Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

@article{citeulike:2926178, abstract = {Abstract\ \ The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7\ ×\ 15\ ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the ‘quality’ of the starting structure seems mainly to influence the simulation stability of the transmembrane β-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for \>50\% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal α-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a ∼10\ ns timescale.}, author = {Cox, Katherine and Bond, Peter and Grottesi, Alessandro and Baaden, Marc and Sansom, Mark }, citeulike-article-id = {2926178}, doi = {http://dx.doi.org/10.1007/s00249-007-0185-8}, journal = {European Biophysics Journal}, keywords = {compare, md, membrane, protein, simulation}, month = {February}, number = {2}, pages = {131--141}, posted-at = {2008-06-25 16:48:52}, priority = {2}, title = {Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers}, url = {http://dx.doi.org/10.1007/s00249-007-0185-8}, volume = {37}, year = {2008} }

TY - JOUR ID - citeulike:2926178 L3 - citeulike-article-id:2926178 N2 - Abstract  The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7 × 15 ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the ‘quality’ of the starting structure seems mainly to influence the simulation stability of the transmembrane β-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for >50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal α-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a ∼10 ns timescale. IS - 2 JF - European Biophysics Journal EP - 141 TI - Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers VL - 37 SP - 131 KW - compare KW - md KW - membrane KW - protein KW - simulation AU - Cox, Katherine AU - Bond, Peter AU - Grottesi, Alessandro AU - Baaden, Marc AU - Sansom, Mark PY - 2008/02/11/ UR - http://dx.doi.org/10.1007/s00249-007-0185-8 ER -