAL EXAMPLES UStNC SOLVENT-SENSmVE PROBES 

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Protamines. Strongly basic, low mol. wt. proteins which contain high levels of arginine, but no sulphur-containing amino-acids. They are soluble proteins, associated with nucleic acids and are obtained in large quantity from fish spermatozoa. 

Northrup S H and Erickson H P 1992 Kinetics of protein-protein association explained by Brownian dynamics computer simulation Proc. Natl Acad. Sci. USA 89 3338-42... 

Interest in vaccine development has centered around the asexual erothrocytic stage of the life cycle, especially the mero2oite. Several proteins associated with these stages have been identified and produced by recombinant techniques (92,93). The most prominent is the MSA-1 protein of the mero2oite. A clinical trial with this protein is being planned (93). 

Here,. Ai(X) is the partial SASA of atom i (which depends on the solute configuration X), and Yi is an atomic free energy per unit area associated with atom i. We refer to those models as full SASA. Because it is so simple, this approach is widely used in computations on biomolecules [96-98]. Variations of the solvent-exposed area models are the shell model of Scheraga [99,100], the excluded-volume model of Colonna-Cesari and Sander [101,102], and the Gaussian model of Lazaridis and Karplus [103]. Full SASA models have been used for investigating the thermal denaturation of proteins [103] and to examine protein-protein association [104]. 

The augmentation of a p sheet in one protein by a strand emanating from another is a mode of protein association not restricted to viral shells. Small domains involved in intracellular signal transduction bind to "arms" of other proteins by presenting the edge of a sheet on which those arms can form an additional strand. 

Van den Berg, G.B. Hanemajer, J.H. and Smolders, C.A., "Ultrafiltration of Protein Solutions the Role of Protein Association in Rejection and Osmotic Pressure," Journal of Membrane Science, 31 (1987) 307-320. 

Cho, K. W., Colepicolo, P., and Hastings, J. W. (1989). Autoinduction and aldehyde chain-length effects on the bioluminescent emission from the yellow protein associated with luciferase in Vibrio fischeri strain Y-lb. Photochetn. Photobiol. 50 671-677. 

The antimuscarinic drug atropine, and its derivative ipratropiumbromide, can also be used for antiarrhyth-mic treatment. Muscarinic receptors (M2 subtype) are mainly present in supraventricular tissue and in the AV node. They inhibit adenylylcyclase via G proteins and thereby reduce intracellular cAMP. On the other hand, activation of the M2 receptor leads to opening of hyperpolarizing Ik.acii and inhibits the pacemaker current If probably via the (3y-subunit of the Gi protein associated with this receptor. The results are hyperpolarization and slower spontaneous depolarization. Muscarinic receptor antagonists like atropine lead to increased heart rate and accelerated atrioventricular conduction. There are no or only slight effects on the ventricular electrophysiology. 

Enzymes 7,9, and 13 form a trifunctional protein associated with the inner face of the inner mitochondrial membrane. Very-long-chain acyl-CoA dehydrogenase is also associated with other inner mitochondrial membranes while the other enzymes are in the matrix and may be loosely associated with the inner face of the inner membrane. A medium-chain 2-enoyl-CoA hydratase may also be present in the mitochondrial matrix. 

The nuclear-encoded proteins are inserted into both inner and outer mitochondrial membranes, the intermembrane space, and the matrix and there are several different mechanisms involved. As mentioned above there is no apparent requirement for a presequence on proteins which insert specifically into the mitochondrial outer membrane. For proteins destined for the inner mitochondrial membrane, a stop-transfer mechanism is proposed. Thus some information in the peptide must stop the complete transfer of the protein into the mitochondrial matrix, enabling the protein to remain in the inner mitochondrial membrane. For some proteins in the intermembrane space (for example the Rieske iron-sulphur protein associated with the outer face of complex III), a particularly complicated import pathway... 

Combination of the Perrin function, p often referred as the frictional ratio due to shape with the frictional ratio (f/fo) enables the degree of expansion of the molecule (vh/ w ) to be estimated, where Vh, (cw / g) is the volume of the swollen molecule (Polysaccharide or protein + associated solvent) per unit mass of polysaccharide and v is the partial specific volume (essentially the anhydrous molecule) ... 

Sheaffer AK, Newcomb WW, Gao M, Yu D, Weller SK, Brown JC, Tenney DJ (2001) Herpes simplex virus DNA cleavage and packaging proteins associate with the procapsid prior to its maturation. J Virol 75 687-698... 

Singh, N.K., Bracket, C.A.S., Hasegawa, P.M., Handa, A.K., Bruckel, S., Hermondson, M.A., Pfankoch, E., Regnier, F.E. Bressan, R.A. (1987o). Characterisation of osmotin. A Thaumatin-like protein associated with osmotic adaptation in plant cells. Plant Physiology, 85, 528-36. 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

The formation of the PIC described above is based on the sequential addition of purified components in in vitro experiments. An essential feature of this model is that the assembly takes place on the DNA template. Accordingly, transcription activators, which have autonomous DNA binding and activation domains (see Chapter 39), are thought to function by stimulating either PIC formation or PIC function. The TAF coactivators are viewed as bridging factors that communicate between the upstream activators, the proteins associated with pol II, or the many other components of TFIID. This view, which assumes that there is stepwise assembly of the PIC—promoted by various interactions between activators, coactivators, and PIC components— is illustrated in panel A of Figure 37-10. This model was supported by observations that many of these proteins could indeed bind to one another in vitro. 

In principle, the use of addressable, pooled GST fusion proteins could be used to identify proteins associated with any biochemical activity, assuming that the fusion protein is soluble, folded and functional. The method has the additional advantage that, once the GST fusion clones are constructed, it is a rapid technique. The authors state that only two weeks are required to purify the 64 pools and the assays can be accomplished in a day (Martzen et al., 1999). In addition, the method is sensitive because only 96 recombinant proteins are assayed at one time in contrast to the use of cell lysates where thousands of proteins are present. This leads to a much higher concentration of each protein, which greatly facilitates detection of a biochemical activity (Martzen et al., 1999). 

Shackelton LM, Mann DM, Millis AJ 1995 Identification of a 38kDa heparin-binding glycoprotein (gp38k) in differentiating vascular smooth muscle cells as a member of a group of proteins associated with tissue remodeling. J Biol Chem 270 13076—13083... 

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