Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RADĚJ, Ondřej SKŘEHOTA and Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins. In 8th European Conference on Computational Chemistry. 2010.

Basic information

• Original name: Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins
• Name in Czech: Rychlé metody výpočtů nábojů: parametrizace EEM pro uplatnění na proteiny
• Authors: IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RADĚJ, Ondřej SKŘEHOTA and Jaroslav KOČA.
• Edition: 8th European Conference on Computational Chemistry, 2010.

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10600 1.6 Biological sciences
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• Keywords in English: atomic charge; EEM; parameterization
• Tags: International impact

Abstract

Atomic charges, although not physical observables, are called upon to explain many molecular properties and are used by many computational chemistry software packages. The quantum chemical approach to calculating various types of atomic charges can be very precise, but extremely time demanding; in any case, its applicability to biomolecules is restricted by the size of the systems. One of the already available alternative solutions is the Electronegativity Equalization Method (EEM), which allows for the fast calculation of partial atomic charges with remarkable precision [1], provided that the proper parameters have been previously determined. Previous studies in this respect have made great progress since the original development of EEM by improving the formalism [2], increasing the number of covered atom types [3], testing the amenability of various atomic charge schemes [4], implementing the EEM formalism in modelling software [5] etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at the biomolecular level. We have obtained EEM parameters for the elements commonly found in proteins (C, H, N, O, S) and the Ca ion that may appear as a ligand, for systems whose size is around 1000 atoms. All these systems are parts of very large proteins, and therefore the parameters we have obtained should be able to predict partial atomic charges on full-sized real proteins to a good approximation. We present the complete process of generating these EEM parameters.