Binding monomers

Commonly, new non-covalent MIPs are designed using a generic approach where the functional groups on the binding monomers are chosen according to their complementarity with the chemical groups of the template. In order to... 

The simulations also revealed that flapping motions of one of the loops of the avidin monomer play a crucial role in the mechanism of the unbinding of biotin. The fluctuation time for this loop as well as the relaxation time for many of the processes in proteins can be on the order of microseconds and longer (Eaton et al., 1997). The loop has enough time to fluctuate into an open state on experimental time scales (1 ms), but the fluctuation time is too long for this event to take place on the nanosecond time scale of simulations. To facilitate the exit of biotin from its binding pocket, the conformation of this loop was altered (Izrailev et al., 1997) using the interactive molecular dynamics features of MDScope (Nelson et al., 1995 Nelson et al., 1996 Humphrey et al., 1996). 

Block copolymers are closer to blends of homopolymers in properties, but without the latter s tendency to undergo phase separation. As a matter of fact, diblock copolymers can be used as surfactants to bind immiscible homopolymer blends together and thus improve their mechanical properties. Block copolymers are generally prepared by sequential addition of monomers to living polymers, rather than by depending on the improbable rjr2 > 1 criterion in monomers. 

Fig. 25. Schematic representation of imprinting (a) cross-linking polymerization ia the presence of a template (T) to obtain cavities of specific shape and a defined spatial arrangement of functional groups (binding sites. A—C) (b) cross-linked polymer prepared from the template monomer and ethylene...

Many proteins frequendy require the assistance of other protein molecules called molecular chaperonins, for assuming the fine tertiary stmcture in vivo. In E. coli, two such chaperonin molecules bind transientiy to newly synthesized polypeptide monomers, preventing them from aggregating prematurely, until the polypeptides attain their folded state (10). 

Figure 8.6 The N-terminal domain of lambda repressor, which binds DNA, contains 92 amino acid residues folded into five a helices. Two of these, a2 (blue) and a3 (red) form a helix-turn-hellx motif with a very similar structure to that of lambda Cro shown In Figure 8.4. The complete repressor monomer contains in addition a larger C-termlnal domain. (Adapted from C. Pabo and M. Lewis, Nature 298 443-447, 1982.)...

Monomers of homeodomain proteins bind to DNA through a helix-turn-helix motif... 

The homeodomain frequently binds to DNA as a monomer, in contrast to procaryotic DNA-binding proteins containing tbe belix-turn-helix motif, which usually bind as dimers. In vitro tbe homeodomain binds specifically to... 

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

How is the binding specificity of the heterodimer achieved compared with the specificity of Mat a2 alone The crystal structure rules out the simple model that the contacts made between the Mat a2 homeodomain and DNA are altered as a result of heterodimerization. The contacts between the Mat o2 homeodomain and DNA in the heterodimer complex are virtually indistinguishable from those seen in the structure of the Mat o2 monomer bound to DNA. However, there are at least two significant factors that may account for the increased specificity of the heterodimer. First, the Mat al homeodomain makes significant contacts with the DNA, and the heterodimeric complex will therefore bind more tightly to sites that provide the contacts required by both partners. Second, site-directed mutagenesis experiments have shown that the protein-protein interactions involving the... 

The ability of the leucine zipper proteins to form heterodimers greatly expands the repertoire of DNA-binding specificities that these proteins can display. As illustrated in Figure 10.19, for example, three distinct DNA-binding specificities could, in principle, be generated from two types of monomer, while six could be created from three types of monomer and so on. This is an example of combinatorial control, in which combinations of proteins, rather than individual proteins, control a cellular process. It is one of the most important mechanisms used by eucaryotic cells to control gene expression. 

Figure 10.19 Heterodimerization of leucine zipper proteins can alter their DNA-binding specificity. Leucine zipper homodimers bind to symmetric DNA sequences, as shown In the left-hand and center drawings. These two proteins recognize different DNA sequences, as indicated by the red and blue regions in the DNA. The two different monomers can combine to form a heterodimer that recognizes a hybrid DNA sequence, composed of one red and one blue region.

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