Small protein binding

Rubber also contains almost entirely Z double bonds. Consistent with this fact is the finding that the prenyltransferases catalyzing formation of rubber promote loss of the pro-R proton rather than the pro-S proton of mevalonic acid (see Eq. 22-2). There appear to be two types of prenyltransferase in animal mitochondria giving rise to E and Z double bonds, respectively.64 In contrast, the rubber tree contains a 137-residue protein, the rubber elongation factor. This small protein binds to E prenyltransferases causing them to form Z double bonds.65 The bacterium Micrococcus hit cits synthesizes all E polyprenyl alcohol diphosphates up to the 0 5 nonaprenyl compound solanesyl diphosphate.66... 

Interferon alfa-n3 is an immnnomodnlator. These small proteins bind to specific cell membranes and initiate complex seqnences, intracellnlar events, inclnding induction of certain enzymes that prodnce antiproliferative action against tumor cells and inhibit viral replication in virus-infected cells. They are used in the treatment of condyloma acuminatum. 

Figure 2.19 Organization of polypeptide chains into domains. Small protein molecules like the epidermal growth factor, EGF, comprise only one domain. Others, like the serine proteinase chymotrypsin, are arranged in two domains that are required to form a functional unit (see Chapter 11). Many of the proteins that are involved in blood coagulation and fibrinolysis, such as urokinase, factor IX, and plasminogen, have long polypeptide chains that comprise different combinations of domains homologous to EGF and serine proteinases and, in addition, calcium-binding domains and Kringle domains.

In most four-helix bundle structures, including those shown in Figure 3.7, the a helices are packed against each other according to the "ridges in grooves" model discussed later in this chapter. However, there are also examples where coiled-coil dimers packed by the "knobs in holes" model participate in four-helix bundle structures. A particularly simple illustrative example is the Rop protein, a small RNA-binding protein that is encoded by certain plasmids and is involved in plasmid replication. The monomeric sub unit of Rop is a polypeptide chain of 63 amino acids built up from two... 

There is a second family of small lipid-binding proteins, the P2 family, which include among others cellular retinol- and fatty acid-binding proteins as well as a protein, P2, from myelin in the peripheral nervous system. However, members of this second family have ten antiparallel p strands in their barrels compared with the eight strands found in the barrels of the RBP superfamily. Members of the P2 family show no amino acid sequence homology to members of the RBP superfamily. Nevertheless, their three-dimensional structures have similar architecture and topology, being up-and-down P barrels. 

Five of the six loop regions (G1-G5 in Figure 13.4) that are present at the carboxy end of the p sheet in the Ras structure participate in the GTP binding site. Three of these loops, G1 (residues 10-17), G3 (57-60), and G4 (116-119), contain regions of amino acid sequence conserved among small GTP-binding proteins and the Ga subunits of trimerlc G proteins. 

It is now apparent that bacteria have developed resistance to heavy metals and the detoxifying process is initiated and controlled by metallo-regulatory proteins which are able selectively to recognize metal ions. MerR is a small DNA-binding protein which displays a remarkable sensitivity to Hg +. The metal apparently binds to S atoms of cysteine and this has been a major incentive to recent work on Hg-S chemistry. 

They also bind small molecules and can be involved in protein-protein interactions. PAS domains in other proteins commonly function either as protein interaction sites or small molecule binding domains. Occasionally,... 

In principle, any type of NMR spectroscopy may be used to detect the chemical shift changes upon ligand binding. For very small proteins, 1D-NMR might even... 

Rapamycin is a macrocyclic lactone produced by Streptomyces hygroscopious. This bacterium was originally cultured from a soil sample collected on Easter Island (known locally as Rapa Nui hence the name rapamycin). Parenthetically, rapamycin shares an interesting mode of action with two other antifungal and immunosuppressive compounds, FK506and cyclosporin A. Inside cells, rapamycin first binds to FKBP12, a small protein receptor known as an immunophilin. FKBP12 is not an essential protein but is an important cofactor required for rapamycin to bind and inhibit TOR. 

The diversity of these subcellular actin structures is remarkable and appears to be determined by the interactions of many actin-binding proteins (ABPs) as well as by changes in the concentrations of intracellular signaling molecules such as Ca and cAMP, by small GTP-binding proteins, and by signals arising from mechanical stress. Approximately 50% of the actin molecules in most animal cells are unpolymerized subunits in the cytosolic pool and exist in a state of dynamic equilibrium with labile F-actin filamentous structures (i.e., new structures are formed while existing structures are renewed) (Hall, 1994). 

Hall, A. (1994). Small GTP-binding proteins and the regulation of the actin cytoskeleton. Ann. Rev. Cell Biol. 10,31-54. 

Ridley, A.J., Hall, A. (1992). The small GTP-binding protein rho regulates the assembly of focal adhesions and actin stress fibers in response to growth factors. Cell 70,389-399. 

Metallothioneins are a group of small proteins (about 6.5 kDa), found in the cytosol of cells, particularly of liver, kidney, and intestine. They have a high content of cysteine and can bind copper, zinc, cadmium, and mercury. The SH groups of cysteine are involved in binding the metals. Acute intake (eg, by injection) of copper and of certain other metals increases the amount (induction) of these proteins in tissues, as does administration of certain hormones or cytokines. These proteins may function to store the above metals in a nontoxic form and are involved in their overall metaboHsm in the body. Sequestration of copper also diminishes the amount of this metal available to generate free radicals. 

The HIV-1 coreceptors CXCR4 and CCR5 bind to ligand members of a family of molecules known as chemokines, or chemotactic cytokines. While the hallmark function of these small proteins is the direction of leukocyte trafficking, they can also participate in cellular events such as activation and costimulation (Bajetto et al. 2(X)la). Members of the chemokine family can be classified as either homeostatic or inflammatory based on their temporal expression (Charo and Ransohoff 2006 Kim 2005). Although traditionally the CNS had been thought to be protected from immune acti-... 

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