proteins STRUCTURE O FUNCTION O BIOINFORMATICS PREDICTION REPORT In silico study of the human rhodopsin and meta rhodopsin II/S-arrestin complexes: Impact of single point mutations related to retina degenerative diseases Leonardo Mokarzel-Falco´n, 1,2 Juan Alexander Padro´n-Garcı´a, 2 * Ramo´n Carrasco-Velar, 3 Colin Berry, 4 and Luis A. Montero-Cabrera 2 1 Microbiology and Virology Department, Biology Faculty, Havana University, Havana 10400, Cuba 2 Laboratory of Theoretical and Computational Chemistry, Chemistry Faculty, Havana University, Havana 10400, Cuba 3 Pharmaceutical Chemistry Center, Havana 16042, Cuba 4 School of Biosciences, Cardiff University, Cardiff CF10 3US, Wales, United Kingdom INTRODUCTION G-protein-coupled receptors (GPCRs) are a large class of membrane proteins that constitute the central components of a variety of biological signal transmission pathways. 1–3 Those pathways involve a variety of crucial biological func- tions such as cell proliferation and survival, angiogenesis, and light and odor detection. 4 Arrestins play a key role in the regulation of the signaling and trafficking of the major- ity of GPCRs. 5 In the phototransduction process, a proto- typical GPCR-driven signaling system, visual S-arrestin demonstrates an exquisite selectivity for light-activated phosphorylated rhodopsin, its cognate receptor. 6 However, S-arrestin binding is not an ‘‘all-or-nothing’’ event: it binds with low affinity to light-activated unphosphorylated rho- dopsin and inactive dark phosphorylated rhodopsin. The structural characteristics that control this phase are not completely elucidated, since the crystallographic structures of the bovine rhodopsin and the S-arrestin are solved but the structure of the complex is still unknown. 7 Moreover, the light-activated unphosphorylated rhodopsin, inactive dark phosphorylated rhodopsin, and activated S-arrestin Grant sponsor: Royal Society International Joint Project Grant. *Correspondence to: Juan Alexander Padro´ n-Garcı ´a, Laboratory of Theoretical and Computational Chemistry, Chemistry Faculty, Havana University, Havana 10400, Cuba. E-mail: padrongj@fq.uh.cu Received 25 April 2007; Revised 2 August 2007; Accepted 31 August 2007 Published online 3 January 2008 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/prot.21873 ABSTRACT We propose two models of the human S-arrestin/rhodopsin complex in the inactive dark adapted rhodopsin and meta rhodopsin II form, obtained by homology modeling and knowledge based docking. First, a homology model for the human S-arrestin was built and validated by molecular dy- namics, showing an average root mean square deviation dif- ference from the pattern behavior of 0.76 A ˚ . Then, combin- ing the human S-arrestin model and the modeled structure of the two human rhodopsin forms, we propose two models of interaction for the human S-arrestin/rhodopsin complex. The models involve two S-arrestin regions related to the N domain (residues 68–78; 170–182) and a third constituent of the C domain (248–253), with the rhodopsin C terminus (330–348). Of the 22 single point mutations related to reti- nitis pigmentosa and congenital night blindness located in the cytoplasmatic portion of rhodopsin or in S-arrestin, our models locate 16 in the interaction region and relate two others to possible dimer formation. Our calculations also predict that the light activated complex is more stable than the dark adapted rhodopsin and, therefore, of higher affinity to S-arrestin. Proteins 2008; 70:1133–1141. V VC 2008 Wiley-Liss, Inc. Key words: homology modeling; knowledge based docking; retinitis pigmentosa; congenital night blindness; G-protein- coupled receptors; single point mutations; molecular dynam- ics; GRAMM; Stc; fold-X. V VC 2008 WILEY-LISS, INC. PROTEINS 1133