scripting_documentation/RosettaScripts/Movers/SpliceOutAntibody

Table of Contents

Author

Gideon Lapidoth; glapidoth@gmail.com; PI: Sarel J. Fleishman; sarel@weizmann.ac.il

References

Baran, Dror, M. Gabriele Pszolla, Gideon D. Lapidoth, Christoffer Norn, Orly Dym, Tamar Unger, Shira Albeck, Michael D. Tyka, and Sarel J. Fleishman. 2017. “Principles for Computational Design of Binding Antibodies.” Proceedings of the National Academy of Sciences of the United States of America 114 (41): 10900–905.
Lapidoth, Gideon D., Dror Baran, Gabriele M. Pszolla, Christoffer Norn, Assaf Alon, Michael D. Tyka, and Sarel J. Fleishman. 2015. “AbDesign: An Algorithm for Combinatorial Backbone Design Guided by Natural Conformations and Sequences.” Proteins 83 (8): 1385–1406.
Norn, Christoffer H., Gideon Lapidoth, and Sarel J. Fleishman. 2017. “High-Accuracy Modeling of Antibody Structures by a Search for Minimum-Energy Recombination of Backbone Fragments.” Proteins 85 (1): 30–38.

Overview

Brief

This mover is the core mover of the "AbDesign"[1-2] and "AbPredict"[3] algorithms for designing and modeling antibodies' variable domain (Fv), comprised of a the variable light and heavy chains. Both methods use a combinatorial backbone optimization algorithm, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, rather than attempting to construct backbone conformations from scratch. Briefly, all the experimentally determined antibody structures are downloaded from the Protein Data Bank (PDB) and segmented along structurally conserved positions: the disulfide cysteines at the core of the variable domain's light and heavy chains, creating 4 segments comprising of CDR's 1&2 and the intervening scaffold (VH and VL) and CDR 3 (H3 and L3). These four segments are then recombined combinatorially to produce a highly conformationally diverse set of novel antibody models. The models are then energetically optimized using Monte-Carlo sampling. At each step a random segment conformation is sampled from a pre-computed database. The SpliceOutAntibody mover is used to create the conformation database. The conformation database is specific to a template antibody. Any PDB structure can be used as the template antibody, which serves as starting point or frame of reference onto which the different antibody backbones conformation are sampled onto. For each segment (VL, L3, VH, and H3) of each of the natural antibodies we extract the backbone dihedral angles (phi, psi and omega) from the source antibody and replace the segment in the template with the source segment’s dihedral angles, introducing a main-chain cut site in a randomly chosen position in the inserted segment. Where the inserted segment is longer than the template antibody segment, residues are added to the model using idealized bond lengths and angles. We then refine the main chain using either cyclic-coordinate descent (CCD) mover on minmover.

<SpliceOutAntibody name="(&string;)" tolerance="(0.23 &real;)"
        ignore_chain_break="(false &bool;)" debug="(false &bool;)"
        CG_const="(false &bool;)" rb_sensitive="(false &bool;)"
        chain_num="(1 &non_negative_integer;)"
        cut_site="(1 &non_negative_integer;)" segment="(&string;)"
        superimposed="(true &bool;)" add_sequence_constraints_only="(false &bool;)"
        template_file="(&string;)" source_pdb="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        torsion_database="(&string;)" design_shell="(6.0 &real;)"
        repack_shell="(8.0 &real;)" rms_cutoff="(999999 &real;)"
        rms_cutoff_loop="(999999 &real;)"
        cut_secondarystruc="(false &bool;)" 
        design="(false &bool;)" 
        rtmin="(true &bool;)" allow_all_aa="(false &bool;)"
        locked_residue="(&string;)" checkpointing_file="(&string;)"
        splice_filter="(&string;)" mover="(&string;)" tail_mover="(&string;)"
        restrict_to_repacking_chain2="(true &bool;)"
        use_sequence_profile="(true &bool;)" >
    <Segments name="(&string;)" current_segment="(&string;)" >
        <segment name="(&string;)" pdb_profile_match="(&string;)" profiles="(&string;)" />
    </Segments>
</SpliceOutAntibody>

tolerance: Splice mover preforms an internal check of peptide bond length in the new segment. If the bond length is more than the set tolerance the mover reports failure
ignore_chain_break: If true, will ignore deviation in bond length. This is not recommended and usually used for debugging.
debug: If true output is more verbose and PDB structures are dumped
CG_const: If true apply coordinate constraint on C-gammas of the segment during CCD/minimization
rb_sensitive: if true, align the current pose to the template pdb
chain_num: The pose's chain onto which the new segment is added.
cut_site: residue number of where to place cut, used mainly for debugging.
segment: which segment are are changing (VL, VH, L3, H3)
superimposed: superimpose source pdb onto current pose.
scorefxn: Name of score function to use
add_sequence_constraints_only: If true does not build new segment. just build sequence profile for the pose and applies sequence constraints.
template_file: The PDB file of the reference PDB (the one used to build to conformation database)
source_pdb: The PDB file from which the segment conformation is extracted
task_operations: A comma separated list of TaskOperations to use.
torsion_database: Name of conformation file to saveto
design_shell: Design shell radius around new segment conformation.
repack_shell: Repack shell radius around new segment conformation.
rms_cutoff: The RMS cut-off between the new segment added to the pose and the segment in the source PDB. if the RMS is above a certain cut-off the mover reports failure. This parameter only refers to the secondary structure elements
rms_cutoff_loop: The RMS cut-off between the new segment added to the pose and the segment in the source PDB - only loop region.
randomize_cut: if true cut will be placed randomly in the segment
cut_secondarystruc: if true cut can be placed in secondary structure element.
rtmin: apply rtmin after CCD/minmover
splice_filter: name of filter used to test of mover finished successfully.
mover: Which mover to use to close the segment (CCD/minmover)
tail_mover: Which mover to use to change the tail segment conformation of VL/VH
restrict_to_repacking_chain2: If true do not design chain2
use_sequence_profile: If true build PSSM and apply sequence profile on pose

Example

Currently, this mover is only accessible via RosettaScripts. The SpliceOutAntibody definition below will generate a new L1_L2 conformation and apply it to the pose antibody. The new segment's conformation will be stored in the _L1_L2.db file. The CCD and tail movers need to be defined in the XML as well.

An example RosettaScripts tag is below:

<SpliceOutAntibody name="spliceout" source_pdb="%%source%%" torsion_database="db/%%name%%_L1_L2.db" scorefxn="talaris_cal" rms_cutoff="0.3" rms_cutoff_loop="0.3" splice_filter="chainbreak_val" template_file="%%start_pdb%%" task_operations="init,seqprofcons" debug="0" mover="ccd" tail_mover="tail" segment="L1_L2" use_sequence_profile="1" superimposed="1" > 
	</SpliceOutAntibody>