BMC Molecular and Cell Biology

Table 4 Hydrogen bonds between the SOX2 protein and DNA before and after MD simulation

From: Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions

Complex name	Before simulation				After simulation
Complex name	Index	SOX2	Dist. [Å]	Human DNA	SOX2	Dist. [Å]	Human DNA
Derived A-allele DNA-SOX2	1	ARG43	3.02	DT	ARG40	1.81	DG
	2	ARG43	2.95	DG	LYS42	1.81	DT
	3	ARG43	2.95	DT	ARG43	1.93	DT
	4	ARG43	3.07	DT	ARG43	1.76	DT
	5	ASN46	3.8	DA	ARG43	2.03	DG
	6	ALA47	3.68	DA	ASN46	2.98	DA
	7	ARG56	2.88	DT	ARG56	1.73	DG
	8	ASN68	2.97	DG	ASN68	2.2	DT
	9	LYS73	2.15	DA	LYS73	1.83	DC
	10	ARG113	3.01	DT	LYS80	1.75	DC
	11	ARG114	3	DG	ARG98	2.11	DT
	12	LYS115	2.26	DA	ARG98	1.69	DT
	13	-	-	-	ARG113	2.28	DT
	14	-	-	-	ARG113	2.32	DG
	15	-	-	-	ARG113	1.76	DT
	Before simulation				After simulation
Ancestral T-allele DNA -SOX2	Index	SOX2	Dist. [Å]	Neanderthal DNA	SOX2	Dist. [Å]	Neanderthal DNA
	1	ARG43	3.5	DT	ARG40	1.93	DT
	2	ARG43	3.68	DT	LYS42	1.9	DG
	3	ARG43	2.97	DA	ARG43	2.06	DT
	4	ARG56	3.75	DT	ASN68	1.73	DT
	5	ASN68	3.74	DC	LYS73	2.3	DC
	6	ASN68	3	DC	LYS73	1.93	DT
	7	ASN68	2.43	DG	LYS87	1.83	DC
	8	-	-	-	ARG98	1.75	DA
	9	-	-	-	ARG98	1.63	DA
	10	-	-	-	ARG113	2.26	DG
	11	-	-	-	ARG113	2.09	DT
	12	-	-	-	ARG113	1.82	DT

The table depict inter-molecular hydrogen bonding differences between the two complexes based on 5000 structural frames obtained from molecular dynamics (MD) simulation during the 0.00 ns to 100.00 ns. Dist. Å (angstrom) illustrates distance between the hydrogen bonded donor atom and acceptor atom or length of hydrogen bond. D (A, C, T, G) denotes Deoxyribonucleotides

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