TABLE 2.

Definition of the parameters used in the two-helix model of proteins embedded in lipid bilayers

Parameter	Range/value	Unit	Description
N0	26	–	The position of a reference amino acid residue. The projection of its Cα to the helix axis of the protein O gives the origin of the coordinate system of the protein. Position n0 = 26 was selected for the transmembrane domain of M13 major coat protein.
h	1.5	Å	Translation per amino acid residue along the helix; 1.5 Å for a perfect α-helix.
nr	3.6	–	Number of amino acid residues per one turn; 3.6 for a perfect α-helix.
nD	26	–	Donor position; position of amino acid residue given by the donor. For M13 coat protein the donor is Trp-26, which is located in the transmembrane domain.
nA	1–50	–	Acceptor position; position of amino acid residue labeled by the acceptor. For the transmembrane domain of M13 coat protein, the acceptor positions are 24, 38, and 46.
lD	6.5	Å	Donor arm, the average distance from the donor moiety to the helix axis. A value lD = 6.5 Å was taken (7).
lA	9.5	Å	Acceptor arm, the average distance from the acceptor moiety to the helix axis. A value lA = 9.5 Å was taken (7).
nk	1–25	–	Position of helix kink; position of amino acid residue from which the N-terminal helix starts.
θ	18	°	Protein tilt angle; the angle between the helix axis and the normal to the membrane. The value of 18° is found in the previous study (3).
d	8.5	Å	Distance from the origin of the coordinate system of the protein to the centre of the bilayer is 8.5 Å (3).
ψ	60	°	Protein tilt direction; the direction of the protein transmembrane domain tilting is ∼60° as found earlier (3,7).
NP	500	–	Number of proteins in the system. All simulations were performed for models containing 500 proteins.
SL	72	Å2	Area occupied by a lipid in one leaflet of a bilayer; the average area for the DOPC/DOPG system is 72 Å2 (17).
L	0.0–1.0	–	Lipid loss; ratio of lipids lost during dialysis to their initial quantity.
DP	10	Å	Protein exclusion distance; minimal protein-protein distance. For M13 coat protein a value DP = 10 Å was taken.
rLP	≥0	–	Lipid to protein molar ratio.
rul	≥0	–	Ratio between the number of unlabeled and labeled proteins.
k	0	–	Protein-protein association probability, defined as the percentage of clustered proteins with respect to the total number of proteins, for considered case ∼0 (3,30).
R0	24	Å	Förster distance. A value of 24 Å is calculated using the data about the photophysical properties of the donor and acceptor.
ϕ	0–90	°	N-terminal helix tilt angle; the angle between the main axes of the two protein domains.
ξ	−180–180	°	N-terminal helix tilt direction; the direction of the N-terminal helix with respect to the x axis of the protein axis system.
ω	−180–180	°	N-terminal helix coaxial rotation; the turning angle of N-terminal helix around its main axis defining the direction of amino acid residues (toward water or lipid phase). The case ω = 0° corresponds to an ideal α-helix, bent at position nk by angle ϕ.

In the simulations the parameters n_k, ϕ, ω, ξ, and L are varied. Parameters n_A, r_LP and r_ul are determined by the experiment; the other parameters are taken from previous work (3) and are fixed as shown in the table.