Detergent organisation in crystals of monomeric outer membrane phospholipase A

Snijder, H.J.; Timmins, Peter; Kalk, K.H.; Dijkstra, Bauke W.

doi:10.1016/s1047-8477(02)00579-8

Cited by 20 publications

(6 citation statements)

References 40 publications

(47 reference statements)

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“…This result is consistent with experimental observations [82-86], including NMR studies of detergent-embedded residues of OmpX [82], analysis of the thickness of the detergent belt in crystals of OmpLA [83], and neutron scattering studies using contrast variation of LPS bilayers [84, 85]. …”

Section: Discussionsupporting

confidence: 89%

Structural adaptations of proteins to different biological membranes

Pogozheva

Tristram-Nagle

Mosberg

et al. 2013

Biochimica et Biophysica Acta (BBA) - Biomembranes

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To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5 Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22 Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4 Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8 Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds.

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Section: Discussionsupporting

confidence: 89%

Structural adaptations of proteins to different biological membranes

Pogozheva

Tristram-Nagle

Mosberg

et al. 2013

Biochimica et Biophysica Acta (BBA) - Biomembranes

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“…Moreover, the calculated membrane boundary planes of the proteins closely correspond to the borders of the detergent monolayer. For example, these planes pass through the aromatic rings of Trp78, Trp98, Phe109, and Phe122 residues in monomeric phospholipase A (OmpLA) in agreement with neutron diffraction (Snijder et al 2003).…”

Section: Comparison With Studies Of Tm Proteins In Detergentssupporting

confidence: 62%

Positioning of proteins in membranes: A computational approach

et al. 2006

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A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were ;1 Å and 2°, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 Å depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26°in asymmetric structures. Calculated hydrophobic boundaries of proteins are located ;5 Å lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database: http://opm.phar.umich.edu/.

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“…Membrane exposed and inward residues were predicted by a grid-based algorithm, and HDGB models were modified to treat the surface residues with implicit membrane and inside residues with bulk implicit water. Based on proteins for which the width of membranes near membrane proteins has been determined from experimental methods, − we found a good match with the experiments using our new HDGB-based protocol and better agreement than with the established OPM and PDBTM protocols. In the following, the protocol for predicting hydrophobic lengths is described before test results are presented and discussed.…”

Section: Introductionsupporting

confidence: 52%

Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model

Dutagaci

Feig

2017

J. Chem. Inf. Model.

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A protocol for predicting the hydrophobic length of membrane proteins using the heterogeneous dielectric generalized Born (HDGB) implicit membrane model is presented. The method involves optimal positioning in the membrane and identification of lipid-facing and inward-facing residues, followed by energy optimization of the implicit membrane model to obtain the hydrophobic length from the optimal membrane width. The latest HDGB version 3 (HDGBv3) and HDGB van der Waals (HDGBvdW) models were applied to a test set containing 15 proteins (seven β-barrel and eight α-helical proteins), for which matching membrane widths are available from experiment, and an additional set contains ten α-helical and ten β-barrel proteins without any experimental data. The results with the HDGB model compare favorably with predictions from methods used in the Orientations of Proteins in Membranes (OPM) and Protein Data Bank of Transmembrane Proteins (PDB-TM) databases.

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Detergent organisation in crystals of monomeric outer membrane phospholipase A

Cited by 20 publications

References 40 publications

Structural adaptations of proteins to different biological membranes

Structural adaptations of proteins to different biological membranes

Positioning of proteins in membranes: A computational approach

Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model

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