Introduction Features Methods and Definitions Precision Classification Comparision with experimental data Comparision with other computational methods Topology definitions Acknowledgements

Methods and Definitions

Transmembrane proteins

Each protein is considered as rigid body that freely floats in a hydrophobic slab of adjustable thickness.

Orientation of the protein was determined by minimizing its transfer energy, ΔG_transfer, with respect to d, z₀, Θ and φ variables in a coordinate system whose axis Z coincides with the bilayer normal:

Figure 1. Schematic representation of a transmembrane protein in a hydrophobic slab.
d, shift along the bilayer normal; D, hydrophobic thickness (D=2z₀); φ, rotation angle; τ, tilt angle.

where ASA_i is the accessible surface area of atom i. σ_i^W-M is solvation parameter of atom i (its transfer energy from water to membrane interior expressed in kcal/mol per Å²). d is shift of the protein center along the Z axis. z₀ is half of membrane hydrophobic thickness. τ tilt angle of protein axis relative to Z axis. φ rotation angle defines the direction of the tilt.

Longitudinal axes of TM proteins are calculated as vector averages of TM segment vectors.

Peripheral/Monotopic proteins

These proteins do not span the membrane. Therefore, they have no hydrophobic thickness, and their ΔG_transfer depends on only three variables (φ, τ and d). Instead of the hydrophobic thickness, we present maximal membrane penetration depths of their atoms (D) in all Tables and Figure 3. The longitudinal axis of a peripheral protein (Figure 1) is defined as an axis that provides minimal moment of inertia (this is different from definition of a longitudinal axis of a transmembrane α-bundle or β-barrel). Transfer energies of peripheral proteins were calculated without ligands, except for 1joc, 1bwn, 1h6h and 1rsy.

The membrane water-penetration profile, f(z_i), was taken in the Boltzmann sigmoidal form that fits results of EPR studies on spin-labeled phospholipids (λ ∼0.9 Å, Marsh 2002):

Marsh D. (2001) Polarity and permeation profiles in lipid membranes Proc. Nat. Acad. Sci. USA 98: 7777-7782.

solvation parameters, σ_i , were derived from partition coefficients of organic compounds between water and 1,9-decadiene and between water and hexadecene (Table 1).
contributions of pore-facing residues were eliminated.
ionization energies of lipid-facing charged groups were calculated and included in solvation parameters of their polar atoms.

**Table 1.** Atomic solvation parameters (σ) applied for simulations of transmembrane proteins.
Scale	σ,cal/mol A²
Scale	C-sp3	C-sp2	S	N	O
Water-hexadecene (detergent scale)^a	25	19	-13	-55	-63
Water-decadiene (lipid bilayer scale)^a	22.6	19	-10	-53	-57

^a Lomize A.L., Pogozheva I.D., and Mosberg H.I. (2004) Quantification of helix-helix binding affinities in micelles and lipid bilayers. Protein Sci. 13: 2600-2612.