MODELING BIOMOLECULES APPLICATIONS IN COMPUTATIONAL BIOPHYSICS Steve Mielke

MODELING BIOMOLECULES APPLICATIONS IN COMPUTATIONAL BIOPHYSICS Steve Mielke, Ph. D. School of Natural Sciences St. Edward’s University SCIE 1199, March 1, 2016

DNA Variable side chain BIOPOLYMERS Proteins Human insulin Amino acids Structure – Function Relationship

ROLES OF BIOMOLECULAR STRUCTURE Protein Electrochemistry DNA Packaging Homology model of PSII core structure http: //www. nature. com/nrneph/journal/v 6/n 6/images/nrneph. 2010. 55 -f 2. jpg Mielke, et al. , 2013

ROLES OF BIOMOLECULAR STRUCTURE DNA Superhelicity Lk = Tw + Wr bp 2050 - 2110 β-lactamase coding Dra. I cleavage sites Tanaka, et al. , 2008

BIOMOLECULAR DYNAMICS: PROTEIN INTERACTIONS DNA Replication (DNA Polymerase) DNA- DNA Transcription (RNA Polymerase) Twin Supercoiling Domain Wu, et al. , 1988 FUSE element, human c-Myc proto-oncogene

COMPUTER SIMULATIONS OF DYNAMICALLY SUPERHELICAL DNA Mielke, et al. , 2008 • Coarse-grained DNA model: One or two chains of interacting hydrodynamic spheres, whose positions (ri) and rotation angles (ϕi) are time-evolved using numerical solutions of Brownian dynamics equations of motion. • t: time; δt: time step; Dt, r: translational and rotational diffusion coefficients; Fi, Ti: forces, torques; Ri, fi: stochastic translational and rotational displacements

SIMULATION RESULTS • … • … Mielke, et al. , 2004 Mielke, et al. , 2005

FUTURE Mielke, et al. , 2008