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oai:www.ideals.illinois.edu:2142/85424 2023-07-11 col_2142_5131 col_2142_14828 com_2142_5130 com_2142_14827 com_2142_14793 com_2142_8903

Schulten, Klaus J. Balaeff, Alexander Alexandrovich 2015-09-25T22:46:02Z 2015-09-25T22:46:02Z 10000-01-01 2002 2002 A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending anisotropy, and electrostatic properties. All the model parameters are considered to be functions of the loop arclength, so that the DNA sequence-specific properties can be modeled. The developed theory is applied to predict the structure of the DNA loop connecting the protein-bound DNA segments in the crystal structure of the lac repressor-DNA complex. The lac repressor system is used to extensively analyze the parameters and approximations of the model. The capabilities of the model are used to mimic the binding of catabolite gene activator protein (CAP) within the lac repressor loop and to explain the cooperativity in DNA binding between the two proteins. The possibilities for further development of the model and its general applicability in biomolecular modeling are discussed, especially with regard to multi-scale simulations of protein-DNA complexes. Made available in DSpace on 2015-09-25T22:46:02Z (GMT). No. of bitstreams: 2 license.txt: 4848 bytes, checksum: 96035ab3f5e1c23cc7138a224ce498bd (MD5) 3069971.pdf: 4240032 bytes, checksum: 9d74b89c4ede2cbbcfd887da6be963c8 (MD5) Previous issue date: 2002 Embargo set by: Seth Robbins for item 86705 Lift date: Forever Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs U of I Only 88 p. Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2002. http://hdl.handle.net/2142/85424 (MiAaPQ)AAI3069971 eng Engineering, Biomedical Application of the Theory of Elasticity to Modeling of Protein -Dna Interactions text Biophysics and Computational Biology Biophysics and Computational Biology University of Illinois at Urbana-Champaign Dissertation Ph.D.