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Improving protein structure prediction, refinement and quality assessment techniques

Leelananda S. P., Pawłowski M., Faraggi E., Kloczkowski A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

231--243

Several novel techniques have been combined to improve protein structure prediction, structural refinement and quality assessment of protein models. We discuss in brief the development of four-body potentials that take into account dense packing and cooperativity of interactions of proteins, and its success. We have developed a metho d that uses whole protein information filtered through machine learning to score protein models base d on their likeness to native structure. Here we consider electrostatic interactions and residue depth, and use these for structure prediction. These potentials were tested to be succe ssful in CASP 9 and CASP 10. We have also developed a Quality Assessment technique, MQAP single, which is a quasi-single-model MQAP , by combining advantages of both “pure” single-model MQAP s and clustering MQAP s. This technique can be used in ranking and assessing the absolute global quality of single protein models. This model (Pawlowski-Kloczkowski) was ranked 3rd in Model Quality Assessment in CASP 10. Consideration of protein flexibility and its fluctuation dynamics improves protein structure prediction and leads to better refinement of computational models of proteins. Here we also discuss how Anisotropic Network Model ( ANM ) of protein fluctuation dynamics and Go-like model of energy score can be used for novel protein structure refinement.

Ion Move Brownian Dynamics (IMBD) : Simulations of Ion Transport

Kurczyńska M., Kotulska M.

Acta of Bioengineering and Biomechanics

2014

Vol. 16, no. 4

107--115

Purpose: Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also time-efficient. Methods: The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Results: Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. Conclusions: IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.