8. If there are missing residues in the initial subunit, i.e., inherited
from crystal or NMR structures, IMP will replace these missing
residues using flexible beads. The movement of these beads are
controlled by the “bead_max_trans” variable (see Note 13).
9. A list of subunits will need to be given to IMP via a “rigid_bodies” list. In the current format, each subunit will be permitted
translational and rotational movement independently from the
other subunits. Several examples of rigid body groups that can
be set are shown in Fig. 7c.
10. Next, lines 57–102 are needed to set the coarse-grained representation of the subunits. Each subunit listed in “topology.txt”
will be replaced by a bead model which will take into account
the “bead_size” parameter as its resolution.
11. Each subunit is automatically given a color for loop on line 74.
12. The ability of each subunit and flexible bead to move is set up
by lines 93–102.
13. Finally, the restraint section “Define Scoring Function Components” defines the variables necessary for restraint-guided
modeling.
3.7 Modeling
Restraints
1. The first restraint is the excluded volume restraint—this prevents unrealistic overlapping in space through calculating the
volume of each subunit per iteration and avoiding steps which
promote overlap.
2. The excluded volume restraint is computationally expensive to
calculate, and thus, the volume is approximated by bead resolution (by default set to 20) on line 115.
3. Lines 117 and 118 add the restraint to the bead model.
4. Next, we will add two cross-link restraints to our tryptophan
synthase system, xl1 and xl2.
5. xl1 is the stoichiometry restraint which will enforce alpha–
beta–beta–alpha connectivity in our modeling. The xl1
restraint can be adjusted by variables listed in Table 2.
6. The “length” variable passed into xl1 is defined by the approximate distance between the alpha and beta subunits as measured
from their centers (approximately equal to the sum radius of
alpha and beta subunits). This distance is approximate and
serves to enforce the topology of the system by preventing
the subunits from moving too far away from their designated
binding partners.
7. The xl2 restraint includes cross-links determined for the tryptophan synthase complex. Lines 146–158 are parametrized
identically to xl1; however, the distance threshold “length,”
“slope,” and “label” has been altered.
Mass Spectrometry-Based Protein Modelling
233
from crystal or NMR structures, IMP will replace these missing
residues using flexible beads. The movement of these beads are
controlled by the “bead_max_trans” variable (see Note 13).
9. A list of subunits will need to be given to IMP via a “rigid_bodies” list. In the current format, each subunit will be permitted
translational and rotational movement independently from the
other subunits. Several examples of rigid body groups that can
be set are shown in Fig. 7c.
10. Next, lines 57–102 are needed to set the coarse-grained representation of the subunits. Each subunit listed in “topology.txt”
will be replaced by a bead model which will take into account
the “bead_size” parameter as its resolution.
11. Each subunit is automatically given a color for loop on line 74.
12. The ability of each subunit and flexible bead to move is set up
by lines 93–102.
13. Finally, the restraint section “Define Scoring Function Components” defines the variables necessary for restraint-guided
modeling.
3.7 Modeling
Restraints
1. The first restraint is the excluded volume restraint—this prevents unrealistic overlapping in space through calculating the
volume of each subunit per iteration and avoiding steps which
promote overlap.
2. The excluded volume restraint is computationally expensive to
calculate, and thus, the volume is approximated by bead resolution (by default set to 20) on line 115.
3. Lines 117 and 118 add the restraint to the bead model.
4. Next, we will add two cross-link restraints to our tryptophan
synthase system, xl1 and xl2.
5. xl1 is the stoichiometry restraint which will enforce alpha–
beta–beta–alpha connectivity in our modeling. The xl1
restraint can be adjusted by variables listed in Table 2.
6. The “length” variable passed into xl1 is defined by the approximate distance between the alpha and beta subunits as measured
from their centers (approximately equal to the sum radius of
alpha and beta subunits). This distance is approximate and
serves to enforce the topology of the system by preventing
the subunits from moving too far away from their designated
binding partners.
7. The xl2 restraint includes cross-links determined for the tryptophan synthase complex. Lines 146–158 are parametrized
identically to xl1; however, the distance threshold “length,”
“slope,” and “label” has been altered.
Mass Spectrometry-Based Protein Modelling
233