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Comparative Study
. 2006 Jun;15(6):1318-33.
doi: 10.1110/ps.062126106.

Positioning of proteins in membranes: a computational approach

Andrei L Lomize  1 , Irina D Pogozheva, Mikhail A Lomize, Henry I Mosberg
Affiliations
Comparative Study

Positioning of proteins in membranes: a computational approach

Andrei L Lomize et al. Protein Sci. 2006 Jun.

Abstract

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 approximately 1 A and 2 degrees, 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 A 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 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A 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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Figures

Figure 1.
Figure 1.
Schematic representation of a TM protein in a hydrophobic slab. Parameters that define the arrangement of a TM protein in the membrane hydrocarbon core: d, shift along the bilayer normal; τ, tilt angle; ϕ, rotational angle; and D = 2z0, hydrophobic thickness of the protein.
Figure 2.
Figure 2.
Comparison of calculated and experimental membrane penetration depths of spin-labeled Cys residues in TM proteins. Five TM proteins were studied: MscL channel (1msl, open square), FepA receptor (1fep, black triangle), KcsA channel (1r3j, gray triangle), bacteriorhodopsin (1py6, black diamond), and BtuB porin (1nqe, black circle). The experimental distances are taken from the original publications (Altenbach et al. 1990, 1994; Greenhalgh et al. 1991; Klug et al. 1997; Perozo et al. 1998, 2001; Fanucci et al. 2002) but counted relative to the depth where parameter Φ is equal to zero. Points with zero depth correspond to residues that have been identified as first or last in the membrane-embedded segments of α-helices of β-strands. Calculated depths are defined as distances from Cβ-atoms of the corresponding residues to the closest boundary plane.
Figure 3.
Figure 3.
Comparison of calculated membrane core boundaries with experimental data for lactose permease (1pv6) in lipid bilayer (A,B), for rhodopsin (1gzm) in native membrane (C) and in detergent (D), and for OmpX (1qj8) in detergent (E). The boundaries are indicated by blue dots for the inner membrane side and red dots for the outer membrane side. (A) Cys-substituted residues in lactose permease, which were modified by cross-linking thiosulfonate agents (Cβ-atoms are colored red). (B) Residues of lactose permease that can be modified by NEM are colored red, residues inaccessible to NEM are colored blue, and lipid-accessible residues identified in spin-labeling studies are colored green. (C) Residues of rhodopsin that were modified by hydrophilic (red) and hydrophobic (blue) chemical probes in native photoreceptor membranes. (D) Spin-labeled residues of rhodopsin in detergent assigned to nonpolar and polar environments by EPR are colored blue and red, respectively (residues with undefined environment are colored gray). (E) NH and CH3 groups of OmpX that form NOEs with hydrophobic tails of DHPC are colored blue and green, respectively. NH groups that interact with head groups of DHPC are colored red. (F) A schematic representation of a protein in a native membrane (left) or in detergent (right).
Figure 4.
Figure 4.
Hydrophobic thickness or membrane penetration depth (Dcalc) vs. transfer energy (ΔGtransf) plot for transmembrane (α-helical and β-barrel), integral monotopic, and peripheral proteins.
Figure 5.
Figure 5.
Dependence of fluctuations of hydrophobic thickness (A) and tilt angle (B) on the size of TM proteins. Transfer energy divided by hydrophobic thickness is roughly proportional to the length of the outer perimeter in TM proteins.
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