Effects of macromolecular crowding on biochemical reaction equilibria: a molecular thermodynamic perspective.
A molecular thermodynamic model is developed to investigate the effects of macromolecular crowding on biochemical reactions. Three types of reactions, representing protein folding/conformational isomerization, coagulation/coalescence, and polymerization/association, are considered. The reactants, products, and crowders are modeled as coarse-grained spherical particles or as polymer chains, interacting through hard-sphere interactions with or without nonbonded square-well interactions, and the effects of crowder size and chain length as well as product size are examined. The results predicted by this model are consistent with experimentally observed crowding effects based on preferential binding or preferential exclusion of the crowders. Although simple hard-core excluded-volume arguments do in general predict the qualitative aspects of the crowding effects, the results show that other intermolecular interactions can substantially alter the extent of enhancement or reduction of the equilibrium and can even change the direction of the shift. An advantage of the approach presented here is that competing reactions can be incorporated within the model.
Hu
Zhongqiao
Z
Department of Chemical and Biomolecular Engineering and The Singapore-MIT Alliance, National University of Singapore, Singapore.
Jiang
Jianwen
J
Rajagopalan
Raj
R
D000596:Amino Acids / Q000737:chemistry; D001703:Biophysics / Q000379:methods*; D007700:Kinetics; D046911:Macromolecular Substances / Q000737:chemistry; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry
D000596:Amino Acids; D046911:Macromolecular Substances; D011506:Proteins; D025801:Ubiquitin