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# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
# G. Bellesia, AI Jewett, and J-E Shea,
# Protein Science, Vol19 141-154 (2010)
#
# Strategy:
#
#1) First I'll define some building blocks (A16, B16, T3)
# which are helices, sheets and turns of a predetermined length)
#
#2) Then I'll copy and paste them together to build
# a 4-helix bundle (or a 4-strand beta-barrel).
# This approach is optional. If your protein has helices which are not
# identical, you should probably just include all 4 helices in a single
# "Data Atoms" section and don't try to subdivide the protein into pieces.)
1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
# A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
A16 {
# AtomID MoleculeID AtomType Charge X Y Z
write('Data Atoms') {
$atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0
$atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6
$atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2
$atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8
$atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4
$atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0
$atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6
$atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2
$atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8
$atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4
$atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0
$atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6
$atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2
$atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8
$atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4
$atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0
}
write('Data Bonds') {
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
}
} # A16
T3 { # T3 is a "turn" region consisting of 3 beads
# AtomID MoleculeID AtomType Charge X Y Z
write('Data Atoms') {
$atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0
$atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44
$atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0
}
write('Data Bonds') {
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
}
} # T3
# ----- Now build a larger molecule using A16 and T3 -------
# Create a 4-Helix bundle.
# In this version, the hydrophobic beads are poing outward.
# I oriented them this way because I want to place this protein in a membrane.
# (There is another file in this directory containing alternate version
# of this same molecule with the hydrophobic beads pointing inward.)
4HelixInsideOut {
helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6)
turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
write('Data Bonds') {
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
}
create_var { $mol } # molecule ID number shared by all atoms in this protein
} # 4HelixInsideOut
# -------------- Force-Field Parameters ------------
# Units and force-field styles for this protein model
# (These can be overridden later.)
write_once("In Init") {
units real
atom_style full
bond_style hybrid harmonic
angle_style hybrid harmonic
dihedral_style hybrid class2
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
pair_modify mix arithmetic
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
}
# --- Distance Units ---
# In this version of the model, sigma (the bond-length
# and particle diameter) is rounded to 6.0 Angstroms.
#
# --- Energy & Temperature Units ---
# In this protein model, "epsilon" represents the free energy
# bonus for bringing two hydrophobic amino acids together.
# Here I choose to set epsilon to 1.806551818181818 kCal/mole.
# This value was chosen so that a temperature of 300 Kelvin lies at
# 0.33 epsilon, which is the unfolding temperature of the marginally stable
# "ASF1" protein model from the Bellesia et al 2010 paper.
# This choice insures that both the "ASF1" model from that paper,
# as well as the much more stable "AUF2" protein we use here (which
# unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
# in the bulk at least. (However it's not clear that these energy
# parameters will work well for a protein in membrane. Perhaps I'll
# run some tests and fine tune these parameters for this scenario.)
# 2-body (non-bonded) interactions:
#
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
#
# i j pairstylename eps sig K L
#
write_once("In Settings") {
# Override any pair_coeff and bond_coeff
# statements from the 1beadProteSci2010 model
# (Because the energies &distances in that model
# were in the wrong units.)
pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0
}
# The exact value of the bond_coeff does not matter too much as long as
# it is "stiff enough". Here I use a softer bond spring than the one
# used in the paper so that I can increase the time step.
# I also use a relatively soft spring to constrain the bond angles.
# bond_coeff bondType bondstylename k r0
write_once("In Settings") {
bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 6.0
}
# angleType atomtypes1 2 3 bondtypes1 2
write_once("Data Angles By Type") {
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
}
# angle_coeff angleType anglestylename k theta0
write_once("In Settings") {
angle_coeff @angle:backbone harmonic 100.0 105.0
}
# dihedralType atomtypes1 2 3 4 bondtypes1 2 3
write_once("Data Dihedrals By Type") {
# For a chain of sH and sL atoms, use the @dihedral:delta65_0
# parameters. (This corresponds to the "AUF2" model from the
# Bellesia et. al 2010 paper. Note: If you want the "AF" model,
# then change this to "delta60_0".)
@dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * *
# If tN atoms are present, use the @dihedral:turn parameters
@dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * *
@dihedral:turn @atom:tN @atom:tN @atom:* @atom:* * * *
@dihedral:turn @atom:tN @atom:tN @atom:tN @atom:* * * *
@dihedral:turn @atom:tN @atom:tN @atom:tN @atom:tN * * *
}
write_once("In Settings") {
dihedral_coeff @dihedral:delta60_0 class2 2.167862 120.0 0 0 2.167862 180.0
dihedral_coeff @dihedral:delta65_0 class2 2.167862 115.0 0 0 2.167862 180.0
dihedral_coeff @dihedral:turn class2 0 0 0 0 0.361310 180.0
# Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
# All of the cross-terms (for the class2 force-field) are zero (see docs):
dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0
dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0
dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0
dihedral_coeff @dihedral:delta65_0 class2 mbt 0 0 0 0
dihedral_coeff @dihedral:delta65_0 class2 ebt 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:delta65_0 class2 at 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:delta65_0 class2 aat 0 0 0
dihedral_coeff @dihedral:delta65_0 class2 bb13 0 0 0
dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0
dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0
dihedral_coeff @dihedral:turn class2 aat 0 0 0
dihedral_coeff @dihedral:turn class2 bb13 0 0 0
}
# --- Mass Units ---
# Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down):
write_once("Data Masses") {
@atom:1beadProtSci2010/sH 100.0
@atom:1beadProtSci2010/sL 100.0
@atom:1beadProtSci2010/tN 100.0
}
} # 1beadProtSci2010 (namespace)
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