title: Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory.
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.
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. iuporov@gmail.com.|Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia. iuporov@gmail.com.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Uporov
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. nforlemu@ggc.edu.|Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA. nforlemu@ggc.edu.
authors.forename: Neville Y
authors.initials: NY
authors.lastname: Forlemu
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. rahul.nori@my.und.edu.
authors.forename: Rahul
authors.initials: R
authors.lastname: Nori
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. tsvetan.aleksandrov@gmail.com.
authors.forename: Tsvetan
authors.initials: T
authors.lastname: Aleksandrov
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. boris.sango@my.und.edu.
authors.forename: Boris A
authors.initials: BA
authors.lastname: Sango
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. yvonne.mbote@okbu.edu.|James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA. yvonne.mbote@okbu.edu.
authors.forename: Yvonne E Bongfen
authors.initials: YE
authors.lastname: Mbote
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. sandeeppothuganti@gmail.com.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Pothuganti
authors.affiliation: Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA. kathryn.thomasson@und.edu.
authors.forename: Kathryn A
authors.initials: KA
authors.lastname: Thomasson
mesh_terms: D000465:Algorithms; D002942:Circular Dichroism / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D055590:Electromagnetic Phenomena; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D009113:Muramidase
keywords: computer program; dipole interaction model; far-UV circular dichroism; other secondary structures; theoretical circular dichroism calculations; α-helical proteins; α/β proteins; β-sheet proteins