Prediction of Protein-Protein Binding Interfaces - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 103

Chapter 6
Prediction of Protein-Protein Binding Interfaces

Damian Marchewka , Wiktor Jurkowski , Mateusz Banach, and Irena
Roterman-Konieczna

Keywords HADDOCK ￿ ZDOCK ￿ RosettaDock ￿ Oil drop ￿ Sequence conservation
￿ Mutagenesis ￿ Epitope mapping ￿ H-D exchange ￿ Crosslinking experiments
￿ Solvated docking ￿ Ambiguous Interaction Restraints (AIRs) ￿ Rotamer packing ￿ Side-
chain rotamer probabilities ￿ Monte Carlo-based modeling package ￿ Geometric
alignment ￿ Fast Fourier Transform algorithms ￿ CHARMM forcefields ￿ Homodimer
￿ Pair-wise interaction ￿ Lock-key ￿ Fuzzy oil drop

6.1 Introduction

When it comes to regulating protein activity, complexation mechanisms are just as
important as ligand binding. Most proteins never exist in isolation - instead they
serve as building blocks for more complex systems. Some proteins form multimers
to ensure maintain spatial alignment (required e.g. for phase separation in the dual
lipid layer and formation of hydrophilic compartments in ion channels (Unwin
2005 ; Jasti et al.. 2007 )); others may require temporary binding of cofactors (e.g.
regulation of transcription factors (Huxford et al. 1998 )), or are part of complicated
protein machinery (e.g. proton-driven rotors in ATP synthases (Boyer 1997 ; Oster
and Wang 1999, 2003 ) ).

D. Marchewka ￿ M. Banach ￿ I. Roterman-Konieczna ( * )
Department of Bioinformatics and Telemedicine , Jagiellonian
University - Medical College , Lazarza 16 , 31-530 Cracow , Poland
e-mail: [e-mail]
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University,
Reymonta 4 , 30-059 Cracow , Poland
W. Jurkowski
Computational Biology Group, Luxembourg Centre for Systems
Biomedicine, University of Luxembourg, Campus Belval 7, avenue des
Hauts-Fourneaux , L-4362 Esch-Belval , Luxembourg