[gmx-users] Side chains protein interaction: determine the type of interaction of two amino acids at the atomic level

milad bagheri milad9bagheri at gmail.com
Mon Dec 31 14:15:05 CET 2018

Dear researcher

I want to check the effect of an SNP (Single-nucleotide polymorphism) in my
protein structure. To do this, I once simulated a protein in the Wild Type
state and once again mutated for 100 nanoseconds.

After performing the MD, The defect of many articles I have read in
literatures, For analysis, the most attention to these articles was on a
Very brief explanation of the RMSD chart or RMSF and other ... But this is
not enough for me and I want to better understand the truth of the
interaction of amino acids, and so I can interpret the protein structure
after molecular dynamics simulation.

To clarify what the question is in my mind, I want to make a clear example:

Suppose that the VAL amino acid is located in the beta-sheet area, which
interaction With amino acids(TRP, CYS) located in the opposite beta-sheet,
In general, I know that interaction between valine and tryptophan is
*aromatic-aliphatic,* *But I want to explore this interaction at the atomic
level(such as Partial charge,Covalent bond.Hydrogen bond,London
attractions, Functional group of aminoacids,* *To be able to guess what
kind of interaction between VAL amino acid and TRP at the atomic level,* In
the first attempt, I examined the distance between the two atoms
interacting with the chimera software. The distance between the two atoms
was very variable, which based on the law of Lennard Jones, When two atoms
are at a distance with energy at the lowest level, then the two atoms are
in a stable state.

I want to know what atomic structural parameters should be considered for
comparing wild and mutated amino acids to determine whether the mutation
was suitable for the protein, or not(Does the desired SNP cause stability
of the protein structure?)

How to compare two amino acids?

Please advise or introduce a book to for me

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