Core chain atoms

By this definition, every core chain atom necessarily has at least one adjacent core chain atom. Figure 31 illustrates the core chain atoms of a simple structure. 

Figure 31 The core chain atoms (dots) of a simple structure.

Most difficult, choosing the capping substituents such that they preserve the chain character of the terminal core chain atoms and satisfy zigzag requirements. 

Identify core chain atoms according to the definition above. 

B. Loop over the core chain atoms. For each, get the angles of its substituents in CCW order and assign the atom to the first of the following four categories that applies ... 

Correct for fixed angle spacing. If the seed atom is a core chain atom, decrement NumSub, and increase the angular demand by the chain angle. 

Algorithm 9 Substituent Placement When Seed Atom Is a Core Chain Atom... 

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

Chls and all tetrapyrroles are heteroaromatic compounds and the aromatic character of the underlying tetrapyrrole moiety and the reactivity of the functional groups in the side chains govern their chemistry. Three different classes of tetrapyrroles, differentiated by their oxidation level, occur in nature porphyrins (11, e.g. hemes), chlorins (12, e.g. chls) and bacteriochlorins (13, e.g. bchls). As a cyclic tetrapyrrole with a fused five-membered ring, the overall reactivity of chi is that of a standard phytochlorin 7. Such compounds are capable of coordinating almost any known metal with the core nitrogen atoms. Together with the conformational flexibility of the macrocycle and the variability of its side chains, this accounts for their unique role in photosynthesis and applications ... 

The structure of thermolysin-inhibitor complexes has shown the presence of a deep PI specificity pocket and the details of hydrogen bonding between enzyme and inhibitor [28]. Side-chain atoms of the enzyme are involved in interaction with the inhibitor amides and the inhibitor conformation is such that the subsites PI and P2 both point into the enzyme core (Rg-9). 

Lindorff-Larsen et al.110 analyzed the NMR structure ensemble by a generalized Lindemann criterion111 to define the mobility of side chain atoms. The result suggested that the side chain atoms have liquid-like mobility even in the core of protein, whereas the backbone atoms uniformly have a solid-like rigidity. As they proposed, the addition of thermodynamic properties for target function of structure calculation can increase the quality and usefulness of NMR structures. 

As discussed in Section 10, the side chain atoms presumably have high mobility even in protein core.110 In the near future, the quality check criteria for NMR structures will be developed including the dynamic properties. 

For each bath mode, the contribution to the norm from each atom can be calculated from the normalized eigenvectors. Modes with a total contribution larger than 0.5 from the side chain atoms were identified as side chain dominant modes those with a contribution larger than 0.8 from the side chain atoms were identified as side chain localized modes. Similar definitions can be made for porphine core atoms or the two isopropionate groups. Table 9.6 summarizes the results for the dominant modes or the localized modes for those modes involved in the important energy transfer pathways in V4 and V7 modes relaxation. 

As in the trp repressor-consensus ODNA complex, residues 4 to 19 (monomer I) and residues 504 and 519 (monomer II) appear as a coil in our structure due to the lack of NOE constraints. All backbone atom positions in the core (helices A, B, C and F) are well defined in both monomers. The backbone atom positions in helix D are not as well defined as those in the rest of the sequence. Both the backbone and side chain atoms at the N-terminal part of helix C and the turn between helices C and D have larger than average RMSD values, as a consequence of the reduced number of constraints in these regions. 

A chain consists of a run of one or more contiguous core atoms plus two capping substituents, which lie on either end of the core chain. (Although two or more chains may appear to coincide at an atom, that atom is... 

Figure 7 Proposed PYMOL model illustrating that the cavity generated on replacing the Leu layer directly above the metal binding site with a sterically less demanding amino acid (e.g., Ala) could more easily accommodate a coordinated water molecule. Shown are the main chain atoms represented as helical ribbons (green), the Leu/Ala side chains in the hydrophobic core as space filling spheres, the Cys side chains (stick form) with the thiol group (orange) coordinated to the Cd(II) (violet) with a bound water (red).

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