This project intends to apply methods of theoretical chemistry and statistical methodologies to the study of biomolecular structures and interactions. Systems of interest include DNA and DNA metabolizing enzymes, mammalian p450 enzymes, the Zn finger domain of BRCA1, the Gla domain of the coagulation proteins, and the p21 product of the ras oncogene. Methods of approach include quantum calculations as well as classical force field approaches, database searching techniques, and molecular graphics. Due to its high charge concentration and flexibility, DNA has been very difficult to simulate realistically. Recent developments in the treatment of long range electrostatics have allowed us to produce long stable simulations of DNA. We plan to look into structural questions involving damaged DNA. We are modeling mammalian p450's using the homologous bacterial proteins. These enzymes as a class interact with a wide variety of substrates, and yet their specificity can be finely tuned by specific amino acid substitutions. In the absence of a known structure of a mammalian p450 we are focussing on a geometric model of the binding pocket. The model is based on the known structure of a bacterial p450. The p21 protein is a molecular """"""""switch"""""""" central to a variety of growth and developmental signaling pathways in human tissues. The """"""""switch"""""""" operates by means of a hydrolysis of the GTP cofactor. Our interest is in the intrinsic rate of hydrolysis in normal and mutant p21.

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Intramural Research (Z01)
Project #
1Z01ES043010-11
Application #
2574343
Study Section
Special Emphasis Panel (SBB)
Project Start
Project End
Budget Start
Budget End
Support Year
11
Fiscal Year
1996
Total Cost
Indirect Cost
City
State
Country
United States
Zip Code
Min, Jungki; Perera, Lalith; Krahn, Juno M et al. (2018) Probing Dominant Negative Behavior of Glucocorticoid Receptor ? through a Hybrid Structural and Biochemical Approach. Mol Cell Biol :
Li, Yin; Perera, Lalith; Coons, Laurel A et al. (2018) Differential in Vitro Biological Action, Coregulator Interactions, and Molecular Dynamic Analysis of Bisphenol A (BPA), BPAF, and BPS Ligand-ER? Complexes. Environ Health Perspect 126:017012
Perera, Lalith; Li, Yin; Coons, Laurel A et al. (2017) Binding of bisphenol A, bisphenol AF, and bisphenol S on the androgen receptor: Coregulator recruitment and stimulation of potential interaction sites. Toxicol In Vitro 44:287-302
Perera, Lalith; Beard, William A; Pedersen, Lee G et al. (2017) Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites. Inorg Chem 56:313-320
Perera, Lalith; Freudenthal, Bret D; Beard, William A et al. (2017) Revealing the role of the product metal in DNA polymerase ? catalysis. Nucleic Acids Res 45:2736-2745
Almaliti, Jehad; Al-Hamashi, Ayad A; Negmeldin, Ahmed T et al. (2016) Largazole Analogues Embodying Radical Changes in the Depsipeptide Ring: Development of a More Selective and Highly Potent Analogue. J Med Chem 59:10642-10660
Takaku, Motoki; Grimm, Sara A; Shimbo, Takashi et al. (2016) GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biol 17:36
Perera, Lalith; Freudenthal, Bret D; Beard, William A et al. (2015) Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proc Natl Acad Sci U S A 112:E5228-36
Perera, Lalith; Beard, William A; Pedersen, Lee G et al. (2014) Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. Adv Protein Chem Struct Biol 97:83-113
Perdivara, Irina; Perera, Lalith; Sricholpech, Marnisa et al. (2013) Unusual fragmentation pathways in collagen glycopeptides. J Am Soc Mass Spectrom 24:1072-81

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