Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Analysis of DNA Deformations in Transcription Factor-DNA Complexes

Interactions between proteins and DNA are a key component of fundamental biological processes such as transcriptional regulation. DNA bending and other deformations are commonly observed in experimental structures of protein-DNA complexes, but the relation of these deformation upon binding to the interactions between the protein and DNA is not well understood, in particular, how much of the DNA shape is intrinsic to the sequence versus induced by binding of the protein. To investigate this question, we examined structural features of transcription factor-DNA complexes contained in the Protein Data Bank. Our dataset of about 700 X-ray structures were categorized according to the transcription factor classes. Geometrical parameters of the bound DNA recognition sequences were determined from the experimental structure and also calculated using the HT shape prediction method DNAshape (Zhou et al., 2013). Structural, chemical, and electrostatic features of the protein binding sites were also calculated. The calculated shape features of the bound DNA sequences were compared with the predicted shape features and correlations between the DNA bending and features of the protein interface within each superclass were investigated.

Zhou,T., Yang,L., Lu,Y., Dror,I., Dantas Machado,A.C., Ghane,T., Di Felice,R. and Rohs,R. (2013) DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res., 41, W56-W62.

Jared Sagendorf1
Helen M. Berman1, 2
Remo Rohs1

1 Molecular and Computational Biology Program
Department of Biological Sciences
Southern California
Los Angeles, CA 90089
2Center for Integrative Proteomics Research
Department of Chemistry and Chemical Biology
Rutgers University
Piscataway, NJ 08854