Peptide charge distribution

Sokalski, W. A., D. A. Keller, R. L. Ornstein, and R. Rein. 1993. Multipole Correction of Atomic Monopole Models of Molecular Charge Distribution. I. Peptides. J. Comput. Chem. 14, 970-976. 

Detergents commonly used to form micelles that are amenable to high-resolution NMR are summarized in Tab. 5.2, and the chemical structures of the most commonly used detergents are presented in Fig. 5.2. Unfortunately, only a few of those needed for use with nonisotopically enriched peptides are commercially available in deuterated form. Most frequently, the zwitterionic DPC or the negatively charged SDS have been used as membrane mimetics. Mixtures of DPC doped with small amounts of SDS may be used to modulate the charge distribution on the micelle surface. It should be emphasized here... 

Consensus features were identified from comparison of sequence homologies of known sulfation sites 110139 and from in vitro sulfation of synthetic peptides using TPST-enriched membrane preparations 11-13 as well as from analysis of mutations. 14 These structural features mainly consist of a preferential type of charge distribution around the sulfation site, i.e. acidic residues on the amino-terminal side of the tyrosine, particularly in position 1. Full accessibility of the site to the TPST in surface-exposed loops and the absence of disulfide bridges in the proximity are also important for sulfation. 

Transition state analogues are essentially stable molecules which resemble, in geometry and in charge distribution, metastable intermediates of the enzymic reaction. The actual transition state of the reaction will be close in structure to the metastable intermediate, and will quite likely vary slightly between different substrates accepted by the same enzyme. There will not be a unique transition state for all transformations catalysed by one particular enzyme, neither of course will there be a unique transition state for different enzymes catalysing the hydrolysis of peptide links in a protein. There will nevertheless be some similarities in mechanism, and so structures containing a tetrahedral centre have been designed to inhibit a variety of proteinases, where a tetrahedral intermediate is always presumed. Differences exist in the pathway to, and breakdown of, the tetrahedral intermediate, and its stabilization, between thiol and serine proteinases, zinc proteinases, and aspartic proteinases. 

Figure 2. The peptide moiety showing charge distributions on each of four atoms. The result is a permanent (ground state) dipole moment indicated by the arrow with the head of the arrow pointing in the positive direction. On absorption of a photon, the electron distribution changes. This results in the atoms having a new distribution of charge and the excited state will have a different dipole moment. The difference dipole moment (between the ground and excited states) is called the electric transition dipole moment, /i,., and its magnitude can be calculated from the area of the absorption curve as shown in Figure 3.

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