[Frontiers in Bioscience 12, 3419-3430, May 1, 2007]

Structural and electrostatic properties of ubiquitination and related pathways

Peter J. Winn1, Mai Zahran1,2,3, James N. D. Battey4, Yanxiang Zhou1,5, Rebecca C. Wade 1, Amit Banerjee6,7

1 EML Research gGmbH, Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany, 2 Department of Molecular and Genomic Bioinformatics, Denis Diderot University - Paris 7, Paris, France, 3 Computational Biochemistry, IWR, University of Heidelberg, 69120 Heidelberg, Germany, 4 Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland, 5 Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany, 6 Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit MI 48201-2417, USA, 7 Department of International Medical Education and Development, Rheinische Friedrich-Wilhelms-Universitaet, Faculty of Medicine, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Molecular electrostatic potential as a predictor of protein function
3.1. Examples of electrostatic potential as a predictor of function
3.2. Calculating and comparing electrostatic potentials
3.3. Electrostatic potentials and UFP ligation
3.4. Electrostatically key residues
3.5. Electrostatic potential and E2 function
3.6. Other UFP related proteins and their electrostatic potentials
3.7. The relationship between sequence and electrostatic potential
3.8. A webserver of ubiquitin related structures and electrostatic potentials
3.9. Ensuring the suitability of protein structures for calculating and comparing electrostatic potentials
4. Perspective
5. Acknowledgment
6. Reference

1. ABSTRACT

Post-translational modification by ubiquitin and ubiquitin-like (UBL) proteins is a key mechanism for cellular control. The specificity of the enzymes of ubiquitination and their close paralogs is dependent on their molecular electrostatic potentials. For example, analysis of molecular electrostatic potentials and electrostatically key residues can account for the selectivity of different E1s (activating enzymes) and of different SUMO proteases. The molecular interactions of the ubiquitin conjugating enzymes, the ubiquitin family proteins (UFP) and UBL domains are discussed in detail. An interesting observation is that the Non Canonical Ubiquitin Conjugating Enzymes (NCUBEs) have electrostatic potentials that are more similar to the UBC9 orthologs, the SUMO conjugating enzymes, than they are to other ubiquitin conjugating enzymes. It had previously been suggested that UBC9 may select for SUMO based on its difference in electrostatic potential as compared to other E2s but the NCUBE exception suggests that this may not be the case. The web site http://www.ubiquitin-resource.org/ allows users to find the E2s most electrostatically similar to a query E2. Where possible, models have been made for all E2 domains in the SMART database (http://smart.embl-heidelberg.de/). A brief overview of molecular electrostatic potentials and their application to understanding protein function is also given.