Molecular Simulation of Biopolymers: Application to Bacterial Chromosome and Biomaterials

Swain, Pinakinarayan A P and Majumdar, Saptarshi (2020) Molecular Simulation of Biopolymers: Application to Bacterial Chromosome and Biomaterials. PhD thesis, Indian Institute of Technology Hyderabad.

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Abstract

Polymers have a wide range of applications in everyday life. They are also essential components of biological systems. Molecular dynamics simulation is a technique to study the properties of the polymers. In this thesis, we use molecular dynamics simulations to understand the statics and dynamics of three different polymers. First, we study chromosome structure and dynamics in E. coli. Recent experiments on live cells grown in micro-confinements, study the morphology and segregation of chromosomes with a combination of genetic and biochemical manipulations. The antibiotic-treated bacteria do not undergo cell division, and using DNAc, the replication of DNA can be switched off at high temperatures. In the absence of replication, chromosome size shows non-linear growth and a subsequent gradual saturation as cell length increases. When replication is allowed, chromosome segregation takes place in the undivided cell approximately to its 1/4-th and 3/4-th positions lengthwise. To explain these fascinating results, we used a model where the chromosome is treated as a polymer with side loops and cytosol as passive crowders. The entropic effect due to confinement and crowders captures the observed morphology, localization, and segregation of chromosomes successfully. However, experiments show higher positional fluctuations of the chromosome than the equilibrium estimate. This could be because of the presence of active forces in the cell. Next, we use molecular dynamics simulation to study the pH-responsive behavior of gelatin, a polymer frequently used in biomedical applications. We look at the static properties of gelatin in aqueous salt solutions at three different pH, 1.2, 7, and 10. At the isoelectric point (pH=7), we observe a monotonic increase in the size of the polymer with an increase in salt concentration. At pH=1.2, the addition of salt leads to a collapse of the polymer. In the negative polyelectrolyte regime (pH=10), we observe a “collapse-reexpansion” behavior. The mechanism behind this reexpansion behavior is the screening of repulsion between the net charges followed by the screening of attraction of oppositely charged ions with increasing salt concentration. The shift in the peak of radial distribution function calculated between monomers and salt ions confirms this spatial reorganization. We use dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) experiments to verify the simulation predictions. Lastly, we study the translocation dynamics of G-protein by coarse-grained molecular simulation. A series of exciting experiments in HeLa cells revealed that the G protein bg subunits detach from the plasma membrane (PM) and translocate reversibly to internal membranes. Based on the terminal amino acid sequences of g subunit, their rate of translocation showed an order of magnitude difference. By performing coarse-grained molecular dynamics simulation, we explore how amino acid sequences of Gg give rise to this difference in translocation. The equilibrium size of the slowest and fastest Gg subunits was calculated and found not be significantly different from each other. We hypothesize that the external force essential for directional transport is due to the dissociation of protein from the PM. The differences in bond dissociation rates lead to differences in external forces, making the translocation rates of Gbg distinctly different. The effect of increasing the agonist concentration is modeled by increasing the numer of subunits dislodges from the PM. We also study the effect of macromolecular crowding on the translocation dynamics. An Increase in crowder concentration leads to a higher exclusion volume, which slows down in the translocation rate.

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