Biological systems often represent macromolecular assemblies that require enormous resources to be simulated by all-atom methods. To simulate such aggregates, one has to use reduced representations of proteins and DNA. One such representation is an elastic rod model of DNA. We applied a classical Kirchhoff system of equations [30] to describe DNA in terms of its center-line, curvatures and twist*. We used a continuation method [31] to solve the equations, modifying parameters and boundary conditions from the values for which an exact solution is known to the desired values. A particular challenge was to use the anisotropic model of DNA cross-section, as such representation renders the DNA twist non-uniformly distributed along the center-line. In addition, we modified the equations to include the intrinsic twist and curvatures of DNA. We applied the method to the DNA segment bound by lactose repressor (see the Highlight section of this report). The use of boundary condit ions obtained from the crystal structure [25] revealed two possible shapes of the DNA loop. The successful solution of the Kirchhoff system of equations suggests that they may be applied to other biological systems, e.g., DNA wrapped around nucleosomes. Since the bifurcation of the solution to the Kirchhoff equations may pose a problem in future applications, we have modified the equations by extracting the oscillatory component of the solution caused by the intrinsic twist of the DNA.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
3P41RR005969-09S2
Application #
6122375
Study Section
Project Start
1998-08-01
Project End
1999-07-31
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
9
Fiscal Year
1999
Total Cost
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
Radak, Brian K; Chipot, Christophe; Suh, Donghyuk et al. (2017) Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 13:5933-5944
Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V et al. (2016) Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry 55:5714-5725
Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
Poudel, Kumud R; Dong, Yongming; Yu, Hang et al. (2016) A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 27:2119-32
Vermaas, Josh V; Taguchi, Alexander T; Dikanov, Sergei A et al. (2015) Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Biochemistry 54:2104-16
Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P et al. (2015) Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 9:10598-611
Shen, Rong; Han, Wei; Fiorin, Giacomo et al. (2015) Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 11:e1004368

Showing the most recent 10 out of 371 publications