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Int. J. Mol. Sci. 2015, 16(9), 21237-21276; doi:10.3390/ijms160921237

Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

1
Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA
2
Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia
3
Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA
4
James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Ritva Tikkanen
Received: 3 January 2015 / Revised: 9 June 2015 / Accepted: 30 June 2015 / Published: 7 September 2015
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
View Full-Text   |   Download PDF [3290 KB, uploaded 7 September 2015]   |  

Abstract

The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima. View Full-Text
Keywords: dipole interaction model; far-UV circular dichroism; theoretical circular dichroism calculations; computer program; α-helical proteins; β-sheet proteins; α/β proteins; other secondary structures dipole interaction model; far-UV circular dichroism; theoretical circular dichroism calculations; computer program; α-helical proteins; β-sheet proteins; α/β proteins; other secondary structures
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Uporov, I.V.; Forlemu, N.Y.; Nori, R.; Aleksandrov, T.; Sango, B.A.; Mbote, Y.E.B.; Pothuganti, S.; Thomasson, K.A. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int. J. Mol. Sci. 2015, 16, 21237-21276.

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