Protein Folding in Solution

In this exercise, you will calculate the protein folding free energy using thermodynamic integration, a method based on molecular dynamics (MD). The protein will be described by the empirical force field, CHARMM22, http://mackerell.umaryland.edu/charmm_ff.shtml

A model protein you will have to deal with is the alanine decapeptide. The folding/unfolding will be achieved by stretching/compressing the chain. This in practice can be achieved by constraining the distance between the end carbon atoms in the protein and performing different simulations for each value of the distance. The atoms are the number 11 and 91, which are the carbon atoms of the carbonyl groups at the edges of the protein. The distance between these atoms is the collective variable chosen for the system. At each distance one runs a constrained MD to extract the time-averaged forces acting on the collective variable, $F(x)$. Then, a free energy difference can be calculated via thermodynamic integration (TI):

\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}

Here $a$ and $b$ are the initial and the final values of the collective variable. TI is a general method, which can be applied to a variety of processes, e.g. phase transitions, electron transfer etc.

Download the files: deca_ala_ex3.tar.gz

in the directory deca_ala you will find

deca_ala.pdb (protein data base) file contains the coordinates

deca_ala.psf (protein structure file) file contains connectivity data

par_all27_prot_lipid.inp contains the force field parameters. You will be using the CHARMM v.22, a popular force field for biologically relevant systems.

md_std.inp is the CP2K input file

Open the deca_ala.pdb protein data bank format file with vmd. Create a new representation for the protein, e.g. of type Ribbon to observe the alpha-helix.

Although the image below shows the deca-alanine in water, it is expensive to run thermodynamic integration for a solvated protein with many values of the constraints on small laptops. So we will run TI for the protein in the gas-phase.

Here you are asked to run several MD simulations for different values of the distance between atoms 11 and 91, in each run it will be constrained. In the original file md_std.inp the distance is set to $14.37$ Å as is in the deca_ala.pdb file. This is the first step to carry out the termodynamic integration, as described in the equation above.

We have made the script run_ti_jobs.sh to run these simulations, which you can find inside the compressed file deca_ala.tar.gz. Take a look at the script and familiarize yourself with it. At which values are we constraining the distances between the carbon atoms? In this case we are performing 5 different simulations, each with a different value of the constraint. You can edit this script to use a larger or smaller number of constraints and to increase or reduce the upper and/or lower bound of integration. Can you guess where in the script we are specifying the values of the constraints?

run_ti_jobs.sh

#!/bin/bash -l
for d in $(seq 16 1 20); do
  mkdir $d
  cp deca_ala/* $d/.
  cd $d
  sed -e "s|14.37|${d}|" md_std.inp > d_${d}.inp
  cp2k.sopt -i d_${d}.inp -o d_${d}.out 
  cd ..
done

Look into the main input file of cp2k md_std.inp, and try to understand the keywords used as much as possible, by now you should be able to understand most of it, and you can experiment changing some of the keywords to see what happens. Look in particular at the definition of the section CONSTRAINT where the target value of the distance between the two carbon atoms at the edges of the proteins are constrained for instance to 14.37, and at the COLVAR section where the the collective variable for the distance between the two C atoms is defined.

constraint section

 &CONSTRAINT
    &COLLECTIVE
      COLVAR 1
      INTERMOLECULAR
      TARGET [angstrom] 14.37
    &END COLLECTIVE
    &LAGRANGE_MULTIPLIERS
      COMMON_ITERATION_LEVELS 1
    &END
 &END CONSTRAINT

colvar section

    &COLVAR
      &DISTANCE
        ATOMS 11 91
      &END DISTANCE
    &END

⇒ Each constrained MD will produce a .LagrangeMultLog-files, which look like this:

Shake  Lagrangian Multipliers:           -63.547262596
Rattle Lagrangian Multipliers:            63.240598387
Shake  Lagrangian Multipliers:            -0.326901815
Rattle Lagrangian Multipliers:            -0.318145579

• From these files you can calculate the average Lagrange multiplier of the Shake-algorithm and the standard error like this:

grep Shake yourprojectname.LagrangeMultLog | awk '{c++ ; s=s+$4; sq=sq+$4*$4 }END{print s/c, sqrt(sq/c - s*s/(c*c))/(sqrt(c)) }'

• The average Lagrange multiplier is the average force $F(x)$ required to constrain the atoms at the distance $x$. First of all, plot the force $F(x)$ with its standard error as a function of the collective variable to see if the simulation carried out so far is statistically relevant or the relative error is too large.
• From the forces, the free energy difference can be obtained via thermodynamic integration between the two states. Given that state $a$ and $b$ are the initial and the final values of the collective variable, extract the free energy difference from

\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}

• Also, extract the free energy profile as a function of the collective variable $x^\prime$. To do this, one can choose the minimum value of the collective variable, as the lower bound of the integral and plot the free energy as a function of $x^\prime$, the upper bound of the integral, according to the same relation

\begin{equation} \Delta A(x^\prime) = -\int_a^{x^\prime} F(x)\, dx \end{equation}

• Discuss the form of the free energy profile and comment on what is the most stable state of the protein. Is it more stable when it is stretched or when it is in the $\alpha$-helix conformation? Is this result physical? Explain why or why not. How can the presence of water affect the conformation of the protein?
• Tip 1: the most stable state will be that where the free energy is at the global minimum.
• Tip 2: In order to understand whether the result obtained from thermodynamic integration is physical or not, have a look at the .xyz files for some of the constrained MD trajectories and think about what are the fundamental interactions between the constituents of the protein that we are taking into account with the CHARMM force field (e.g. electrostatic, van-der Waals, covalent bonds) and how these may contribute to the stabilization of the protein in a given state.
• The two articles at the links below show how the free energy profile should look like, using thermodynamic integration or a different enhanced sampling method. Compare the free energy profile obtained from your simulations to either of those papers. Most likely, the free energy profile you obtained will not be as converged as theirs. What are some possible reasons for this, and how can one obtain better converged free energy profiles?
• Paper 1: https://arxiv.org/pdf/0711.2726.pdf see figure 2, solid line obtained with thermodynamic integration, using the same force field (CHARMM v.22) used here. This paper however, uses a different collective variable, i.e. the distance between the N-atoms at the opposite edges.
• Paper 2: https://pubs.acs.org/doi/pdf/10.1021/ct5002076 see figure 1, obtained with umbrella sampling and adaptive bias force sampling, for two versions of the CHARMM force field, v.22 and v.36. The collective variable in this case is the same as the one specified in our input.
• Finally, in principle we could have performed a direct MD simulation (as we did in the past exercises) to compute the free energy profile as a function of the distance between two of the atoms at the opposite edges of the protein (the collective variable we chose for this particular problem). Instead, we chose to perform an enhanced simulation technique. Can you think of a problem we would face if we had decided to perform a direct MD simulation? What could be a possible way to overcome this problem?