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Main chain torsion angles

Figure 8.6 Ramachandran plot of the crystal I ographi model of ALBP. The main-chain torsional angle (N-C, bond) is plotted versus (C-C, bond). The following symbols are used (.) nonglycine residues (+) glycine residues. The enclosed areas of the plot show sterically allowed angles. Reprinted with permission from Z. Xu et al. (1992) Biochemistry 31, 3484-3492. Copyright 1992 American Chemical Society. Figure 8.6 Ramachandran plot of the crystal I ographi model of ALBP. The main-chain torsional angle (N-C, bond) is plotted versus (C-C, bond). The following symbols are used (.) nonglycine residues (+) glycine residues. The enclosed areas of the plot show sterically allowed angles. Reprinted with permission from Z. Xu et al. (1992) Biochemistry 31, 3484-3492. Copyright 1992 American Chemical Society.
Validation of the biasing potential on pentane in vacuum Pentane has only two main configurational degrees of freedom, 0, and 02, the main chain torsional angles. Thus, it is the simplest model which can be used to test and validate the ID and 2D biasing techniques described above. Also the computed PMFs for rotation of butane and pentane in vacuum (data not shown)... [Pg.883]

Secondary structures [39, 40] are regular local structure elements identified in the 1950s [41, 42] which are characteristic abstractions for proteins and believed to be of great importance for the 3D folding. Secondary structure elements are defined via characteristic main chain torsion angles. Usually, three discrete states, a-helix (H), /i-strand (E, extended), or other (L, loop) are distinguished [1] (see Chapter 5 for details). [Pg.257]

Figure 5.1. Notation for torsion angles of biopolymer chains. Torsion angles ( and ift) that affect the main chain conformations of biopolymers are shown for polysaccharide (a), polypeptide (b), and polynucleotide (c) chains according to the IUBMB notation. The two torsion angles, and ij>, specified around the phosphodiesteric bonds of nucleic acids correspond to a and respectively. Reproduced from IUBMB at http //www.chem.gmw. ac.uk/iubmb. Figure 5.1. Notation for torsion angles of biopolymer chains. Torsion angles (<f> and ift) that affect the main chain conformations of biopolymers are shown for polysaccharide (a), polypeptide (b), and polynucleotide (c) chains according to the IUBMB notation. The two torsion angles, <j> and ij>, specified around the phosphodiesteric bonds of nucleic acids correspond to a and respectively. Reproduced from IUBMB at http //www.chem.gmw. ac.uk/iubmb.
Figure 2. Ball and stick representation of the blocked Ala-Pro-Tyr peptide in extended conformation. The aliphatic carbons are labelled according to the lUPAC definition. The cis and trans methylene protons (compared to the a proton) of proline and tyrosine are indexed 1 and 2 respectively. The main backbone and side chain torsional angles referred to in the text are indicated by arrows. Figure 2. Ball and stick representation of the blocked Ala-Pro-Tyr peptide in extended conformation. The aliphatic carbons are labelled according to the lUPAC definition. The cis and trans methylene protons (compared to the a proton) of proline and tyrosine are indexed 1 and 2 respectively. The main backbone and side chain torsional angles referred to in the text are indicated by arrows.
The four residue linker between two strands (E-L4-E) shows distinct clusters. One fourth of the L2 residues of the first sub-cluster are either Asp, Gly or Ser/Thr/Pro. The main chain torsions preferred are oCr for the first three residues and (Xl for the last residue. For the linker H-L4-E, one of the sub clusters shows a very strong preference for Pro at the second position (about half of observed L2), which constrains the < ) angle to be negative as observed and Asp at the third position (again about half of observed L3 residues). The E-L4-H linker is similar to the first cluster of the H-L4-E linker but the difference lies in the strong preference of Pro at... [Pg.675]

When A A or B B, the symmetry is lower and the only possible line repetition groups are s(M/N) and tc for isotactic and syndiotactic polymers, respectively, in both cis and trans configurations. In these cases, two independent torsion angles in the main chain define the regular conformation (Oi and 02 in Figure 2.15). [Pg.96]


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See also in sourсe #XX -- [ Pg.31 ]




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Chain angle

Main-chain

Torsion angl

Torsion angle

Torsional angles

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