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I would like to create a figure displaying the binding pathways of a ligand between a lipid bilayer and a protein.

  • Ligand moves into the membrane and back into the extracellular environment (in equilibrium)
  • Ligand moves from within the membrane into the binding pocket of the protein (in equilibrium)
  • Ligand moves from the protein binding pocket into the extracellular environment (in equilibrium)

These three pathways in turn are in equilibrium with each other - I've drawn a (very) rough idea here.

Rough idea

I don't really know where to start!

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    Hello and welcome to TEX. Please read here how to ask a question and increase your changes of getting an answer. Your pic is possible to draw in Tikz but it will need a lot of time and effort. Here you can find a solution how to draw lipid layers and vesicles. You can start with this. In my opinion LaTex may not be the best option for drawing complex biological scientific cartoons, especially when you are a beginner.
    – Roland
    Commented Dec 15, 2020 at 2:02

1 Answer 1

7

Starting from this code here I came to this result. I think it is a start:

\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{decorations,decorations.pathreplacing}
\usepackage{chemfig}
\usepgflibrary{arrows}


\begin{document}

%%%%%%Source of lipid layer: https://texample.net/tikz/examples/lipid-vesicle Published 2009-03-05 | Author: Henrik Skov Midtiby. Modified by Roland Tresky 2020-12-16

    \pgfdeclaredecoration{lipidleaflet}{initial}
    {
        % Place as many segments as possible along the path to decorate
        % the minimum distance between two segments is set to 7 pt.
        \state{initial}[width=\pgfdecoratedpathlength/floor(\pgfdecoratedpathlength/7pt)]
        {
            % Draw the two acyl chains
            \pgfpathmoveto{\pgfpoint{-1pt}{0pt}}
            \pgfpathlineto{\pgfpoint{-1pt}{-10pt}}
            \pgfpathmoveto{\pgfpoint{1pt}{0pt}}
            \pgfpathlineto{\pgfpoint{1pt}{-10pt}}
            % Draw the head group
            \pgfpathmoveto{\pgfpoint{1pt}{0pt}}
            \pgfpathcircle{\pgfpoint{0pt}{2pt}}{2.5pt}\pgfusepath{fill,stroke}
        }
        \state{final}
        {
            \pgfpathmoveto{\pgfpointdecoratedpathlast}
        }
    }
    
    \begin{tikzpicture}[node distance=2cm]
            
%%%%%%%%% Lipid bilayer right
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (-1, -2.8) -- (2, -2.8);
        \draw[decorate, decoration={lipidleaflet}]
        (-1, -2) -- (2, -2);
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (3, -2.8) -- (6, -2.8);
        \draw[decorate, decoration={lipidleaflet}]
        (3, -2) -- (6, -2);
        %\draw (0, -3.5) node {Lipid bilayer};
        
        %membraneprotein
        \draw[rounded corners,red!60,fill=red!60] (2,-1.5) rectangle (2.8,-3);
        \draw[cyan,fill=cyan] (2.2,-1.4) circle (4pt);
        
        %constants
        \node (A) at (0, 0) {K\textsubscript{mb}};
        \node (B) at (2, 0) {K\textsubscript{bm}};
        \draw[>=triangle 45, <->] (0.5,0) -- (1.5,0);
        
        %double arrow
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick, shorten >=3pt] (2.1,-1.1) -- (1.1,-0.4);
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick, shorten >=3pt] (1.1,-0.5) -- (2.1,-1.2);
        
        %arrow
        \draw[{Triangle[length=2mm, width=1mm]}-{Triangle[length=2mm, width=1mm]},shorten >=5pt] (-1.4,-2.4) -- (-3,-2.4);
        
        
%%%%%%%%% Lipid bilayer left
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (-6,-2.8) -- (-3, -2.8);
        \draw[decorate, decoration={lipidleaflet}]
        (-6, -2) -- (-3, -2);
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (-10, -2.8) -- (-7, -2.8);
        \draw[decorate, decoration={lipidleaflet}]
        (-10, -2) -- (-7, -2);
        
        %membraneprotein
        \draw[rounded corners,red!60,fill=red!60] (-7,-1.5) rectangle (-6.2,-3);
        \draw[cyan,fill=cyan] (-8,-0.4) circle (4pt);
        
        %double arrow
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick, shorten >=3pt] (-8,-1.6) -- (-8,-0.6);
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick, shorten >=3pt] (-8.1,-0.7) -- (-8.1,-1.7);
        
        %constants
        \node (A) at (-9, 0) {K\textsubscript{am}};
        \node (B) at (-7, 0) {K\textsubscript{ma}};
        \draw[>=triangle 45, <->] (-8.5,0) -- (-7.5,0);
        
%%%%%%%%% Lipid bilayer below
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (-1.4,-6.8) -- (2, -6.8);
        \draw[decorate, decoration={lipidleaflet}]
        (-1.4, -6) -- (2, -6);
        \draw[decorate, decoration={lipidleaflet, mirror}]
        (-5.8, -6.8) -- (-2.4, -6.8);
        \draw[decorate, decoration={lipidleaflet}]
        (-5.8,-6) -- (-2.4,-6);
        
        %membraneprotein
        \draw[rounded corners,red!60,fill=red!60] (-2.4,-7) rectangle (-1.6,-5.6);
        \draw[cyan,fill=cyan] (-2.3,-5.5) circle (4pt);
        
        %double arrow
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick,shorten >=3pt] (-3.45,-6.2) -- (-2.45,-5.6);
        \draw[-{Stealth[right][length=2mm, width=1mm]},red,thick,shorten >=3pt] (-2.6,-5.6) -- (-3.6,-6.2);
        
        %constants
        \node (A) at (-3, -8) {K\textsubscript{ab}};
        \node (B) at (-1, -8) {K\textsubscript{ba}};
        \draw[>=triangle 45, <->] (-2.5,-8) -- (-1.5,-8);
        
        %arrow
        \draw[{Triangle[length=2mm, width=1mm]}-{Triangle[length=2mm, width=1mm]},shorten >=5pt] (-6,-3.5) -- (-4,-5);
        
        %arrow
        \draw[{Triangle[length=2mm, width=1mm]}-{Triangle[length=2mm, width=1mm]},shorten >=5pt] (2,-3.5) -- (0,-5);
        
    \end{tikzpicture}
    
\end{document} 

enter image description here

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    Now that's some really cool TikZ @Roland... I might end up using it in my lectures...
    – v_manz
    Commented Dec 20, 2020 at 22:04

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