Journal of the Korean Magnetic Resonance Society 2011, 15, 80-89 * To whom correspondence should be addressed. E-mail : wson@cha.ac.kr 80 DOI : 10.6564/JKMRS.2011.15.1.080 3D Structure of STAM1 UIM-ubiquitin Complex Using RosettaDock Jongsoo Lim 2 , Jong-Jae Yi 1 , Hee-Chul Ahn 2 , Jin-Kyu Rhee 3 , and Woo Sung Son 1* 1 College of Pharmacy, CHA University, 198-1, Donggyo-dong, Pocheon-si, Gyeonggi-do 487-801, Republic of Korea 2 College of Pharmacy, Dongguk University-Seoul, Goyang, Gyeonggi 410-820, Republic of Korea 3 Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (Received May 5, 2011; accepted May 27, 2011) Abstract : 3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences. Keywords : RosettaDock; Protein-Protein Complex; Ubiquitin; STAM1; ESCRT; lysosomal degradation; UIM; VHS domain INTRODUCTION One of the important post-translational modifications is ubiquitination of proteins and this modification regulates a variety of cellular processes 1 . During ubiquitin-mediated selective trafficking of membrane proteins, ubiquitinated membrane proteins should be delivered inside of the