Molecular recognition structures

Keywords Hydrogen bond, Supramolecular synthesis. Molecular recognition. Structure comparison, Structure prediction. 

Supramolecular chemistry (molecular recognition, structure and assembly, and functional systems) 06AR(B)148. 

Murata, T., Morita, Y, Yakiyama, Y, Fukui, K., Yamochi, H., Saito, G., and Nakasuji, K. 2007. Hydrogen-bond interaction in organic conductors Redox activation, molecular recognition, structural regulation, and proton transfer in donor-acceptor charge-transfer complexes of TTF-imidazole. /. Am. Chem. Soc. 129 10837-10846. 

EMPl, selected by phage display from random peptide libraries, demonstrates that a dimer of a 20-residue peptide can mimic the function of a monomeric 166-residue protein. In contrast to the minimized Z domain, this selected peptide shares neither the sequence nor the structure of the natural hormone. Thus, there can be a number of ways to solve a molecular recognition problem, and combinatorial methods such as phage display allow us to sort through a multitude of structural scaffolds to discover novel solutions. 

Another example of the shape similarity effect on molecular recognition involves the similarity between the structures of the binding sites. Investigation was made for four reaction systems I-IV each consisting of a 1 1 mixture of thiols HS—X and HS—Y... 

Proteins derive their powerful and diverse capacity for molecular recognition and catalysis from their ability to fold into defined secondary and tertiary structures and display specific functional groups at precise locations in space. Functional protein domains are typically 50-200 residues in length and utilize a specific sequence of side chains to encode folded structures that have a compact hydrophobic core and a hydrophilic surface. Mimicry of protein structure and function by non-natural ohgomers such as peptoids wiU not only require the synthesis of >50mers with a variety of side chains, but wiU also require these non-natural sequences to adopt, in water, tertiary structures that are rich in secondary structure. 

Efforts to investigate the questions posed here will lead to more useful peptoid designs while simultaneously leading to a better fundamental understanding of molecular recognition and sequence/structure/function relationships in non-natural, sequence-specific peptidomimetic ohgomers. 

Finally, to produce the structural and functional devices of the cell, polypeptides are synthesized by ribosomal translation of the mRNA. The supramolecular complex of the E. coli ribosome consists of 52 protein and three RNA molecules. The power of programmed molecular recognition is impressively demonstrated by the fact that aU of the individual 55 ribosomal building blocks spontaneously assemble to form the functional supramolecular complex by means of noncovalent interactions. The ribosome contains two subunits, the 308 subunit, with a molecular weight of about 930 kDa, and the 1590-kDa 50S subunit, forming particles of about 25-nm diameter. The resolution of the well-defined three-dimensional structure of the ribosome and the exact topographical constitution of its components are still under active investigation. Nevertheless, the localization of the multiple enzymatic domains, e.g., the peptidyl transferase, are well known, and thus the fundamental functions of the entire supramolecular machine is understood [24]. 

Afshar M., Hubbard R. and Demaille J. (1998). Towards structural models of molecular recognition in olfactory receptors. Biochimie 80, 129-135. 

These are considered to be functionally competent protein domains owing to their ability to maintain their structure and molecular recognition properties independent of the full-length protein (Cohen GB, Ren R, Baltimore D. Modular binding domains in signal transduction proteins. Cell 1995 80 237-248). 

---