Computing Theoretical Circular Dichroism of Proteins using the Dipole Interaction Model (DINAMO) with a United Atom Approachстатья

Статья опубликована в высокорейтинговом журнале

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Дата последнего поиска статьи во внешних источниках: 19 октября 2015 г.

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[1] Computing theoretical circular dichroism of proteins using the dipole interaction model (dinamo) with a united atom approach / N. Rahul, I. V. Uporov, N. Y. Forlemu et al. // Biophysical Journal. — 2014. — Vol. 106, no. 2. — P. 613a–614a. The dipole interaction model is a classical electromagnetic theory for calculating the π-π∗ transitions of peptides and proteins. DInaMo reduces all amide chromophores to single points with anisotropic polarizability and all nonchromophoric aliphatic atoms to points with isotropic polarizability; all other atoms are ignored. By determining interactions among the chromophoric and nonchromphoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of the CD spectrum for each molecule. DInaMo software is being modified to reduce computational demand by collapsing hydrogens into the atoms to which they are bound (i.e., united atom). Crystal structures of proteins containing less than 300 residues are energy minimized using NAMD. Hydrogens attached to various groups (e.g., CH3, CH2, or CH groups) are then deleted programmatically. Deleted hydrogen polarizabilities are either ignored or added to the atom to which they are bound. Theoretically predicted CD for a variety of proteins (26 different structures, examples pictured below) are compared with synchrotron radiation CD data. Theory agrees with experiment showing bands with similar morphology and absorption maxima for the π-π∗ transitions. [ DOI ]

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