DOI: 10.5061/dryad.wh70rxx0j
title: Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutant

description: Striga hermonthica is a parasitic weed that destroys billions of dollars’
 worth of staple crops every year. Its rapid proliferation stems from an
 enhanced ability to metabolize strigolactones (SLs), plant hormones that
 direct root branching and shoot growth. Striga’s SL receptor, ShHTL7,
 bears more similarity to the staple crop karrikin receptor KAI2 than to SL
 receptor D14, though KAI2 variants in plants like Arabidopsis thaliana
 show minimal SL sensitivity. Recently, studies have indicated that a small
 number of point mutations to HTL7 residues can confer SL sensitivity to
 AtKAI2. Here, we analyze both wild-type AtKAI2 and SL-sensitive mutant
 Var64 through all-atom, long-timescale molecular dynamics simulations to
 determine the effects of these mutations on receptor function at a
 molecular level. We demonstrate that the mutations stabilize SL binding by
 about 2 kcal/mol. They also result in a doubling of the average pocket
 volume and eliminate the dependence of binding on certain pocket
 conformational arrangements. While the probability of certain non-binding
 SL-receptor interactions increases in the mutant compared with the
 wild-type, the rate of binding also increases by a factor of ten. All
 these changes account for the increased SL sensitivity in mutant KAI2 and
 suggest mechanisms for increasing functionality of host crop SL receptors.
description: # Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple
 mutant Dataset DOI: [10.5061/dryad.wh70rxx0j](10.5061/dryad.wh70rxx0j) ##
 Description of the data and file structure The repository contains all of
 the features data (.npy files), featurization scripts (.py) and scripts
 used to plot the figures in the manuscript: [Mechanistic Basis for
 Enhanced Strigolactone Sensitivity in KAI2 Triple
 Mutant](https://doi.org/10.1101/2023.01.18.524622). ### Files and
 variables #### File: WT\_Adaptive\_Sampling.zip **Description:** This zip
 folder contains the information for rounds 1-3 using adaptive sampling
 with K-means clustering to explore the landscape for WT KAI2. Within this
 zip folder is 3 folders: * `Features` contains the `*.tar.gz` features
 files for Mutant and Ligand Features in `.npy` form. * Mutant features
 contain 615 `.npy` files of Residue pair 153-190, 157-190, and 153-157
 distances. * Ligand features are 1025 `.npy` files of all pairs of
 Residues 2345, 2406, 2490, A-ring, D-ring, and GR24 distances. *
 `Analysis` contains all `.py` files used to generate the `.npy` files in
 `Features`. * `Plotting` contains all `.py` files used to generate the
 Figures for the manuscript and supporting information. #### File:
 WT\_Exploration.zip **Description:** This zip folder contains the
 information for the 4th extensive round of simulations for WT KAI2. Within
 this zip folder is 3 folders: * `Features` contains the `*.tar.gz`
 features files for Mutant and Ligand Features in `.npy` form. * CatTriad
 features are 4,269 `.npy` files on catalytic triad contact distances. *
 DLoopLig features are 8,538 `.npy` files on D-loop vs. Ligand contact
 distances. * Ligand features are 5,692 `.npy` files of Ligand distances
 from the binding pocket features. * Mutations features are 4,269 `.npy`
 files on contact distances between key mutations in the protein. * T1T2
 features are 4,269 `.npy` files on T1 vs T2 helix contact distances. *
 DLoop features are 8,538 `.npy` files on inter D-loop contact distances. *
 F26 features are 4,269 `.npy` files on contact distances between many key
 residues and the F26 residue. * Ligand2 features are 4,269 `.npy` files on
 additional relevant contacts, primarily between the T1T2 helices and the
 ligand GR24. * Pocket features are 2,846 `.npy` files on contact distances
 within the protein binding pocket. * T1T2Lig features are 17,076 `.npy`
 files on contact distances between the ligand and the T1 and T2 helices of
 the protein. * `Analysis` contains all `.py` files used to generate the
 `.npy` files in `Features`. * `Plotting` contains all `.py` files used to
 generate the Figures for the manuscript and supporting information. ####
 File: Mutant\_Adaptive\_Sampling.zip **Description:** This zip folder
 contains the information for rounds 1-3 using adaptive sampling with
 K-means clustering to explore the landscape for Mutant KAI2. Within this
 zip folder is 3 folders: * `Features` contains the `*.tar.gz` features
 files for Mutant and Ligand Features in `.npy` form. * Mutant features
 contain 615 `.npy` files of Residue pair 153-190, 157-190, and 153-157
 distances. * Ligand features are 1025 `.npy` files of all pairs of
 Residues 95, 2345, 2401, 2891, A-ring, D-ring, and GR24 distances. *
 `Analysis` contains all `.py` files used to generate the `.npy` files in
 `Features`. * `Plotting` contains all `.py` files used to generate the
 Figures for the manuscript and supporting information. #### File:
 Mutant\_Exploration.zip **Description:** This zip folder contains the
 information for the 4th extensive round of simulations for Mutant KAI2.
 Within this zip folder is 3 folders: * `Features` contains the `*.tar.gz`
 features files for Mutant and Ligand Features in `.npy` form. * CatTriad
 features are 4,377 `.npy` files on catalytic triad contact distances. *
 DLoopLig features are 8,754 `.npy` files on D-loop vs. Ligand contact
 distances. * Ligand features are 5,8636 `.npy` files of Ligand distances
 from the binding pocket features. * Mutations features are 4,377 `.npy`
 files on contact distances between key mutations in the protein. * T1T2
 features are 4,377 `.npy` files on T1 vs T2 helix contact distances. *
 DLoop features are 8,754 `.npy` files on inter D-loop contact distances. *
 F26 features are 4,377 `.npy` files on contact distances between many key
 residues and the F26 residue. * Ligand2 features are 4,377 `.npy` files on
 additional relevant contacts, primarily between the T1T2 helices and the
 ligand GR24. * Pocket features are 2,918 `.npy` files on contact distances
 within the protein binding pocket. * T1T2Lig features are 17,508 `.npy`
 files on contact distances between the ligand and the T1 and T2 helices of
 the protein. * `Analysis` contains all `.py` files used to generate the
 `.npy` files in `Features`. * `Plotting` contains all `.py` files used to
 generate the Figures for the manuscript and supporting information. ####
 File: Pyemma.yml **Description:** This `.yml` file creates a conda
 environment with the necessary package versions to execute all `.py` files
 provided within the zip folders. Assuming the user has conda, to generate
 the environment please execute: `conda env create -f pyemma.yml -n
 my_custom_env_name` where `my_custom_environ_name` is the name you would
 like for the conda environment. ## Code/software All code provided can be
 executed via the terminal using `python {code}.py`. For the exact software
 required to execute the code, a `pyemma.yml` file of the conda environment
 used has been provided with the dataset. To extract the data (and print to
 screen) from a numpy `.npy` file, an example code execution in python
 would be: `import numpy as np` `data = np.load (‘path/to/numpy_file.npy’,
 allow_pickle=True)` `print(data)` ## Access information Other publicly
 accessible locations of the data: * All stripped trajectories for this
 manuscript are available on
 [Box](https://uofi.box.com/s/zvchi4sqx09ql662olwv6hrftdw5tp3a).