Structural Ligand-Protien and Energy
Study of Kanamycin A with an Aminoglycoside 2'-n-acetyltransferase protein
Aminoglycoside 2'-n-acetyltransferase(PBD code:- 1M4I) is a dimeric protein, which has two main subunits that mirror each other. It catalyzes the acetylation of the 2’ Hydroxyl or amino group of aminoglycosides. The aminoglycosides that are found to be a substrate for this protein are tobramycin, Kanamycin A and ribostamycin. Each subunits binds to one substrate molecule, in this paper Kanamycin A(Het:- 1KNY) is studied, and Acetyl COA. The reaction is dependent on Acetyl COA. Aminoglycoside 2'-n-acetyltransferase is an important enzyme in tuberculosis bacteria because it deactivates many antibiotics with it’s catalytic acitivity.
Using MM2 single point calculations to find the steric energy summary for Kanamycin A when it is complexed with the protein, and in its gas phase, the following data is collected:-
Steric energy summary for Kanamycin A:-
Table 1.0
Structure of Kanamycin A when Structure
of Kanamycin A in the
complexed with the protein:-
gas phase:-
Figure 1 Figure 2
Comparison of the Steric energy components of Kanamycin A:-
By looking at the total energies of Kanamycin A when it is complexed with the protein, and when it is in it’s free form, it is shown that there is a significant difference. Kanamycin A’s total energy drops to 31.4 from 150.65 when in it’s minimum conformation energy. Visually it is shown that both structures are different, though the exact nature of the change is not evident without overlap.
By looking at the specific energy components, it is
concluded that the greatest contributors are the stretch and bend frequency.
Stretch occurs when bonds are compressed or stretched beyond their optimal
length. This can occur from interactions with other molecules, in this case
from the interactions of Kanamycin with the protein, which distorts the natural
geometry of Kanamycin.
The Vander wall force interactions is the next greatest contributor. This occurs from the repulsion between the electron clouds of adjacent molecules.
The torsion energy which refers to the energy of dihedral angles, is the next greatest contributor. If two dihedral angles have large functional groups, strain can occur from mechanical interaction of the atoms bumping into each other if they are too close or repulsion from their electron clouds. Relatively, the contribution from the torsion angle is very small though.
Following
is the Wiring Diagram for the protein Aminoglycoside 2'-n-acetyltransferase:-
Figure 3
The
red dots above each letter that stands for an amino acid residue of the protein
stands for an interaction between the protein and the hetro-compound. Not all
the red dots shown above are between Kanamycin A and the protein though,
because Aminoglycoside 2'-n-acetyltransferase also binds with Acetyl-COA.
Aminoglycoside
2'-n-acetyltransferase contains two Kanamycin ligands. Both molecules are
arrayed similarly in two mirror image chains of the protein. The Kanamycin
molecules are named Kan 500 and 501. The lig Plot of Kanamycin A 500 looks like
this:-
Figure 4
Kanamycin
501 is similarly arrayed, and Figure 4 is said to also represent 501 on the
PDB-Sum webpage.
Next
is a ball and Stick model of Kanamycin A, within the protein.
Figure 5
Same
Compound with the interacting amino acid residues shown in yellow:-
Figure 6
Interactions
between Kanamycin A and the amino acid residues shown closer up, with hydrogen
bonds in green dotted lines.
Figure 7
Table
2 lists the specific amino acids residues of the protein, that are interacting
with Kanamycin A. By looking at the interacting atoms, the most likely
interaction is figured out.
|
Amino acid Residue |
Hetero compound atoms |
Nature of Interaction |
|
Asp 35 |
N-C |
2
Hydrogen bonds between the nitrogen hydrogens and the lone electronpairs of
the Asp Oxygens |
|
Phe 32 |
Non-aromatic
ring |
2 Phe
aromatic rings could stack with the hexane ring of Kanamycin |
|
Phe 36 |
“ |
“ |
|
Gly 83 |
-O |
Hydrogen
bonding between the nitrogen of the Gly and the Oxygen |
|
Glu 82 |
-OH |
Hydrogen
bonding between the oxygen of Glu and HO- of Kanamcyin |
|
Ser 117 |
-OH |
Hydrogen
bonding between oxygen lone pair on Ser and hydrogen of –OH |
|
Asp 151 |
-OH |
Asp is
HBD with oxygen on Hetero compound |
|
Asp 152 |
-NH2 |
Lone pair
hydrogen is HBD with hydrogen of N |
|
Trp 181 |
-NH2 |
Oxygen of
TRP hydrogen bonds with H on the Hetero Nitrogen |
Table
2
Bibliography:-
PDB ID: 1M4I
Vetting, M.W., Hegde, S.S., Javid-Majd, F., Blanchard, J.S., Roderick, S.L.
Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis in complex with coenzyme A and aminoglycoside substrates.
Nat Struct Biol 2002 Sep ;9(9);653-8.
Vetting, M.W., Hegde, S.S., Javid-Majd, F., Blanchard, J.S.,
Roderick, S.L. Nature Structural Biology. 2002, 9, 653. “Aminoglycoside 2'-N-acetyltransferase from Mycobacterium
tuberculosis in complex with coenzyme A and aminoglycoside substrates”
http://www.nature.com/nsmb/journal/v9/n9/pdf/nsb830.pdf
Laskowski R A, Chistyakov V V,
Kanamycin A Lig Plot
Interactions. PDB SUM.