ABCMdb

PMID: 17116404

Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS
Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
J Struct Biol. 2007 Mar;157(3):593-605. Epub 2006 Oct 20., [PubMed]

Sentences

No. Mutations Sentence Comment

11 ABCC7 p.Ile231Asp In an I231D mutant, the M3-M4 hairpin is additionally stabilized via an inter-helix Q207/D231 interaction. Login to comment 94 ABCC7 p.Ile231Asp ABCC7 p.Ile231Asp Simulation Duration (ns) Number of lipids/waters Approximate bilayer/micelle formation time (ns) WALP16 3 £ 200 256 DPPC + 3,187 W 10, 8, 26 WALP19 3 £ 200 256 DPPC + 3,228 W 144, 49, 41 WALP23 3 £ 200 256 DPPC + 3,133 W 8, 40, 33 LS3 3 £ 200 256 DPPC + 3,333 W 20, 80, 40 Vpu 3 £ 200 256 DPPC + 3,117 W 7, 14, 20 Fd 3 £ 200 256 DPPC + 3,150 W 60, 16, 92 CFTR M3-M4 WT 3 £ 500 64 DPC + 15,551 W 60, 90, 100 CFTR M3-M4 I231D 1 £ 500, 64 DPC + 15,546 W 200 2 £ 200 120, 100 LacY CG 1 £ 200 217 DPPC + 2,504 W 20 LacY AT 1 £ 50 173 DMPC + 14,845 W - lipid bilayers (Im and Brooks, 2005;Nymeyer et al., 2005;Petrache et al., 2002). Login to comment 147 ABCC7 p.Ile231Asp (B) Start and end snapshots for the CFTR M3-M4 I231D simulation. Login to comment 148 ABCC7 p.Ile231Asp ABCC7 p.Ile231Asp (B) Start and end snapshots for the CFTR M3-M4 I231D simulation. Login to comment 149 ABCC7 p.Ile231Asp The initial structure is the starting model of the CFTR M3-M4 I231D mutant, modelled (based on secondary structure predictions) as two -helices connected by an extended loop. Login to comment 219 ABCC7 p.Val232Asp It is thought that the Q207 sidechain in M3 may form an interhelical H-bond with a CF-phenotypic mutant V232D in M4 (Therien et al., 2001). Login to comment 220 ABCC7 p.Val232Asp ABCC7 p.Ile231Asp It is thought that the Q207 sidechain in M3 may form an interhelical H-bond with a CF-phenotypic mutant V232D in M4 (Therien et al., 2001). Login to comment 221 ABCC7 p.Ile231Asp ABCC7 p.Ile231Asp Asp-scanning mutagenesis, in which Asp was placed in M4 successively at residues 221-241, combined with gel shift assays to assess H-bonding suggested that the I231D formed the strongest predicted hydrogen bond with Q207 (Choi et al., 2004). Login to comment 222 ABCC7 p.Ile231Asp To explore the nature of -helical hairpin formation in CFTR M3-M4 we therefore performed two simulations, of CFTR M3-M4 WT and of the I231D mutant. Login to comment 232 ABCC7 p.Ile231Asp Interestingly, the average time for formation of a stable micelle was &#bb;80 ns for the WT, but &#bb;140ns for the I231D mutant. Login to comment 233 ABCC7 p.Ile231Asp Interestingly, the average time for formation of a stable micelle was »80 ns for the WT, but »140ns for the I231D mutant. Login to comment 241 ABCC7 p.Ile231Asp (A) Distributions of distance between the sidechain particles for residues 207 and 231 for simulations CFTR M3-M4 WT (black line) and M3-M4 I231D (grey line). Login to comment 242 ABCC7 p.Ile231Asp (A) Distributions of distance between the sidechain particles for residues 207 and 231 for simulations CFTR M3-M4 WT (black line) and M3-M4 I231D (grey line). Login to comment 243 ABCC7 p.Ile231Asp For the WT snapshot the two spheres represent the Q207 and I231 sidechain particles, for the I231D snapshot they correspond to Q207 and D231. Login to comment 244 ABCC7 p.Ile231Asp For the WT snapshot the two spheres represent the Q207 and I231 sidechain particles, for the I231D snapshot they correspond to Q207 and D231. Login to comment