Page 64 - GPD-3-1

Gene & Protein in Disease In silico application of the CoM method

Equation I can be applied to compute monomer [1] heterodimer. The program reads the complete heterodimer
(M ) and monomer[2] (M )CoM: structure, provided by.gro file. For each monomer in the
1 2
t
t z )
t
com ( x , y , t and system, separate index files can be compiled, provided by
M 1 M 1 M 1 M 1 the residues’ range selection option ri, such as: ri 1-597
t
com (( x , y , M 2 t (for monomer M ) and ri 598-791 (for monomer M ). The
t
t z ) . Equation II can be
M2
2
M 2
1
M 2
used to compute the CoM distance between monomers M program generates.ndx file, followed by -o output flag.
1
and M during the course of MD simulation. Typical command use would be:
2
1 gmx make_ndx -f npt.gro -o index.ndx
t
2
( x x ( y 2
t )
t
d d M M1, 2 () M 1 2 M 2 M 1 2 Having split monomers into separate index groups
t
t
com
t
t )

y ( z z M 2 t ) (by default indexed as groups 18 and 19), gmx distance
M 2
M 1
(II) program can be used to compute the distance between
monomers’ CoM, during the course of the simulation.
For the sake of simplicity, we use d (t) and d (t) The following command computes and writes down the
com,W
com,M
to denote the CoM distance between monomers in the distance between monomers’ CoM in.xvg file, having
wild-type and mutant heterodimer. provided.xtc and.tpr files as input arguments and having
At first, we use d (t) to distinguish between non- selected corresponding monomers from the.ndx file:
com
convergent and convergent system’s dynamics. During the gmx distance -f md.xtc -s md.tpr -n index.ndx -oall
non-convergent phase, monomers have not yet entered a output_file.xvg -select ‘com of group 18 plus com of group 19’
mutually stable conformation, and large movements are
likely to occur that will result in sharp d (t) oscillations. d The obtained CoM distance results in.xvg format:
(for the wild-type heterodimer) and d com,M (mutant
com
On the other hand, once they have entered a mutually heterodimer) that can be plotted in MS Excel. One can
com,W
stable conformation, the CoM distance is preserved at
a relatively constant level, resulting in smooth d (t) use the plot to identify the earliest time point t eq., when
com
transitions. both heterodimers enter stable conformation. We can
identify the binding affinity impact of induced protein
Given that t is the earliest time point that marks mutations, depending on which of the conditions (a), (b),
eq
the joint beginning of the convergent phase in both or (c) becomes true.
heterodimers, we compare average(d com,M (t≥t )) against
eq.
average(d com,W (t≥t )), in order to draw a conclusion about 3. In silico experiment: Systems preparation
eq.
the binding affinity change in comparative context, based and MD simulation
on the fulfillment of condition (a), (b), or (c):
(a) If average(d com,M (t≥t ))>average(d com,W (t≥t )): Induced For the purpose of the experiment, Protein Data Bank
eq.
15
eq.
mutation(s) decrease intermolecular biding affinity; (https://www.rcsb.org) structure: 6M0J, was used as
(b) If average(d com,M (t≥t ))<average(d com,W (t≥t )): Induced a wild-type molecular complex. 6M0J heterodimer
eq.
eq.
mutation(s) increase intermolecular biding affinity; (https://www.rcsb.org/structure/6m0j) includes two
(c) If average(d com,M (t≥t ))≈average(d com,W (t≥t )): Induced monomers, namely, chain A (hACE2 receptor, residues
eq.
eq.
mutation(s) do not substantially alter intermolecular range: [19 – 615]) and chain E (SARS-CoV-2 S-protein
binding affinity. RBD, residues range: [333 – 526]); N-acetyl-D-glucosamine
ligands; and additional metal ions, such as zinc cations.
2.2. Method implementation in GROMCAS MD Amino acids included in the 6M0J model represent the key
simulation software interface of hACE2-RBD interactions.
The method can be implemented in GROMACS MD PyMol software (https://pymol.org/2/, version 2.5.4)
simulation software, using the following output files: was used to clean up all non-protein content and mutate
(a) .xtc file: compressed MD trajectory file; wild-type K417 (Lys417) in SARS-CoV-2 S-protein to Y417
(b) .tpr file: portable binary run input file that contains (Tyr417). In spite of 3D molecule visualization, PyMol also
the initial structure, the topology and simulation enables easy content modification. PyMol mutagenesis
parameters; tool was used to mutate wild-type K417 (Lys417) to Y417
(c) .gro file: that contains molecular structure in (Tyr417) in the SARS-CoV-2 S-protein.
Gromos87 file format. Both heterodimers, bearing K417/Y417 in the S-protein,
The first step is to call gmx make_ndx program to followed equal preparation procedure. Heterodimers were
create separate index groups for the monomers in each dissolved under the SPC/E (simple point-charge/extended)
Volume 3 Issue 1 (2024) 3 https://doi.org/10.36922/gpd.2657