ProtoSyn Protein Mutation

In this demo we can use ProtoSyn.jl to mutate amino acids. Different rotamers can be selected for the mutated residue. To use ProtoSyn here you currently have to use a workaround. The getprotosyn() function downloads the source code, then you can include it. In the future hopefully it will be built in.

Copy-pastable code

using BioMakie
using GLMakie
using BioStructures
BioMakie.getprotosyn()
include("../protosyn.jl")
struc = retrievepdb("2vb1")
chn = collectresidues(struc[1]["A"], standardselector)
writepdb("2vb1x.pdb", chn)
rot_lib = ProtoSyn.Peptides.load_dunbrack()
res_lib = ProtoSyn.load_grammar_from_file(ProtoSyn.resource_dir*"/Peptides/grammars.yml", "default")
pose = ProtoSyn.Peptides.load("2vb1x.pdb"; bonds_by_distance=true) |> Observable
ProtoSyn.Peptides.cap!(pose[])
ProtoSyn.Peptides.assign_default_atom_names!(pose[])
ProtoSyn.sort_atoms_by_graph!(pose[])
ProtoSyn.Peptides.Calculators.Electrostatics.assign_default_charges!(pose[], res_lib)
pdata = plottingdata(pose)
fig = Figure(resolution = (985,700))
layout = fig[1,1] = GridLayout(11,7)
selected = @lift pdata[:resids][][$(pdata[:selected])] |> unique
selection_text = lift(selected) do sel
    if length(sel) == 0
        return ""
    else
        return "$(string(pose[].graph[1][sel[1]]))"
    end
end
_plotstruc!(layout[1:10,1:5], pdata; resolution = (600,700))
title = Label(layout[1,6:7]; text = "Mutate Residue", fontsize = 30)
selection_label = Label(layout[2,6:7]; text = "Selection:", fontsize = 20)
vselection = Label(layout[3,6:7]; text = selection_text, fontsize = 16)
clear_button = Button(layout[4,6:7]; label = "Clear selection",
                    buttoncolor = :pink, fontsize = 18,
                    width = 140, height = 50)
mutation_label = Label(layout[5,6:7]; text = "Mutate selection to:", fontsize = 20)
mutate_menu = Menu(layout[6,6:7]; options = BioMakie.res3letters[1:20],
                        cell_color_active = to_color(:lightblue),
                        cell_color_hover = to_color(:lightgreen),
                        selection_cell_color_inactive = to_color(:lightblue)
)
mutate_button = Button(layout[7,6:7]; label = "Mutate!",
                    buttoncolor = :lightgreen, fontsize = 18, width = 80, height = 50
)
rotamer = Observable(1)
rotamer_label = Label(layout[8:9,6]; text = "Change rotamer:", fontsize = 20)
rotamer_button1 = Button(layout[8,7]; label = "ꜛ",
                    buttoncolor = :lightgreen, fontsize = 40,
                    tellwidth = false, width = 70, height = 40
)
rotamer_button2 = Button(layout[9,7]; label = "ꜜ",
                    buttoncolor = :lightgreen, fontsize = 40,
                    tellwidth = false, width = 70, height = 40
)
on(clear_button.clicks) do s
    pdata[:selected][] = Vector{Bool}(undef,length(pdata[:selected][])) .= false
end
on(mutate_button.clicks) do s
    selection_text[] = "$(string(pose[].graph[1][selected[][1]]))"
    mutletter = BioMakie.resletterdict[mutate_menu.selection[]]
    ProtoSyn.Peptides.mutate!(pose[], pose[].graph[1][selected[][1]], res_lib, [mutletter])
    fixpose!(pose)
end
on(rotamer_button1.clicks) do s
    if length(selected[]) == 0
        println("No selection")
    else
        phi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.phi(pose[].graph[1][selected[][1]]))
        psi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.psi(pose[].graph[1][selected[][1]]))
        stack = rot_lib["$(pose[].graph[1][selected[][1]].name)"][phi, psi]
        nrotamers = length(stack.rotamers)
        if rotamer[] < nrotamers
            rotamer[] = rotamer[] + 1
        end
        ProtoSyn.Peptides.apply!(pose[].state, stack[rotamer[]], pose[].graph[1][selected[][1]])
        fixpose!(pose)
    end
end
on(rotamer_button2.clicks) do s
    if length(selected[]) == 0
        println("No selection")
    else
        phi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.phi(pose[].graph[1][selected[][1]]))
        psi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.psi(pose[].graph[1][selected[][1]]))
        stack = rot_lib["$(pose[].graph[1][selected[][1]].name)"][phi, psi]
        nrotamers = length(stack.rotamers)
        if rotamer[] > nrotamers
            rotamer[] = rotamer[] - 1
        end
        ProtoSyn.Peptides.apply!(pose[].state, stack[rotamer[]], pose[].graph[1][selected[][1]])
        fixpose!(pose)
    end
end

