Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Novel geometric approaches to uniquely characterize DNA binding interfaces

Protein nucleic-acid interactions play a critical role in all steps of the gene expression pathway. DNA binding proteins interact with DNA via distinct regions on their surface that are characterized by an ensemble of chemical, physical and geometrical properties. In previous studies we have developed unique approaches to characterize DNA binding proteins combining geometric and/or electrostatic features (Stawiski et al., 2003, Shazman et al., 2007, Shazman and Mandel-Gutfreund 2010). Here I will present a novel approach we have recently developed to characterize protein structures by the distribution of their overlapping local surface patches. In this approach the protein surface is represented by a bag of overlapping surface patches, which are defined by a central surface residue and its nearest surface neighbors. Using a similar approach to FragBag, a method used to retrieve proteins structure neighbors based on short contiguous backbone segments (Budowski-Tal etal., 2010), we characterize each protein by a ‘bag-of-surface patches’- a vector representing the distribution of different patches which appear on the protein surface. The similarity between two proteins is finally measured by the distance between their corresponding vectors of surface patches. Our results, based on a large benchmark of protein domains, show that the method has a great advantage over other methods for detecting remote function relationships between proteins based solely on the protein surface. We further show the applicability of the method to uniquely identify DNA binding interfaces accurately and efficiently.


  1. Stawiski, E.W., Gregoret, L.M. and Mandel-Gutfreund, Y. (2003). Annotating nucleic acid-binding function based on protein structure. J Mol Biol, 326, 1065-1079
  2. Shazman, S., Celniker, G., Haber, O., Glaser, F. and Mandel-Gutfreund, Y. (2007). Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res, 35, W526-530
  3. Shazman S, Elber G, Mandel-Gutfreund Y. (2011). From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res. 39:7390.
  4. Budowski-Tal, I., Nov, Y. & Kolodny, R. (2010). FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. PNAS, 107, 3481-3486.

Yael Mandel-Gutfreund

Faculty of Biology Technion, Haifa, Israel 32000

Ph: 972-4-8293958
Fx: 972-4-8225153
Email: yaelmg@tx.technion.ac.il