TY - JOUR
T1 - Macromolecular crowding effects in flexible polymer solutions
AU - Majumdar, Bibhab Bandhu
AU - Ebbinghaus, Simon
AU - Heyden, Matthias
N1 - Funding Information:
This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.
Publisher Copyright:
© 2018 World Scientific Publishing Company.
PY - 2018/5/1
Y1 - 2018/5/1
N2 - Biological environments are often "crowded" due to high concentrations (300-400g/L) of macromolecules. Computational modeling approaches like Molecular Dynamics (MD), rigid-body Brownian Dynamics and Monte Carlo simulations have recently emerged, which allow to study the effects macromolecular crowding at a microscopic level and to provide complementary information to experiments. Here, we use a recently introduced multiple-conformation Monte Carlo (mcMC) approach in order to study the influence of intermolecular interactions on the structural equilibrium of flexible polyethylene glycol (PEG) polymers under self-crowding conditions. The large conformational space accessible to PEG polymers allows us to evaluate the general applicability of the mcMC approach, which describes the intramolecular degrees of freedom by a finite-size ensemble of discrete conformations. Despite the simplicity of the approach, we show that influences of intermolecular interactions on the intramolecular free energy surface can be described qualitatively using mcMC. By varying the magnitude of distinct terms in the intermolecular potential, we can further study the compensating effects of repulsive and nonspecific attractive intermolecular interactions, which favor compact and extended polymer states, respectively. We use our simulation results to derive an analytical model that describes the effects of intermolecular interactions on the stability of PEG polymer conformations as a function of the radius of gyration and the corresponding solvent accessible surface. We use this model to confirm the role of molecular surfaces for attractive interactions that can counteract excluded volume effects. Extrapolation of the model further allows for the analysis of scenarios that are not easily accessible to direct simulations as described here.
AB - Biological environments are often "crowded" due to high concentrations (300-400g/L) of macromolecules. Computational modeling approaches like Molecular Dynamics (MD), rigid-body Brownian Dynamics and Monte Carlo simulations have recently emerged, which allow to study the effects macromolecular crowding at a microscopic level and to provide complementary information to experiments. Here, we use a recently introduced multiple-conformation Monte Carlo (mcMC) approach in order to study the influence of intermolecular interactions on the structural equilibrium of flexible polyethylene glycol (PEG) polymers under self-crowding conditions. The large conformational space accessible to PEG polymers allows us to evaluate the general applicability of the mcMC approach, which describes the intramolecular degrees of freedom by a finite-size ensemble of discrete conformations. Despite the simplicity of the approach, we show that influences of intermolecular interactions on the intramolecular free energy surface can be described qualitatively using mcMC. By varying the magnitude of distinct terms in the intermolecular potential, we can further study the compensating effects of repulsive and nonspecific attractive intermolecular interactions, which favor compact and extended polymer states, respectively. We use our simulation results to derive an analytical model that describes the effects of intermolecular interactions on the stability of PEG polymer conformations as a function of the radius of gyration and the corresponding solvent accessible surface. We use this model to confirm the role of molecular surfaces for attractive interactions that can counteract excluded volume effects. Extrapolation of the model further allows for the analysis of scenarios that are not easily accessible to direct simulations as described here.
KW - Excluded-volume effects
KW - Free energy
KW - Monte Carlo simulations
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U2 - 10.1142/S0219633618400060
DO - 10.1142/S0219633618400060
M3 - Article
AN - SCOPUS:85047105030
SN - 0219-6336
VL - 17
JO - Journal of Theoretical and Computational Chemistry
JF - Journal of Theoretical and Computational Chemistry
IS - 3
M1 - 1840006
ER -