Tertiary structure, stabilization

R. H., Draper, D. E. The RNA-binding domain of ribosomal protein Lll recognizes an rRNA tertiary structure stabilized by both fhiostrepton and magnesium ion. Nucleic Adds Res 2000, 28, 1778—... 

Klostermeier, D., and Millar, D. P. (2001). Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms Different energetic contributions from a ribose zipper motif. Biochemistry 40, 11211—11218. 

Leipply, D., and Draper, D. E. (2009). The dependence of RNA tertiary structure stability on Mg(2+) concentration Interpretation of the Hill equation and coefficient (submitted). 

Tertiary structure also refers to the overall shape of a molecule, especially to structures stabilized by disulfide bridges (cystine) formed by the oxidation of cysteine mercapto groups. 

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

The immunoglobulin structure in Figure 6.45 represents the confluence of all the details of protein structure that have been thus far discussed. As for all proteins, the primary structure determines other aspects of structure. There are numerous elements of secondary structure, including /3-sheets and tight turns. The tertiary structure consists of 12 distinct domains, and the protein adopts a heterotetrameric quaternary structure. To make matters more interesting, both intrasubunit and intersubunit disulfide linkages act to stabilize the discrete domains and to stabilize the tetramer itself. 

A correlation of enhanced synthesis of polyamines with rapid growth or cell proliferation has been observed 21. From a physiological point of view, polyamines are implicated as regulators of cell proliferative activity 22). It is well known that polyamines, as protonated polycations, can bind with nucleotide and nucleic acid anions 23 241 to affect biochemical reactivities and stabilize tertiary structures 25,26). 

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

The three-dimensional conformation of a protein is called its tertiary structure. An a-helix can be either twisted, folded, or folded and twisted into a definite geometric pattern. These structures are stabilized by dispersion forces, hydrogen bonding, and other intermo-lecular forces. 

Covalent bridging of biopolymers is one of the widely occurring prindples in nature for increasing the stability of the tertiary structure, for example the disulfide bridges in keratin and ribonuclease. 

It is well known that native collagen containes tripeptide sequences, which alone are not capable of building up a triple helix (e.g. Gly-Pro-Leu, Gly-Pro-Ser) when they exist as homopolypeptides. The synthesis of threefold covalently bridged peptide chains opens up the possibility of investigating the folding properties of such weak helix formers, because the bridging reduces the entropy loss during triple-helix formation and thereby increases the thermodynamic stability of the tertiary structure. Therefore, we have... 

The S-S bond between two divalent sulfur atoms plays an important role as the main stabilizer of the tertiary structure of many proteins. The simplest chemically stable compounds of this class are HSSH and CH3SSCH3. The structures of these two disulfanes have been established by microwave spectroscopy and electron diffraction experiments. 

In a first step towards the design of / -peptides tyligomers (oligomers that fold into predictable tertiary structures [8]), carefully controlled interhelical hydrophobic interactions have been utilized to stabilize a / -peptide two-helix bundle (92) [179] (Fig. 2.17). 

C13-0124. Design a protein containing ten amino acids whose tertiary structure would be roughly spherical with a hydrophobic interior and a hydrophilic exterior. Include one S—S bridge that would help stabilize the structure. 

An anthocyanin occurs in solution as a mixture of different secondary structures, a quinonoidal base, a carbinol pseudobase, and a chalcone pseudobase. ° hi addition, different mechanisms for the stabilization of anthocyanins lead to the formation of tertiary structures such as self-association, inter-, and intra-molecular co-pigmentation. ... 

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