MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

Stansfeld, Phillip J.; Goose, Joseph E.; Caffrey, Martin; Carpenter, E.P.; Parker, Joanne L.; Newstead, Simon; Sansom, Mark S. P.

doi:10.1016/j.str.2015.05.006

Cited by 273 publications

(275 citation statements)

References 76 publications

Supporting

Mentioning

265

Contrasting

Order By: Relevance

“…The Martini 2.2 force field 51 was used to run an initial 1 μs Coarse Grained (CG) MD simulation to permit the assembly and equilibration of a 1---palmitoly, 2---cis---vaccenyl, phosphatidylglycerol (PVPG): 1---palmitoly, 2---cis---vaccenyl, phosphatidylethanolamine (PVPE) bilayers around the BamABCDE complexes 52 . Using the self---assembled system as a guide the coordinates of the BAM complexes were inserted into an asymmetric model E. coli OM, comprised of PVPE, PVPG, Cardiolipin in the periplasmic leaflet and the inner core of Rd1 LPS lipids in the outer leaflet 53 , using Alchembed 54 .…”

Section: Molecular Modelling and Simulationsmentioning

confidence: 99%

Structural basis of outer membrane protein insertion by the BAM complex

Dong

et al. 2016

Nature

263

462

View full text Add to dashboard Cite

3Outer membrane proteins (OMPs) play important roles in Gram-negative bacteria, mitochondria and chloroplasts in nutrition transport, protein import, secretion, and other fundamental biological processes [1][2][3] . Dysfunction of mitochondria outer membrane proteins are linked to disorders such as diabetes, Parkinsons and other neurodegenerative diseases 4,5 . The OMPs are inserted and folded correctly into the outer membrane (OM) by the conserved OMP85 family proteins [6][7][8] , suggesting that similar insertion mechanisms may be used in Gram-negative bacteria, mitochondria and chloroplasts.In Gram-negative bacteria, OMPs are synthesized in the cytoplasm, and are transported across the inner membrane by SecYEG into the periplasm 8,9 . The seventeen kilodalton (kDa) protein (Skp) and the survival factor A (SurA) chaperones escort the unfolded OMPs across the periplasm to the β-barrel assembly machinery (BAM), which is responsible for insertion and assembly of OMPs into the OM 10-12 . InEscherichia coli, the BAM complex consists of BamA and four lipoprotein subunits, BamB, BamC, BamD and BamE. BamA is comprised of five N-terminal polypeptide transport-associated (POTRA) domains and a C-terminal OMP transmembrane barrel, while the four lipoproteins are affixed to the membrane by N-terminal lipid-modified cysteines. Of these subunits, BamA and BamD are essential 3,6 . One copy of each of these five proteins is required to form the BAM complex with an approximate molecular weight of 200 kDa (Extended Data Fig. 1). In vitro reconstitution of the E.coli BAM complex and functional assays showed that all five subunits are required to obtain the maximum activity of BAM [13][14][15][16] . Furthermore, comparison of the two complexes reveals that the periplasmic units are rotated with respect to the barrel, which appears to be linked to significant conformational changes in the β-strands β1C-β6C of the barrel. Taken together this suggests a novel insertion mechanism whereby rotation of the BAM periplasmic ring promotes insertion of OMPs into the OM. To our knowledge, this is the first reported crystal structure of an intramembrane barrel with a lateral-open conformation.Unique architecture of two E. coli BAM complexes X-ray diffraction data of selenomethionine labelled crystals were collected to 3.9Ångström (Å) resolution and the BAM structure was determined by singlewavelength anomalous dispersion (SAD) and manual molecular replacement (Methods, Extended Data Table 1). The first structure contained four proteins: BamA, BamC, BamD and BamE (Fig. 1a-c), with the electron density and crystal packing indicating that the BamB is absent in the complex. This was confirmed by SDS-PAGE analysis of the crystals (Extended Data Fig. 1 and Supplementary Data Fig. S1). In this model, BamA, BamC, BamD and BamE contain residues E22-I806, C25-K344, E26-S243, and C20-E110, respectively. The machinery is approximately 115 Å in length, 84 Å in width and 132 Å in height (Fig. 1a). 5The architecture of BamACDE resembles a top hat with a...

show abstract

Section: Molecular Modelling and Simulationsmentioning

confidence: 99%

Structural basis of outer membrane protein insertion by the BAM complex

Dong

et al. 2016

Nature

263

462

View full text Add to dashboard Cite

show abstract

“…However, large-scale membrane deformations and lipid translocation are slow processes that are difficult to study with traditional fully atomistic molecular dynamics (MD) simulations, given current computational limitations. To mitigate some of these concerns, Sansom and coworkers (14) used their membrane protein simulation pipeline, MemProtMD, to run less demanding coarse-grained simulations on nhTMEM16. Over the course of 1 µs, the authors observed approximately 15 lipids traverse the hydrophilic groove from the extracellular to the cytoplasmic leaflet of the membrane.…”

mentioning

confidence: 99%

Atomistic insight into lipid translocation by a TMEM16 scramblase

Bethel

Grabe

2016

Proc. Natl. Acad. Sci. U.S.A.

104

159

View full text Add to dashboard Cite

The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane-protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup-dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane-even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation.TMEM16 | lipid scrambling | continuum membrane models | simulation | anoctamin T he compositional asymmetry between the leaflets of the plasma membrane influences the signaling properties of cells. Scramblases are a class of proteins that disrupt membrane asymmetry by facilitating the transfer of phospholipids from one leaflet to the other in an energy-independent manner. These transmembrane proteins play a role in events such as coagulation of the blood and cellular apoptosis by transporting phosphatidylserine (PS) from the inner leaflet to the outer leaflet of the plasma membrane (1). In particular, transmembrane protein 16 (TMEM16) family members have gained recent attention for their role in phospholipid scrambling in platelets and fungi. The TMEM16 family members have diverse functions. For example, TMEM16A and -B are calcium-activated chloride channels, TMEM16F is a nonspecific cation channel and scramblase, and the fungal Aspergillus fumigatus TMEM16 is another dual scramblase/ion channel (2-6).The structure of the Nectria haematococca TMEM16 (nhTMEM16) membrane protein revealed a possible mechanism for phospholipid conduction across the membrane (Fig. 1A) (7). The protein forms a dimer, and each subunit has a hydrophilic groove composed of polar...

show abstract

“…1 C). The simulated protein position closely resembled that obtained using the coarse-grained MemProtMD protocol (57). Because the OPM database (30) outputs the position of the two planes, one cannot expect a perfect agreement.…”

Section: Discussionmentioning

confidence: 55%

“…1 C). We compared the protein insertion position achieved by our atomistic simulation protocol with that reported in the MemProtMD database (57), which relies on a coarse-grained MD simulation lipid partitioning protocol, and observed very similar results (Fig. S7 B).…”

Section: Lipid Partitioning Of the Cu D Atpase Membrane Domainmentioning

confidence: 58%

Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport

Grønberg

Sitsel

Lindahl

et al. 2016

Biophysical Journal

View full text Add to dashboard Cite

Cu þ -specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu þ -binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu þ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu þ delivery. Mutational analyses and simulations in the presence and absence of Cu þ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu þ -transporting P-type ATPases.

show abstract

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

Cited by 273 publications

References 76 publications

Structural basis of outer membrane protein insertion by the BAM complex

Structural basis of outer membrane protein insertion by the BAM complex

Atomistic insight into lipid translocation by a TMEM16 scramblase

Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport

Contact Info

Product

Resources

About