Interaction dimeric

The change in the quaternary structure and the structural change in the 6-F helix as the molecule moves from one state to the other are intimately related. The dimer interactions in the T state are not compatible with the presence of the 6-F helix, which would, if present, clash with the neighbouring dimer. The quaternary structure of the T state requires that the 6-F helix be unwound. Conversely the R state quaternary structure depends on the presence of the 6-F helix. 

Figure 8.4 Cro molecules from bacteriophage lambda form dimers both in solution and in the crystal structure. The main dimer interactions ate between p strands 3 from each subunit. In the diagram one subunit is green and the other is brown. Alpha helices 2 and 3, the helix-turn-helix motifs, are colored blue and red, respectively, in both subunits. (Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.)...

Two such dimers form the tetramer through mainly hydrophobic interactions between the a helices. The p strands are on the outside of the tetramer and are not involved in the dimer-dimer interactions. The arrangement of the four a helices is unusual and provides a rare example of four a helices packed against each other in a way different from the four-helix bundle motif. 

The two zinc ions fulfill important but different functions in the DNA-binding domains. The first zinc ion is important for DNA-bindlng because it properly positions the recognition helix the last two cysteine zinc ligands are part of this helix. The second zinc ion is important for dimerization since the five-residue loop between the first two cysteine zinc ligands is the main component of the dimer interaction area. 

Residues 50-64 of the GAL4 fragment fold into an amphipathic a helix and the dimer interface is formed by the packing of these helices into a coiled coil, like those found in fibrous proteins (Chapters 3 and 14) and also in the leucine zipper families of transcription factors to be described later. The fragment of GAL4 comprising only residues 1-65 does not dimerize in the absence of DNA, but the intact GAL4 molecule does, because in the complete molecule residues between 65 and iOO also contribute to dimer interactions. 

Leucine zippers provide dimerization interactions for some eucaryotic transcription factors... 

Nagano, K., and Tsuji, F. I. (1990). Dimeric interaction of calcium-binding photoprotein aequorin. In Rivier, J. E., and Marshall, G. R. (eds.), Pept. Chem., Struct. Biol., Proc. Am. Pept. Symp., 11th, 1989, pp. 508-509. ESCOM Sci. Pub., Leiden, Netherland. 

Detailed analysis of the lambda repressor led to the important concept that transcription regulatory proteins have several functional domains. For example, lambda repressor binds to DNA with high affinity. Repressor monomers form dimers, dimers interact with each other, and repressor interacts with RNA polymerase. The protein-DNA interface and the three protein-protein interfaces all involve separate and distinct domains of the repressor molecule. As will be noted below (see Figure 39—17), this is a characteristic shared by most (perhaps all) molecules that regulate transcription. 

In the literature, LB films of chlorophyll a have been investigated by many techniques [21,27,28]. In particular, Chapados et al. [29] have studied the aggregation state of chlorophyll a in LB films with electronic and infrared spectroscopies. Their results suggest many points. First, immediately after the fabrication of the film (time zero) the ketone group C = 0 of one chlorophyll a molecule links to the magnesium of an adjacent chlorophyll a molecule to form a dimer. Each dimer interacts via water with another dimer to... 

Schiitz, M., Brdarski, S., Widmark, P.-O., Lindh, R., Karlstrom, G., 1997, The Water Dimer Interaction Energy Convergence to the Basis Set Limit at the Correlated Level , J. Chem. Phys., 107, 4597. 

FIGURE 5-11 Ribbon diagram of an NBD dimer (PDB 160). 3 strands are depicted as arrows and a helices as coiled ribbons. The two nucleotides, shown as stick models, bind to form part of the interface that stabilizes the dimeric interaction. (With permission from Fig. 5 of reference [88].)... 

A recent crystal structure based model [20] for the structure of C-cadherin postulates that the five extracellular domains EC1-EC5 protrude from the cell surface as a curved rod. The structural analysis of C-cadherin reveals that the molecules facing each other across apposed cell surfaces are antiparallel to one another, forming a dimeric interaction termed a strand dimer (Fig. 7-5). This forms the functional unit that is likely to mediate adhesion between cell surfaces. The structure from this recent paper allows the prediction of both cis and trans interfaces that together result in a lattice and not, as previously believed, an adhesion zipper. This new model allows for a mechanism by which adhesion plates or puncta might be generated, such as are formed at CNS synapses [21, 22], adherens junctions and desmosomes [23], all cadherin based organelles. 

Contrary to all other reactions with acids the behaviour of the zwitterion towards vapours of formic acid is intriguing, since no proton transfer is observed. The formic acid vapour uptake generates a material composed of pairs of zwitterion molecules, linked by O-H- - O bonds between the protonated -COOH and the deprotonated -COO() groups [0---0 separation 2.526(4) A] residing on the organometallic moiety. The zwitterion dimers interact with two formic acid molecules via 0-H---0 and C-H---0 hydrogen bonds [0---0 distance 2.541(4),... 

Fig. 63. Departures from local 2-fold symmetry, especially of side chain positions, in the j8 strand dimer interaction of insulin. From Blundell et al. (1972), with permission.

The theory had never been tested on a logical model system. Let us consider in detail one representative case, the superimposable stacking of the two benzene rings, one from each triplet diphenylcarbene molecule. These are considered to represent idealized modes of dimeric interaction of the aromatic ring parts of open-shell molecules in ordered molecular assemblies like crystals, liquid crystals and membranes. 

It is not widely appreciated that the major aspects of core histone interactions were well understood even before the development of the nucleosome model. Evidence for strong H2A H2B dimer interactions and an FI3 H4 tetramer was available in the early seventies (see Ref. [1], Chapter 2). By 1978, the rigorous sedimentation equilibrium studies from Moudrianakis laboratory had elucidated the thermodynamics of octamer formation [7]. What was missing, of course, was any structural information concerning these interactions. This was overcome by arduous X-ray diffraction studies, culminating in the elegantly detailed structures we have today [15,17,18], see also Flarp et al., this volume, p. 13. We now know how the core... 

The active site pocket is defined by a deep channel formed in part by dimer interactions (Fig. 5). Access to the L-Arg binding pocket is open, and there appears to be little need for conformational aijjustments to... 

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