mutation

Load BioMakie and ProtoSyn

Download the protosyn source code from the src directory of BioMakie and include it. This should install a few packages (SplitApplyCombine, Colors, Meshes, GeometryBasics, OrderedCollections, Distances) and then import ProtoSyn.

using BioMakie
using GLMakie

BioMakie.getprotosyn()
include("../protosyn.jl")

Prepare the structure

To simplify things, we will load a structure with BioStructures and save chain "A" as a PDB file. Then we will load the PDB file with ProtoSyn.

using BioStructures
struc = retrievepdb("2vb1")
chn = collectresidues(struc[1]["A"], standardselector)
writepdb("2vb1x.pdb", chn)

pose = ProtoSyn.Peptides.load("2vb1x.pdb"; bonds_by_distance=true) |> Observable

Get plotting data and plot it

pdata = plottingdata(pose)
fig = Figure()
_plotstruc!(fig, pdata)

wildtypearg

Prepare the structure

We can use diagnose to get an idea of what is missing and of inconsistencies in the structure.

ProtoSyn.Peptides.diagnose(pose[])

We have several issues, including charges, naming, and caps, which are the terminal hydrogens. We can use the following functions to address these issues. First we load the library of amino acids, to get the Peptide/protein-specific data, instead of the default generic data.

res_lib = ProtoSyn.load_grammar_from_file(ProtoSyn.resource_dir*"/Peptides/grammars.yml", "default")
ProtoSyn.Peptides.cap!(pose[])
ProtoSyn.Peptides.assign_default_atom_names!(pose[])
ProtoSyn.sort_atoms_by_graph!(pose[])
ProtoSyn.Peptides.Calculators.Electrostatics.assign_default_charges!(pose[], res_lib)

ProtoSyn.Peptides.diagnose(pose[])

Now the issues should say OK, except for the atom-level graph. We can ignore this for now. This fixpose! function below may be convenient for syncing and correcting the structure after making changes. Using pose[] = pose[] can force Makie to update the pose/figure.

function fixpose!(pose::Observable; res_lib=ProtoSyn.load_grammar_from_file(ProtoSyn.resource_dir*"/Peptides/grammars.yml", "default"))
    ProtoSyn.Peptides.cap!(pose[])
    ProtoSyn.Peptides.assign_default_atom_names!(pose[])
    ProtoSyn.sort_atoms_by_graph!(pose[])
    ProtoSyn.Calculators.Electrostatics.assign_default_charges!(pose[],res_lib)
    ProtoSyn.Peptides.sync!(pose[])
    pose[] = pose[]
end

Mutate the structure

Get information about a residue. In this example we will use residue 128 because it is easy to find on the structure. The long side chain of this arginine extends outward the furthest.

pose[].graph[1][128]

Next lets try mutating it to tyrosine. We can use the mutate! function to do this. Combine it with fixpose! to get the updated structure. You should see the side chain change into the phenol ring of tyrosine.

ProtoSyn.Peptides.mutate!(pose[], pose[].graph[1][128], res_lib, ["Y"])
fixpose!(pose)

mutanttyr

To choose different rotamers/orientations, we can use the rotamer library. ProtoSyn provides a stack of the most likely rotamers based on the dihedral angles of the residue.

rot_lib = ProtoSyn.Peptides.load_dunbrack()
phi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.phi(pose[].graph[1][128]))
psi = ProtoSyn.getdihedral(pose[].state, ProtoSyn.Peptides.psi(pose[].graph[1][128]))
stack = rot_lib["TYR"][phi, psi]

ProtoSyn.Peptides.apply!(pose[].state, stack[3], pose[].graph[1][128])
fixpose!(pose)

mutanttyrrotamer

This page was generated using Literate.jl.