Helix 4, stabilization

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

Vila, J. A., Ripoll, D. R., and Scheraga, H. A. (2000). Physical reasons for the unusual a helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sd. USA 97, 13075-13079. 

Hg2 + selectively binds the AT region, apparently due to its great affinity for thymine. Thus, Hg2+ interacts with DNA at nitrogen atoms, replacing hydrogen between the thymine and adenine bases [114]. This interaction results in increased helix stability and an increased diameter of the double helix, approximating the difference between the atomic radius of hydrogen and mercury [116]. 

Hydrogen bonding is a critical part of triple helix stabilization. The triple helix has repetitive backbone hydrogen-bonding networks, but differs from j3 sheets or a helices in that the repeating tripeptide unit consists... 

Table 5 Helix stabilization energies (kcal mol for substituted oPE hexamers calculated with MMFF... 

S. Hildbrand and C. Leumann, Enhancing DNA triple helix stability at neutral pH by the use of oligonucleotides containing a more basic deoxycytidine analog, Angew. Chem. Int. Ed., 35 (1996) 1968-1970. 

Amino Acid Sequence Affects a Helix Stability... 

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