Report

Homework in
Computational Biochemistry

dyatlov.denis95@gmail.com
 Written by Denis Diatlov. University of Barcelona

1st chapter: Enhanced sampling methods (Prof. Rodrigo

Casasnovas)
1. Free energy surface and conformational search.
In this task we have to analyze alanine dipeptide molecule and study two dihedral
angles: phi (φ) and psi (Ψ). In order to do it we have to perform unbiased and
metadynamics simulations (MD). In fact, alanine dipeptide presents in two meta
stable states, which can be seen on following picture. The energy of the state.
Dependent on two parameters – two dihedral angles: phi and psi. The calculations
were carried out using “PLUMED” software.

Figure 1. Dipeptide alanine conformations

Now let’s plot FES 3d curve for the unbiased and MD simulations.

Figure 2. FES of dipeptide alanine for unbiased and MD simulation respectively

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 Written by Denis Diatlov. University of Barcelona
Looking on the figure 2, we can conclude, that graph, obtained from unbiased
simulation is incomplete, instead of MD simulation. Actually, its happed due to we
not allowed system to jump thought the energy barrier. This is limitation of our
sampling. We calculate free energy as:
𝐹 = −𝑘𝑇𝑙𝑛𝑃
when P is probability of finding the system.
The probability to obtain system in “white region” is zero (see figure 3). Thus,
the free energy achieves infinite value and can’t be shown on the plot.

Figure 3. Distribution of the sampled conformations for unbiased and MD simulation

respectively
For the metadynamics simulation we add some energy to the system and it
can jump though the barrier and visit all area, in our case [-pi:pi] for the both axis.
Thus, we can calculate free energy in every space point and obtain the full 3D FES.
Also, we indicated on the Figure 2 (MD case) path from one stable state (ST)
to another one through transition state (TS), which connect its.

2. Collective variables and convergence in Metadynamics.

In this exercise we are going to consider, that we have computational power
only to perform metadynamics on 1 collective variable. Now we should select the
best variable in order to obtain well stationary points with lowest energy. In that case
let’s make two independent calculations and plot two graphics of time evolution of

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phi and psi during the MD in which only phi or psi was biased and also distribution
of sampled conformation.
Dihedral angle, rad

Time, ns*10-3 Time, ns*10-3

Figure 4. Time evolution plots of phi and psi in MD simulations. phi and psi are biased only
respectively.
Dihedral angle, rad

Figure 5. Distribution of sampled conformation phi vs psi in MD. phi ad psi are biased only
respectively.
By looking on the figures 4, 5 we can conclude, that the best CV for this job
is phi dihedral angle. Let’s look at the psi time-evo graph. At first the behavior of
psi looks diffusive in the entire CV space. But, in region 2-4 ns, psi seems to be
caught in the area of the CV space in which it was previously diffusing without
problems. The reason is that the non-biased CV phi after a while has jumped into a
different local minimum. Since phi is not directly biased, one has to wait for this
(slow) degree of freedom to equilibrate before the free energy along psi can converge
difference between basins) to assess the convergence of this metadynamics

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 Written by Denis Diatlov. University of Barcelona
simulation. By looking of figure 5 it can be shown that distribution in phi biased
only graph is very similar to the FES (figure 2), opposite than psi.
Since, we know that there is “bad” and “good” CVs we need to choose the
good one.

Figure 6. Free energy as a function of the dihedral. psi and phi were biased respectively.
By looking on the figure 6 it can be shown that in case of psi the convergence
reached only from time equal to 6 ns approx. In case phi dihedral biased (right
picture) the convergence reached fast and the difference in time is not significantly.
So, we can conclude that we should select phi as CV to be biased

3. Umbrella sampling and binding free energy.

In this task we have to calculate and plot potential of mean force of the
formation (pmf) for benzene-benzene complex.

Figure 7. Plot of the histograms

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Figure 8. Plot of the PMF vs distance.

By looking on the figure 8 it can be shown that benzene-benzene binding

free energy is about 3.0 kcalmol-1 when distance is equal to 0.55 nm or 5.5 A.
We used all 23 windows in order to plot PMF. In case of reducing the
number of histograms we will obtain the less accurate results. Unfortunately, we
have no access to machine, locating in Zaragoza and can`t repeat calculation with
reduced number of histograms.

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 Written by Denis Diatlov. University of Barcelona

2nd chapter. Embedding methods. (Prof. Charles Curutchet)

1. Quantum / molecular mechanics (QM/MM) methods.
In this task we should draw a schematic plot of the PES corresponding to the
pCA – Glu46 hydrogen bond, in the photoactive yellow protein (PYP).
In order to do in we prepared two inputs. We run its to obtain the optimal
geometry of 2 cases: in PYP_pCAH the pCA is protonated and the Glu residue
anionic. And in PYP_GluH file the Glu is the one protonated. The geometry
optimization calculations were carried out in Gaussian 09.

Figure 9. Schematic potential energy surface

By analysing figure 9 we can see, that H-bond is asymmetric and energy varies
as we go from one protonation to another one with preferable GlyH protonated. It is
a standard H-bond, due to the difference of the energy is equal to ~13 kcal/mol.
We have used “oniom” in order run calculations for more than one level of
theory. Am1 for high-level region and UFF for low-level region. We selected
Embedcarge, i.e. use electrostatic embedding. When optimizing only QM region
(keeping MM atoms frozen), the QM atom linked to MM part needs to be frozen
too. All charge of our system equal to -6.
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 Written by Denis Diatlov. University of Barcelona
2. Continuum solvation methods.
The key of this task is investigating dependence of activities of cimetidine
derivatives vs their octanol/water partition coefficient, i.e. logP for two sets of
molecules.
The full set of investigated molecules and their activities presented in the
picture 10.

Figure 10. Set of radicals and activities of molecules.

Obviously, biological activity depends on chemical structure. However, the
chemical compound should have intermediate values of activity. Thus, we prepared
all inputs and carried out calculations in Gaussian 09 software. In these calculations
was used 6-31G* level of theory and B3LYP method. All requested geometries were
prepared be teacher.
Now, let’s obtain the energies from Gaussian and calculate logP by following
formula:
∆ G (wat) − ∆ G(oct)
log 𝑃 = −log
1,364

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 Written by Denis Diatlov. University of Barcelona
Here, we should plot the graph dependence logP vs activity and try to fit it in
order to obtain correlation for set A:

Figure 11. Fitted curve for set A (1-11 molecules) obtained with Matlab 2017b.
By looking on the figure 11, obviously that there is some correlation between
logP and activity. It could be described by second order exponential equation.

Distribution of points for set B

7,50

7,00

6,50

6,00

5,50

5,00

4,50

4,00
2,00 2,10 2,20 2,30 2,40 2,50 2,60 2,70 2,80 2,90 3,00

Figure 12. Distribution of points for set B (1-21 molecules)

By looking on the figure 12, which presents set 1-21, we can’t obtain
correlation between activity and logP. The distribution looks like chaotic points and
can’t be fitted. It’s happened due to values of activity in the set B after 11th begin to

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repeat, making it difficult to determine the dependence. This set is not good for
approximating.
QSAR is powerful method and allows us predict some biological properties,
by using known function (like in set A). However, we need a well model. Set of 11th
compounds are enough for make a relation in order to build mathematical model.
Also, we have used 1-molecular descriptor, but any others descriptors could be used
as well, until we obtain good mathematical correlation, for instance, potential
energy, dipole moment or polarizability.

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