title: Structural fluctuations and thermal stability of proteins in crowded environments: effects of the excluded volume.
abstract: We perform molecular dynamics simulations for a simple coarse-grained model of a protein placed inside of a softly repulsive sphere of radius R. The protein is surrounded either by a number of same molecules or a number of spherical crowding particles that immitate other biomolecules such as the osmolytes. The two descriptions are shown to lead to distinct results when testing thermal stability as assessed by studying the unfolding times as a function of temperature. We consider three examples of proteins and show that crowding increases the thermal stability provided the inter-protein or protein-crowder interactions are repulsive. On the other hand, an introduction of attraction between the proteins is found to destabilize the proteins. Crowding by repulsive crowder particles is seen to enhance the RMSF in certain exposed regions. The effect grows on decreasing the size of the crowding particles. In the absence of crowding the RMSF anticorrelates with the coordination number related to the residue-residue interaction.
authors: Centre for Innovative Research in Medical and Natural Sciences, Medical Faculty of University of Rzeszów, ul. Warzywna 1a, 35-310 Rzeszów, Poland.
authors: Anna
authors: A
authors: Starzyk
authors: Michał
authors: M
authors: Wojciechowski
authors: Marek
authors: M
authors: Cieplak
mesh_terms: D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
chemical_list: D010940:Plant Proteins; D011506:Proteins; C024934:crambin protein, Crambe abyssinica; D009113:Muramidase