Helix formation and

Since these investigations could be carried out only in the crystalline state, the question of the dynamics of the triple-helix formation and of the correlation of its stability with the amino acid sequence could be answered only with the help of other methods working in solution. 

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... 

Figure A2.6 (a) Single strand nucleotide, (b) DNA in double helix formation, and (c) the pairing up of bases on two separate strands via hydrogen bonding to form the double helix.

C-terminal NC domain (NC2)." The deletion of the N-terminal NC domain (NCI) did not abolish the triple helix formation and subsequent association of two molecules into disulfide-bonded hexameric aggregates," an... 

N 116 "The Spatial Configuration of Ordered Polynucleotide Chains. I. Helix Formation and Base Stacking"... 

Further studies of the C-peptide showed that a helix is very strongly affected by pH, due to the presence of ionizable side chains. Helical stabilization occurs when favorable interactions can occur between ionized side chains and the helix dipole, and also when ionization can promote hydrogen bonding between side chains. In the case of C-peptide, two ionized groups (with p/fas near 3.5 and 6.5) promote helix formation and helix content follows a bellshaped curve, with a maximum near pH 5. 81 Increasing concentrations of salt (NaCl) also increases conformational stability. 98 ... 

Spin-lattice relaxation times and 13C chemical shifts were used to study conformational changes of poly-L-lysine, which undergoes a coil-helix transition in a pH range from 9 to 11. In order to adopt a stable helical structure, a minimum number of residues for the formation of hydrogen bonds between the C = 0 and NH backbone groups is necessary therefore for the polypeptide dodecalysine no helix formation was observed. Comparison of the pH-dependences of the 13C chemical shifts of the carbons of poly-L-lysine and (L-Lys)12 shows very similar values for both compounds therefore downfield shifts of the a, / and peptide carbonyl carbons can only be correlated with caution with helix formation and are mainly due to deprotonation effects. On the other hand, a sharp decrease of the 7] values of the carbonyl and some of the side chain carbons is indicative for helix formation [854]. 

Several approaches have been adopted for elucidating the factors involved in helix formation and stability. Perhaps the simplest approaches of these are the statistical approaches as typified by the Chou-Fasman... 

Tepper HL, Voth GA (2005) A coarse-grained model for double-helix molecules in solution, Spontaneous helix formation and equilibrium properties. J. Chem. Phys. 122 124909... 

Wang G, Seidman MM, Glazer PM. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science 1996 271(5250) 802-5. 

Polypeptide (a) is comprised largely of amino acid residues with small side chains. Except for Ala, none of the residues favors helix formation, and Gly destabilizes the a helix. Thus, this polypeptide is more likely to form j3 structures. 

About two thirds of the distance into the CCD of vertebrate dysbindin-1, there is a sequence of about 4—6 aa in which the probability of forming a coiled coil drops sharply ( Figures 2.2-3 and O 2.2-4). Those amino acids appear to constitute what is called a stutter in an alpha helix, which may actually facilitate alpha helix formation and stable coupling with other such helices (Cohen and Parry Brown et al., 1996 Lupas and Gruber, 2005). Using the terminology of Nazarian et al. (2006), we designate the CCD before the stutter as helix 1 (HI) and the remainder of the CCD after the stutter as helix 2 (H2)... 

The NMR studies of nucleic acids can yield information about base sequences, conformations in solution, helix formation, and hydrogen bonding between base pairs. 

Helicity of the polymers in DMSO was observed to be lower than in DMF. This may be explained by the fact that the hydrogen bonds are destroyed by DMSO molecules. The addition of EG to DMSO promotes the helix formation, and the bo value in DMSO-EG (3/2, v/v) approaches the value obtained in DMF. 

Peptide models of a-helices have revealed much about the intrinsic and extrinsic factors that control helix formation in peptides and proteins (1-5). While considerable progress has been made in our understanding of helix formation and stabilization, the same cannot be said of the situation regarding two other important classes of secondary structure p-sheets and p-tums. The reason for this is that there has not yet been a p-sheet model developed that is as simple to prepare and as easy to characterize as a monomeric helix. 

DFPQIMRIKPHQGQHIGE) but not the linear control (PQIMRIKPEIQGQHIGE) competed for receptor binding. The addition of 2, 2, 2-trifluoroethanol to an aqueous solution of cyclo-VEGI stabilized helical conformations in the 1-8 domain. This was unexpected because P-sheet structures and random coil conformations are those observed in macrocyclic peptides. In cyclo-VEGI, Pro-2 induces helix formation and Pro-9 breaks the 1-8 helical domain. 

Figure 1.15 Double-helix formation and entropy. When solutions containing DNA strands with complementary sequences are mixed, the strands react to form double helices. This process results in a loss of entropy from the system, indicating that heat must be released to the surroutrdings to avoid violating the Second Law of Thermodynamics.

Karle, I. L. (2001) Controls exerted by the Aib residue Helix formation and helix reversal. Biopolymers 60, 351-365. 

Many details of this mechanism remain to be determined, but, even in schematic form, it explains several observations. Fig. 5 (see p. 289) and the accompanying text suggest that double-helix formation, and therefore gelation, would be completely blocked by the presence of D-galactose 6-sulfate or 2,6-disulfate in place of a 3,6-anhydride... 

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