Paper Citing NAMD - Abstract
Mnpotra, Jagjeet S.; Qiao, Zhuanhong; Cai, Jian; Lynch, Diane L.; Grossfield, Alan; Leioatts, Nicholas; Hurst, Dow P.; Pitman, Michael C.; Song, Zhao-Hui; Reggio, Patricia H.
Structural Basis of G Protein-coupled Receptor-G(i) Protein Interaction FORMATION OF THE CANNABINOID CB2 RECEPTOR-G(i) PROTEIN COMPLEX
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:20259-20272, JUL 18 2014
In this study, we applied a comprehensive G protein-coupled receptor-G alpha(i) protein chemical cross-linking strategy to map the cannabinoid receptor subtype 2 (CB2)-G alpha(i) interface and then used molecular dynamics simulations to explore the dynamics of complex formation. Three cross-link sites were identified using LC-MS/MS and electrospray ionization-MS/MS as follows: 1) a sulfhydryl cross-link between C3.53(134) in TMH3 and the G alpha(i) C-terminal i-3 residue Cys-351; 2) a lysine cross-link between K6.35(245) in TMH6 and the G alpha(i) C-terminal i-5 residue, Lys-349; and 3) a lysine cross-link between K5.64(215) in TMH5 and the G alpha(i) alpha(4)beta(6) loop residue, Lys-317. To investigate the dynamics and nature of the conformational changes involved in CB2 center dot G(i) complex formation, we carried out microsecond-time scale molecular dynamics simulations of the CB2 R*center dot G alpha(i1)beta(1)gamma(2) complex embedded in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer, using cross-linking information as validation. Our results show that although molecular dynamics simulations started with the G protein orientation in the beta 2-AR*center dot G alpha(s)beta(1)gamma(2) complex crystal structure, the G alpha(i1)beta(1)gamma(2) protein reoriented itself within 300 ns. Two major changes occurred as follows. 1) The G alpha(i1) alpha 5 helix tilt changed due to the outward movement of TMH5 in CB2 R*. 2) A 25 degrees clockwise rotation of G alpha(i1)beta(1)gamma(2) underneath CB2 R* occurred, with rotation ceasing when Pro-139 (IC-2 loop) anchors in a hydrophobic pocket on G alpha(i1) (Val-34, Leu-194, Phe-196, Phe-336, Thr-340, Ile-343, and Ile-344). In this complex, all three experimentally identified cross-links can occur. These findings should be relevant for other class A G protein-coupled receptors that couple to G(i) proteins.
