Proteins dimeric

DIffey W M, Homoelle B J, Edington M D and Beck W F 1998 Excited-state vibrational coherence and anisotropy decay In the bacterlochlorophyll a dimer protein B820 J. Phys. Chem. B 102 2776-86... 

Some of the procaryotic DNA-binding proteins are activated by the binding of an allosteric effector molecule. This event changes the conformation of the dimeric protein, causing the helix-tum-helix motifs to move so that they are 34 A apart and able to bind to the major groove. The dimeric repressor for purine biosynthesis, PurR, induces a sharp bend in DNA upon binding caused by insertion of a helices in the minor groove between the two... 

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

A dimeric protein which can exist in eidier of two. state.s Rq and Tq. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

Cann, J.R., Models of mobility-shift assay of complexes between dimerizing protein and DNA, Electrophoresis, 18, 1092, 1997. 

Figure 3.7 The crystal structure of DtxR, a 226-residue three-domain dimeric protein, is shown. The protein, activated by cobalt (designated 1 and 2), is bound to a 21-bp DNA duplex based on the consensus operator sequence. Two DtxR dimers surround the DNA duplex, which is distorted compared to canonical B-DNA. Only domain 1, involved in DNA-binding, and domain 2, involved in dimer formation, are shown. The helices of the DNA-binding domain are indicated by HI, H2, and H3. H3 binds to the major groove of the DNA. From Pohl et al., 1999, by permission of Academic Press. 

Maragliano, L. Ferrario, M. Ciccotti, G., Effective binding force calculation in dimeric proteins, Mol. Simul. 2004, 30, 807-816... 

Thymidylate Synthase (TS) is a 70 kDa dimeric protein that catalyzes the conversion of 2 -deoxyuridine 5 -monophosphate (dUMP) into 2 -deoxythymidine 5 -monophosphate (dTMP) using 5,10-methylene-5,6,7,8-tetrahydrofolate as cofactor. Inhibitors of TS represent potential... 

The most extensively studied alcohol dehydrogenases are those of mammalian liver. They are dimeric proteins, with each subunit binding two Zn2+ ions, only one of which is catalytically active. This catalytic Zn2+ ion has distorted tetrahedral geometry, coordinated to one histidine and two cysteine residues. The non-catalytic zinc plays a structural role and is coordinated tetrahedrally to four cysteine residues. 

CuIV would allow the two-electron reduction of N20. Good electron-transfer pathways exist from the neighbouring CuA centre in the second subunit of the dimeric protein to Cu and CuIV, to allow rapid re-reduction of the Cuz centre. 

Etanercept (Enbrel, Immunex) is a dimerized protein molecule that consists of a portion of the tumor necrosis factor receptor coupled to the Fc portion of human IgGl (see Section 4.3). It has 934 amino acids and a molecular weight of approximately 150 kDa. 

Figure 1. Derivation of the MWC ligand saturation equation for a dimeric protein.

Figure 2. Top Effect of the magnitude of the allosteric constant on ligand saturation behavior of a dimer obeying the MWC model. Bottom Fraction of total dimeric protein present in various T- and R-species.

A recently characterized single-domain copper protein, auracyanin (Trost et al., 1988), is a dimeric protein which has a visible spectrum more like that of the A. faecalis cupredoxin (pseudoazurin, subgroup II see Table II) than that of either azurin or plastocyanin, but, because of its cysteine content and rhombic EPR, it has been put in the other class in Table II. 

The nature of the copper in these proteins is not totally clear. Dooley et al (1988) reported that the Achromobacter protein may have two kinds of type I sites in a total of three copper sites per dimeric protein, while the A. faecalis protein was reported to be a tetrameric protein with both type I and type II coppers (KakutanielaZ., 1981). Interestingly, the Achromobacter protein is green. Both of these nitrite reductases accept electrons from a cupredoxin. 

In some cases, the ligand itself has a dimeric structure and induces formation of active receptor dimers on binding to the receptor. One example is PDGF, which exists as a disulfide bridge-linked dimeric protein. 

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