Multimer dimer

Before moving furtlier to tire multimer case we should outline one furtlier significant feature of a dimer. Dimer excited states have a well defined rotational strengtli [33, 34] ... 

With tlie development of femtosecond laser teclmology it has become possible to observe in resonance energy transfer some apparent manifestations of tire coupling between nuclear and electronic motions. For example in photosyntlietic preparations such as light-harvesting antennae and reaction centres [32, 46, 47 and 49] such observations are believed to result eitlier from oscillations between tire coupled excitonic levels of dimers (generally multimers), or tire nuclear motions of tire cliromophores. This is a subject tliat is still very much open to debate, and for extensive discussion we refer tire reader for example to [46, 47, 50, 51 and 55]. A simplified view of tire subject can nonetlieless be obtained from tire following semiclassical picture. 

The terms polypeptide and protein are used interchangeably in discussing single polypeptide chains. The term protein broadly defines molecules composed of one or more polypeptide chains. Proteins having only one polypeptide chain are monomeric proteins. Proteins composed of more than one polypeptide chain are multimeric proteins. Multimeric proteins may contain only one kind of polypeptide, in which case they are homomultimeric, or they may be composed of several different kinds of polypeptide chains, in which instance they are heteromultimeric. Greek letters and subscripts are used to denote the polypeptide composition of multimeric proteins. Thus, an ag type protein is a dimer of identical polypeptide subunits, or a homodimer. Hemoglobin (Table 5.1) consists of four polypeptides of two different kinds it is an hetero-multimer. 

Fig. 6-12. Different types of binding sites in polymers eontaining miero- (site B), meso- and maerop-ores (site A) C) Embedded site, D) Site eomplementary to dimer or multimer, E) Indueed binding site, E) Nonseleetive site, G) Residual template.

The ability of a solute to associate with itself can be expressed by the degree of association (/). The / is obtained by dividing the stoichiometric mole fraction of the solute by the effective mole fraction of the solute. Assuming that a single multimer species in equilibrium with a monomer is a dimer,/values range from 1.0 to 2.024). 

Sequence-specific transcription factors often bind as multimers especially as dimers to DNA. This allows binding of mirror-imaged sequences (palindromes) in the DNA that are separated by a few spacer nucleotides. The dimerization is stabilized by hydrophobic motifs within dimerization motifs of each transcription factor molecule. Dependent on the nature of the dimerization domain and the abundance of individual transcription factors homo- or heterodimers can form and bind to palindromes with differential activity. 

FIGURE 2.5 Schematic representation of hydrogen-bonded self-associative structures of higher fatty acids (a) cyclic associative dimer and (b) linear associative multimer. 

Rossotti and co-workers45 introduced the term "oligomers for dimers and even multimers or ra-mers in non-aqueous solutions real examples of such self-aggregates (non-hydrogen bonded) have been reported46 for quaternary ammonium thiocyanates, iodides and perchlorates with ra-mers with n even up to 20. 

The pJuFo system also has the potential to display homodimers or homomultimeric proteins on the surface of the phage. This is possible because the protein of interest is expressed independent of the phage proteins. Therefore, the Fos-ORF fusion protein is secreted to the periplasm, the Fos portion interacts with Jun to attach the protein to the phage, and other copies of the Fos-ORF protein can interact with each other to form a dimer or multimer. However, the successful display of homodimers has not been demonstrated in practice. 

The g-tensor principal values of radical cations were shown to be sensitive to the presence or absence of dimer- and multimer-stacked structures (Petrenko et al. 2005). If face-to-face dimer structures occur (see Scheme 9.7), then a large change occurs in the gyy component compared to the monomer structure. DFT calculations confirm this behavior and permitted an interpretation of the EPR measurements of the principal g-tensor components of the chlorophyll dimers with stacked structures like the P 00 special dimer pair cation radical and the P700 special dimer pair triplet radical in photosystem I. Thus dimers that occur for radical cations can be deduced by monitoring the gyy component. 

Gel-filtration analysis reveals bands of molecular mass 40-70 kDa. These represent dimers (and some multimers) of the IFN-y polypeptide. Its biologically active form appears to be a homodimer in which the two subunits are associated in an antiparallel manner. 

Enzymes may exist as simple monomers, or as homo- or heterodimers, or as multimers. In multimeric enzymes, each component monomer may possess a catalytic site alternatively, the catalytic site may be located at the interface between two or more monomers, or only one monomer of a heteromultimer may possess an active site. It is not uncommon in dimeric or multimeric enzymes containing two or more active sites for some degree of cooperativity to exist between the sites, with respect to the substrate binding or substrate turnover number (Monod et ah, 1965). 

Ions appearing at approximately twice the mass of the parent ion are known as multimers. These usually appear at (2M + H)" owing to the formation of a protonated dimer in the MS. 

As seen from above, the mode of electron trapping in sc CO2 cannot be deduced from the results obtained in the gas phase or matrix isolation studies. It is not obvious whether the solvent radical anion should be similar to multimer cluster anions found in the gas phase, dimer cation(s) in solid matrices, or monomer CO2 anions in inert liquids. Such a situation is typical for other molecular liquids. 

Hydrogen bonds are continually breaking and reforming by thermal agitation and, according to the association model, there exist instantaneous distributions of free monomers Bj, hydrogen-bonded dimers B2 and multimers Bj, which obey the reaction scheme ... 

Most transcription activators bind to DNA as a dimer or higher multimer (see 2.4). The dimerization relies on structural motifs which commonly occur in many different proteins. Examples for dimerization motifs are the helix-loop-hdix motif and the leucine zipper. The dimerization motifs permit the formation of DNA-boimd homodimers or heterodimers, depending upon whether the same or different proteins interact with each other (Fig. 1.38). The different dimers have different requirements for the... 

The minimal functional unit (quite well conserved among all rubiscos) is a homodimer in which the active sites are located at the subunit interface. Residues from both subunits contribute to each active site, which is illustrated in Color Plate 8. All known forms (at present, four different types) consist of these basic dimeric units which are arranged into various larger multimer arrays—dimers, tetramers and even pentamers. The different forms of rubisco all have a common evolutionary origin and existing solid-state structures of the active sites are nearly superimposable. ... 

Several lines of evidence demonstrate that the active unit of integrase is a multimer. It is clear, as an isolated protein in solution, that integrase forms dimers [6,10-12], and it has been shown by sedimentation equilibrium studies that Rous sarcoma virus (RS V) integrase exists in reversible equilibrium between monomeric, dimeric, and tetrameric forms [13]. Protein-protein cross-linking studies of HIV-1 [14] and RSV [15] integrases confirm the existence of protein dimers and tetramers in solution, and in vivo, the yeast GAL4 two-hybrid system has demonstrated that HIV-1 integrase can interact with itself [16]. 

Complementation studies using mutant proteins in vitro provide compelling evidence that the active form of integrase must be at least a dimer [14, 17]. This can be inferred from the result that when certain inactive forms of integrase—generated either by truncation or point mutation—are mixed, robust activity can be reconstituted. This indicates that different monomers in a multimer are capable of providing different essential functions in the context of an active complex. 

It is important for us to keep in mind that biopolymers are generally not monodisperse components. Proteins are typically paucidisperse — mixtures of monomers, dimers and multimers. And polysaccharides are polydisperse their chain lengths and molar masses can be represented as a continuous distribution. For this reason the virial coefficients appearing in equations (5.16) and (5.17) should be interpreted as averages. So the inverse of the number-averaged molar mass of component / is given by... 

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