Secondary structure stability

Dolinnaya NG, Fresco JR (1992) Single stranded nucleic acid helical secondary structure stabilized by ionic bonds d(A -G)10. Proc Natl Acad Sci USA 89 9242-9246... 

Until very recently, the a-helical conformation with 3.6 residues per turn (Figure 2(a)) was considered to be exclusive of poly(a-peptide)s. In these last two decades it has been demonstrated however that poly(j8-peptide)s, specifically those derived from aspartic acid, are also well suited for adopting folded secondary structures stabilized by intramolecular hydrogen bonds [7,8]. In these... 

Proteins have complex molecular structures. The linear sequence of the amino acids comprising a protein is classified as its primary structure. In different proteins, these linear sequences assume conserved structures along the axis of the polypeptide in the form of alpha-helixes, 3j -helix, beta sheets, or random coils, turns which are described as the secondary structure of the protein. These secondary structures are stabilized primarily by hydrogen bonds. For thermodynamic stability, proteins rearrange themselves into tertiary structures comprising several secondary structures stabilized by van der Waal s, electrostatic, or hydrophobic interactions, hydrogen bonding, as well as disulfide cross-links. Some proteins have a fourth structural level called the quaternary structure in which two or more... 

Short-chain alcohols showed the same behavior. The melting temperature of DNA decreases in water/methanol solutions [65]. Furthermore, the midpoint of the solvent denaturation decreased in the order methanol, ethanol and propanol that is, the secondary structure stability was lowered as the length of the aliphatic chain was increased [65]. Following the same line, in another contribution it was realized that an increase in the number or size of alkyl substituents on amides, ureas, carbamates and alcohols increased the denaturating effectiveness towards DNA [61]. The contribution of non-specific hydrophobic interactions to DNA denaturation was then brought up, and in fact it is not surprising that these small hydrophobic molecules... 

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

Section 27 19 Two secondary structures of proteins are particularly prominent The pleated sheet is stabilized by hydrogen bonds between N—H and C=0 groups of adjacent chains The a helix is stabilized by hydrogen bonds within a single polypeptide chain... 

Secondary structure refers to the shape of the molecule as a whole, particularly to those aspects of structure which are stabilized by intramolecular hydrogen bonds. 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

The secondary structures we have described here are all found commonly in proteins in nature. In fact, it is hard to find proteins that do not contain one or more of these structures. The energetic (mostly H-bond) stabilization afforded by a-helices, /3-pleated sheets, and /3-turns is important to proteins, and they seize the opportunity to form such structures wherever possible. 

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. 

Figure 26.5 (a) The o-helical secondary structure of proteins is stabilized by hydrogen bonds between the N—H group of one residue and the C=0 group four residues away, (b) The structure of myoglobin, a globular protein with extensive helical regions that are shown as coiled ribbons in this representation. 

Natural mutation of amino acids in the core of a protein can stabilize the same fold with different complementary amino acid types, but they can also cause a different fold of that particular portion. If the sequence identity is lower than 30% it is much more difficult to identify a homologous structure. Other strategies like secondary structure predictions combined with knowledge-based rules about reciprocal exchange of residues are necessary. If there is a reliable assumption for common fold then it is possible to identify intra- and intermolecular interacting residues by search for correlated complementary mutations of residues by correlated mutation analysis, CMA (see e.g., http //www.fmp-berlin.de/SSFA). 

Such differences in the secondary structure behavior with respect to temperature can be explained by suggesting that molecular close packing of proteins in the film is the main parameter responsible for the thermal stability. In fact, as in the case of BR, we have close packing of molecules even in the solution (membrane fragments) there are practically no differences in the CD spectra of BR solution at least tiU 75°C (denaturation takes place only for the sample heated to 90°C). RC in solution begins to be affected even at 50°C and is completely denatured at 75°C, for the solution contains separated molecules. 

Comparative study of LB films of cytochrome P450 wild type and recombinant revealed similar surface-active properties of the samples. CD spectra have shown that the secondary structure of these proteins is practically identical. Improved thermal stability is also similar for LB films built up from these proteins. Marked differences for LB films of wild type and recombinant protein were observed in surface density and the thickness of the deposited layer. These differences can be explained by improved purity of the recombinant sample. In fact, impurity can disturb layer formation, preventing closest packing and diminishing the surface density and the average monolayer thickness. Decreased purity of... 

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