Proteins tertiary structure, molecular interaction

It is very interesting that large molecules, such as proteins, behave as particles and can be described by ultrasound scattering theory in the very long wavelength limit. Scattering theory is vindicated by the precise and repeatable nature of the data available for these molecules. In particular, it should be pointed out that the molecular adiabatic compressibility is insensitive to individual bonds and is the sum of the intrinsic compressibility of the primary structure (the amino acid sequence), cavities in the tertiary structure and interaction with the solvent (Kharakoz and Sarvazyan, 1993). Velocity and attenuation spectroscopy relate to different aspects of the molecule... 

Metalloproteins constitute a distinct subclass of proteins that are characterized by the presence of single or multiple metal ions bound to the protein by interactions with nitrogen, sulfur, or oxygen atoms of available amino acid residues or are complexed by prosthetic groups, such as heme, that are covalently linked to the protein. These metals function either as catalysts for chemical reactions or as stabilizers of the protein tertiary structure. Protein-bound metals may also be labile and, as such, be subject to transport, transient storage, and donation to other molecular sites of requirement within tissues and cells. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

From the atomic to the macroscopic level chirality is a characteristic feature of biological systems and plays an important role in the interplay of structure and function. Originating from small chiral precursors complex macromolecules such as proteins or DNA have developed during evolution. On a supramolecular level chirality is expressed in molecular organization, e.g. in the secondary and tertiary structure of proteins, in membranes, cells or tissues. On a macroscopic level, it appears in the chirality of our hands or in the asymmetric arrangement of our organs, or in the helicity of snail shells. Nature usually displays a preference for one sense of chirality over the other. This leads to specific interactions called chiral recognition. 

Several laboratories have described systems by which synthetic linear peptide chains self-assemble into desirable secondary and tertiary structures. One self-assembly approach has been the creation of a peptide-amphiphile, whereby a peptide head group has the propensity to form a distinct structural element, while a lipophilic tail serves to align the peptide strands and induce secondary and tertiary structure formation, as well as providing a hydrophobic surface for self-association and/or interaction with other surfaces. The preparation of a dialkyl ester tail first involves the acid-catalyzed condensation of H-Glu-OH with the appropriate fatty acid alcohol to form the dialkyl ester of H-Glu-OH a typical example is shown in Scheme 7. The assembly of peptide-amphiphiles with mono- and dialkyl ester tails is shown in Scheme 8. A series of studies have demonstrated that triple-helical and a-helical protein-like molecular architecture is stabilized in the peptide-amphiphile 44,63-65 ... 

One of the problems with DNA is that it is essentially a linear code that stores information. The functional groups (nucleotides) only interact with each other and, while this can lead to the elegant double helix, it limits the ability of DNA to form different secondary and extensive tertiary structures. RNA is rather more amenable to forming other structural motifs, hence the RNA World theory of molecular evolution, but it appears that only proteins with their varied side chains are able to adopt truly complex structures. 

The ribosomal RNAs are involved in multiple molecular interactions with both protein factors and other RNAs in addition to having an extensive intramolecular secondary structure of their own. These interactions involve not only particular sequence domains but also recognition of secondary and tertiary structural features of the RNA molecule.1-12 Un-... 

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