Proteins denature at high hydrostatic pressures, implying that the unfolded proteins in aqueous solution have lower volume than the folded state. A model that explains pressure unfolding requires water to penetrate the protein interior and disrupt the protein hydrophobic core. I will explore the energetics of water penetration and the effect of pressure on hydrophobic interactions. I will also describe molecular simulations of the reversible folding/unfolding equilibrium as a function of density and temperature of solvated peptides that can form alpha helices (the AK peptide) and beta hairpins (the C terminal domain of protein G). I will characterize the structural, thermodynamic and hydration changes as a function of temperature and pressure. To study protein folding equilibrium thermodynamics we use an extension of the replica exchange molecular dynamics (REMD) method that allows for density and temperature Monte Carlo exchange moves. We studied multiple thermodynamic states, covering a density range from 0.96 g cm-3 to 1.14 g cm-3, and a temperature range from 300 to over 500 K.
I will briefly describe an all atom Go model for DNA molecules of length ~ 1 persistence length (150 bp). Thermal fluctuations in double-stranded DNA induce localized, sequence-dependent openings of its base pairs. These openings have, in certain cases, been associated with the formation of the DNA transcription complex. We describe these fluctuational openings at the atomic level using molecular dynamics (MD) simulation and a Go potential to model the dynamics of DNA. This potential, previously applied to study protein folding, simplifies the non-covalent energetics but includes the configurational entropy and geometrical and steric constraints imposed by the three-dimensional structure. The simplified treatment of the energetics allows for the simulation of large-scale fluctuations of relatively large systems. We simulate known gene promoter DNA sequences and show that bubbles form at the transcription initiation sites. Simulation results are compared to cleavage and transcription assays for the 69~bp promoter AAV P5, which binds the transcription factor Yin Yang~1 (YY1). Our simulations indicate preferential openings in locations associated with transcription initiation and regulation by DNA binding protein complexes.
This work has been done in collaboration with D Paschek, S. Gnanakaran, V Beleva and K. Rasmussen.
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