Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption

Table 2

Side chain-side chain hydrogen bond interactions in the final simulated and refined MDM2-DHFR protein complex in Homo sapiens.

Donor				Acceptor				Parameters
Position	Protein	Residue	Atom	Position	Protein	Residue	Atom	Dd-a	Dh-a
36	D	ARG	NH1	62	M	MET	SD	3.64	4.1
36	D	ARG	NH1	62	M	MET	SD	3.64	3.73
36	D	ARG	NH2	62	M	MET	SD	3.57	3.98
36	D	ARG	NH2	62	M	MET	SD	3.57	3.69
36	D	ARG	NH1	67	M	TYR	OH	2.97	2.29
36	D	ARG	NH1	67	M	TYR	OH	2.97	2.91
162	D	TYR	OH	68	M	ASP	OD1	2.52	9.99
168	D	ASP	OD2	18	M	GLN	NE2	2.75	1.8
168	D	ASP	OD2	18	M	GLN	NE2	2.75	3
17	M	SER	OG	168	D	ASP	OD1	2.53	9.99
18	M	GLN	NE2	168	D	ASP	OD2	2.75	3.43
18	M	GLN	NE2	168	D	ASP	OD2	2.75	1.8
67	M	TYR	OH	37	D	MET	SD	3.31	9.99
70	M	LYS	NZ	130	D	HIS	NE2	3.35	9.99
70	M	LYS	NZ	183	D	GLU	OE1	2.66	9.99
70	M	LYS	NZ	183	D	GLU	OE2	2.8	9.99
70	M	LYS	NZ	185	D	ASN	OD1	2.76	9.99
94	M	LYS	NZ	161	D	GLU	OE2	2.63	9.99

Protein D and protein M represent DHFR and MDM2 proteins from Homo sapiens. Dd-a represents the distance between the “donor” and “acceptor.” Dh-a represents the distance between “hydrogen atom” and “acceptor.” The ATOM records, such as SD and NE, indicate the atomic names according to IUPAC (i.e., PDB) nomenclature as well as the CHARMM atom categories for each of the atoms in the individual residues. At the end of either of the ATOM records, the specific numbers (like NH1, OD2, etc.) represent the partial atomic charge.