Backbone hydrogen bonds

The simulation trajectory shown in Fig. 8b provides an explanation of how the force profile in Fig. 8a arises. During extension from 0 to 10 A the two /9-sheets slid away from each other, each maintaining a stable structure and its intra-sheet backbone hydrogen bonds. As the extension of the domain reached 14 A, the structure within each sheet began to break in one sheet, strands A and G slid peist each other, while in the other sheet, strands A and B slid past each other. The A -G and A-B backbone hydrogen bonds broke nearly simultaneously, producing the large initial force peak seen in Fig. 8a. 

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. 4. Ramachandran plots of glutamines (A) making side chain-to-backbone hydrogen bonds with the next residue in sequence (B). Filled circles denote residues where the glutamine is in the PPII conformation. Open circles denote all residues where the glutamine is not in the PPII conformation.

Glutamine can also be considered an outlier if it forms a side chain-to-backbone hydrogen bond as hypothesized by Stapley and Creamer... 

Other than an effect on backbone solvation, side chains could potentially modulate PPII helix-forming propensities in a number of ways. These include contributions due to side chain conformational entropy and, as discussed previously, side chain-to-backbone hydrogen bonds. Given the extended nature of the PPII conformation, one might expect the side chains to possess significant conformational entropy compared to more compact conformations. The side chain conformational entropy, Y.S ppn (T = 298°K), available to each of the residues simulated in the Ac-Ala-Xaa-Ala-NMe peptides above was estimated using methods outlined in Creamer (2000). In essence, conformational entropy Scan be derived from the distribution of side chain conformations using Boltzmann s equation... 

To explore this issue, Monte Carlo computer simulations were run using the protocol outlined in the previous section. In these simulations, however, a peptide of sequence Ac-Ala-Xaa-Ala-Ala-NMe was employed (Xaa = Gin or Asn), the backbone was not constrained to the PPII conformation, and a side chain-to-backbone hydrogen bond was constrained using a potential function previously used to constrain a-helical backbone-to-backbone hydrogen bonds (Tun and Hermans, 1991 Creamer and Rose, 1994). 

Fig. 6. Ramachandran plots for simulated Ac-Ala-Xaa-Ala-Ala-NMe peptides with Xaa = glutamine or asparagine, with a constrained side chain-to-backbone hydrogen bond. Conformational distribution for glutamine i (A) and for the residue i +1 to which the glutamine is hydrogen-bonded (B). Conformational distribution for asparagine i (C) and for the residue i +1 to which it is hydrogen-bonded (D).

Garcia, A. E., and Sanbonmatsu, K. Y (2002). a-Helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sd. USA 99, 2782-2787. 

Pentynoic acid, 5 34t People. See also Personnel investment in, 21 624 organizational ties to, 21 627-628 People s Republic of China. See also China demand for oil in, 23 530 oil recovery program in, 23 534 Pepper, pipeline levels in, 23 159 Peptide antibiotics, 18 252-253. See also Antimicrobial peptides Peptide backbone hydrogen bonds, in proteins, 20 826 Peptide mapping, 3 840-841 Peptide nucleic acids, 17 631-634... 

Tight turns were first recognized from a theoretical conformational analysis by Venkatachalam (1968). He considered what conformations were available to a system of three linked peptide units (or four successive residues) that could be stabilized by a backbone hydrogen bond between the CO of residue n and the NH of residue n + 3. He... 

The surfaces that form subunit-subunit contacts are very much like parts of a protein interior detailed fit of generally hydrophobic side chains, occasional charge pairing, and both side chain and backbone hydrogen bonds. Twofold symmetry is the most common relationship between subunits. The 2-fold is often exact and can be part of the actual crystallographic symmetry, as for the prealbumin dimer in Fig. 62. However, in many cases (e.g., Tulinsky et al., 1973 Blundell et al., 1972) individual side chains very close to the approximate 2-fold axis must take up nonequivalent positions in order to avoid overlapping (see Fig. 63). Conformational nonequivalence can extend further away from the axis and produce such effects as different... 

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... 

Matrix metalloproteinase structural studies of the P -side inhibitors to date show a common set of inhibitor-enzyme interactions. This can be attributed primarily to the strong directional zinc-binding forces. Further stabilizing forces from the backbone hydrogen-bonding patterns common to a (3 sheet allow for minor adjustments due to the zinc interactions to be made while maintaining a common pharmacophore. 

Fig. 6. (a) Backbone hydrogen bonding scheme as currently delimited. Disulfide bridges are indicated in heavy dashed lines and poor or less certain bonds in light dashed lines. W indicates solvent molecule. Side chain to side chain bonds are not generally indicated. The scheme of bonding currently assigned for 3 -CMP is also... 

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