ilmode

Moving closed-loops with Normal Mode Analysis with constraints in internal coordinates. Local normal mode analysis for fast loop conformational sampling. J.R. López-Blanco1, Y. Dehouck, U. Bastolla, and P. Chacón. J. Chem. Inf. Model. 2022, 62, 18, 4561–4568

Sampling

Move a closed-loop along a given mode direction till reach a give rmsd from the inital conformation:

../sbg/bin/ilmode 3hsz.pdb  81 93 --chain A -i 1 -o _mod1F -m 2 -s 0 -a  1  --rmsd 3.0 --drmsd 0.25 
../sbg/bin/ilmode 3hsz.pdb  81 93 --chain A -i 1 -o _mod1B -m 2 -s 0 -a -1  --rmsd 3.0 --drmsd 0.25   
../scripts/renum_tr.pl 3hsz_mod1F_traj.pdb 3hsz_mod1B_traj.pdb > 3hsz_mod1.pdb

The first command moves forward (-a 1) the 81-93 loop until the rmsd from the initial position is > 3.0 Å (--rmsd 3.0). Every 0.25Å away(--drmsd 0.25) from the initial pose the moved loop coordinates are saved in the 3hsz_mod1F_traj.pdb trajectory file. The second command does the same but backward, and the final one generates a forward-backward trajectory like this:

first.mp4

Note how the loop closure is fully maintained despite the large motion. Please, activate the loop option for a better display (right-click on the play icon). Here there is another example with a different loop in which we compute all the modes:

for ((i=1;i<=17;i++)); 
do
     echo "processing mode $i";
     ../sbg/bin/ilmode 3irs.pdb 66 76 --chain C -m 2 -i $i -a  1 -s 0  --rmsd 3.0 --drmsd 0.25 -o F >> log;
     ../sbg/bin/ilmode 3irs.pdb 66 76 --chain C -m 2 -i $i -a -1 -s 0  --rmsd 3.0 --drmsd 0.25 -o B >> log;
     ../scripts/renum_tr.pl   3irsF_traj.pdb  3irsB_traj.pdb > mode_$i.pdb     
done
 

And here we display the corresponding results all together:

mov1.mp4

Alternatively, to a single mode motion, you can move in the direction defined by a random contribution of all the modes (option -s 1):

../sbg/bin/ilmode 3hsz.pdb  81 93 --chain A -i 1 -o _allF -m 2 -s 1 -a  1  --rmsd 3.0 --drmsd 0.25 
../sbg/bin/ilmode 3hsz.pdb  81 93 --chain A -i 1 -o _allB -m 2 -s 1 -a -1  --rmsd 3.0 --drmsd 0.25
../scripts/renum_tr.pl 3hsz_allF_traj.pdb 3hsz_allB_traj.pdb > 3hsz_all.pdb

Also with option -s 2 can move mutiple times (-nr times) in different random modal directions. For example to obtain only 10 conformations at 1.0Å apart from the original loop conformation use:

../sbg/bin/ilmode 3hsz.pdb  81 93 --chain A -i 1 -o _multiple -m 2 -s 2 -a -1  --rmsd 1.0  --nr 10 

and you can do it at different Rmsd cutoffs, i.e, 1.0Å , 3.0Å , and, 6.0Å:

--rmsd 1.0	--rmsd 3.0	--rmsd 6.0

finally, you can have in the trajectory file all the intermediate conformations by adding --drmsd option.

../sbg/bin/ilmode 3hsz.pdb 81 93 --chain A -i 1 -o _multiple -m 2 -s 2 -a -1 --rmsd 3.0 --drmsd 0.25 --nr 10

Finally, there is no restriction in where to put the restraints and you can move any segment of the protein. Here we move the sub-domain of the adenylate kinase protein using:

../sbg/bin/ilmode 4ake.pdb  109 162 --chain A -i 1 -o _mod1HF -m 2  -a  2  --rmsd 3.0 --drmsd 0.25  --seed 399495214
../sbg/bin/ilmode 4ake.pdb  109 162 --chain A -i 1 -o _mod1HB -m 2  -a -2  --rmsd 3.0 --drmsd 0.25  --seed 399495214
../scripts/renum_tr.pl 4ake_mod1HF_traj.pdb 4ake_mod1HB_traj.pdb >  4ake_mod1H.pdb

4ake.mp4

Morphing

Here we model the transition between two loop conformations deviated 13.0Å away using only the local modes computed by our approach. To this end, the initial structure (3hsz.pdb) is iteratively deformed along the lowest modes while the root mean square deviation (RMSD) to a target structure (3ht0.pdb) is minimized.

ilmode 3hsz.pdb  81 93 --chain A -t 3ht0.pdb -m 2 --skip_missingatoms -a 1 -i 1  --drmsd 0.25  -x  -o  _morph

Initial rmsd=13.0Å	Trajectory	Final rmsd=1.0Å
	morph.mp4

We have reached the target structure despite the only dihedral angles being moved. This and other examples illustrate the potential of this reduced loop-closed modal space for the conformational search. Here you can find another example:

ilmode 3irs.pdb  66 76 --chain C -t 3k4w.pdb -m 2 -a 1 --drmsd 0.25 -x  -o  _morph

Directories and Databases

• test/ Here you can find all the PDB coordinates corresponding to the examples of this tutorial.

• sbg/ Source code and linux binaries

• morph/ Highly variable loops benchmark observed in multiple stable conformations and compiled by Marks, C., et al. Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics 2017;33(9):1346-1353. This set includes 30 loops from 10 to 15 residues long. Each loop case is associated with an ensemble from 2 to 11 different conformations.

• REMD/ Benchmark set of 15 exposed and diverse loops employed to test loop predictions using Replica Exchange Molecular simulations (REMD) with RSFF2C force field (Feng, J.J., et al. Accurate Structure Prediction for Protein Loops Based on Molecular Dynamics Simulations with RSFF2C. J Chem Theory Comput 2021;17(7):4614-4628). These loops had a resolution of <2.0 Å, Rfactor < 0.3, sequence identity <20%, and an average B-factor <35. We extend the length of the loop one residue at both ends to minimize the deviations of the anchors found in the REMD simulations. The size of the loops ranges from 12 to 18 residues. The initial MD structures were prepared via implicit MD simulations at high temperatures to guarantee to be far away from the crystallographic ones (>10 Å). Trajectories (last microsecond), initial REMD structures, and the corresponding simulations were kindly provided by the authors, with structures already superimposed by the anchors.

Source Code

The complete source C++ code of KORPM is under sbg directory. Just execute compile_ilmode.sh script.

Funding

This work was supported by Spanish grants PID2019-109041GB-C21/AEI/10.13039/501100011033