Backbone atoms

Figure 2 A glutamate side chain partitioned into quantum and classical regions. The terminal CH2C02 group IS treated quantum mechanically, and the backbone atoms are treated with the molecular mechanics force field.

Variations on the a helix in which the chain is either more loosely or more tightly coiled, with hydrogen bonds to residues n + 5 or n + 3 instead of n + 4 are called the n helix and 3io helix, respectively. The 3io helix has 3 residues per turn and contains 10 atoms between the hydrogen bond donor and acceptor, hence its name. Both the n helix and the 3to helix occur rarely and usually only at the ends of a helices or as single-turn helices. They are not energetically favorable, since the backbone atoms are too tightly packed in the 3io helix and so loosely packed in the n helix that there is a hole through the middle. Only in the a helix are the backbone atoms properly packed to provide a stable structure. 

Fig. 7. Comparison of the cluster binding fold of the water-soluble Rieske fragment from bovine heart 6ci complex (ISF, left PDB file IRIE) with the structure of ru-bredoxin (middle PDB file 7RXN) and with the zinc-ribbon motif (right PDB file ITFl). The metal binding loops are shown as ball-and-stick models of the backbone atoms.

Figure 6. Stereo pairs of distance geometry structures of RpII. Only backbone atoms are shown.

Figure 4 Sequential assignment of the backbone atoms for the segment Pro-109 to Val-113 of inhibited sfSTR by 4-D HCANNH and 4-D HCA(CO)NNH. Four planes are shown from each spectrum. The assigned backbone atoms are indicated in (A). In (B) the upper four planes in solid lines are from the 4-D HCANNH and the lower four planes in dashed lines are from the 4-D HCA(CO)NNH. The chemical shifts for the four correlated nuclei in each case are shown. The correlations continue for the segment Pro-109 to Pro-129. As Pro lacks a protonated N, this residue serves as a "stop" signal. The correlation of 19 residues with Pro at the N- and C-terminal ends is unique for this segment in the sequence of sfSTR, therefore these backbone atoms are specifically assigned without having to further assign side chain atoms. (From Ref. 5.)...

Figure 11 Potential hydrogen bond partners to the backbone atoms of the inhibitor and the residues of the S/ subsite that are in intermolecular contact with the Pi homophenylalanine.

Figure 3 illustrates the correspondence of the calculated backbone trace with that of the backbone atoms. Figure 4 illustrates the sequence ofthe protein and the occurrence of the two breaks in the chain. 

Third, the introduction of crosslinks between chains confers insolubility and increased solid state rigidity, often accompanied by improved thermal stability. High degrees of crosslinking confer ceramic-type properties on the solid, whether the backbone atoms are carbon atoms or inorganic species. 

We also performed optimization for R2met using the three-layer ONIOM3 (B3LYP HF/STO-3G Amber). In addition to the atoms shown in Figure 2-4, an additional 45 side-chain and backbone atoms were treated at the Hartree-Fock/STO-3G level. The resultant RMS and maximum deviations are 0.23 and 0.36 A, respectively, compared to 0.34 and 0.52 A for QM MM. This indicates that the electronic effects of the protein residues, evaluated only classically in the QM MM (B3LYP Amber) treatment, can be further improved with the use of the ONIOM3 QM QM MM method. 

We use carbon-13 NMR spectrometry to identify the monomer units present in copolymers, their absolute concentrations, the probability that two or more monomer units occur in proximity, and long chain branching concentrations. For instance, in the case of polyethylene, we can not only distinguish and quantify ethyl, butyl, and hexyl branches, but we can also determine whether branches are present on carbon backbone atoms separated by up to four bonds. We can compare the observed adjacency of branches to a theoretical value calculated for random comonomer incorporation. By this method, we can determine whether comonomers are incorporated at random, as blocks, or in some intermediate fashion. 

We can divide commodity plastics into two classes excellent and moderate insulators. Polymers that have negligible polar character, typically those containing only carbon-carbon and carbon-hydrogen bonds, fall into the first class. This group includes polyethylene, polypropylene, and polystyrene. Polymers made from polar monomers are typically modest insulators, due to the interaction of their dipoles with electrical fields. We can further divide moderate insulators into those that have dipoles that involve backbone atoms, such as polyvinyl chloride and polyamides, and those with polar bonds remote from the backbone, such as poly(methyl methacrylate) and poly(vinyl acetate). Dipoles involving backbone atoms are less susceptible to alignment with an electrical field than those remote from the backbone. 

Fig. 5. Molecular dynamics simulations (MD) of dendrimer 23 with 50 repeat units after 300 ps MD. End-to-end distance 9.1 nm, average diameter 4.4 ( 0.2) nm.The backbone atoms are kept in yellow, the terminal phenyl rings in red, and all other atoms in green... 

Figure 7.2 (a) Schematic representation of the structure of B. subtilis ferrochelatase. Domain I is coloured green and domain II blue. The parts of the chain in red build up the walls of the cleft, and the region in yellow makes the connection between the domains. The N- and C-termini are marked, (b) The proposed active site of ferrochelatase with protoporphyrin IX molecule (red) modelled into the site. The backbone atoms of the protein are in purple, the side-chains in blue. Reprinted from Al-Karadaghi et ah, 1997. Copyright (1997), with permission from Elsevier Science. 

The new backbone atom must now be checked for overlap with other atoms on the chain. The distance from every other atom is then calculated. If there is a spin on this atom, terms for the second moment summation are accumulated in this program loop as well. 

All results were obtained from chains of 200 backbone atoms, averaging 100 chains to obtain M2, axial extensions, end-to-end distances, and segmental and chain order parameters and directors. 

The closest physical realization of the system examined above would be a polymer such as poly(vinyl fluoride) doped into poly(ethylene) (observing the r resonance) or poly(trifluoroethylene) doped into poly(tetra-fluorethylene), observing H. Neither of these systems is likely to be sufficiently miscible, and there is the possibility of significant proportions of head-to-head linkages, which would dominate the experimental M2 because of the proximity of the spins on adjacent backbone atoms. 

Each point represents an average of 100 chains of 200 backbone atoms each. In this calculation, 13F spins reside at the coordinates of alternate backbone atoms. 

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