Knottin cyclization: impact on structure and dynamics

BMC Structural Biology

Table 4 Hydrogen bond occurrences during the molecular dynamics simulations

Local structure	Residues	MCoTI-II		lin-MCoTI		EETI-II
3-stranded β -sheet	N33-O13	68.7	3.03	97.6	2.98	99.7	2.95
	N15-O31	98.7	2.94	98.9	2.93	98.8	2.97
	N26-O34	99.9	2.88	99.9	2.90	100.0	2.74
	N34-O26	99.5	2.91	99.6	2.89	97.2	2.98
	N28-O32	95.9	2.98	91.7	3.02	93.5	3.01
β -turns	N25-O22	88.8	3.06	92.3	3.05	89.6	3.13
	N25-O23	7.5	3.20	5.1	3.21	21.6	3.22
	N31-O28	97.0	3.03	96.4	3.04	96.7	3.06
3-10 helix	N20-O17	83.8	3.15	87.2	3.13	97.7	3.05
	N21-O18	81.9	3.17	67.8	3.19	70.6	3.19
	N21-O19	-	-	5.6	3.15	0.2	3.35
C to N linker	N6-O3	36.5	3.15	-	-	-	-
	N6-O4	15.7	3.18	-	-	-	-
Others	N10-08	8.6	2.99
	N11-O9	51.2	2.93	73.4	2.94	29.2	3.03
	N13-O11	13.5	3.12	22.1	3.19	9.2	3.06
Side chains	N16-Asp²⁰	76.1	2.90	81.6	2.94	98.7	2.88
	N17-Asp²⁰	71.7	3.01	50.5	3.02	88.3	3.04
	N27-Asp¹⁸	93.7	2.90	90.9	2.92	22.0	2.97
	Arg¹⁶-Asp²⁰	-	-	21.5	3.00	5.8	2.99
	Arg¹⁷-Asp²⁰	23.2	2.97	5.3	2.95	(Gln¹⁷)
	Lys¹³-Asp²⁰	10.1	2.96	-	-	(Met¹³)
	N32-Asn³⁰	68.8	3.16	70.1	3.16	79.6	3.15
	Lys¹³-O20	32.1	2.89	44.2	2.89	(Met¹³)
	Lys¹³-O14	15.8	2.93	30.8	2.94	(Met¹³)
	Lys¹⁴-O30	-	-	-	-	7.3	3.02
	Lys¹⁴-O31	-	-	-	-	7.4	3.09
	Lys¹⁰-O8	-	-	-	-	6.6	2.96
	Arg¹⁶-O15	10.3	2.95	-	-	-	-
	Arg²⁸-O1	50.5	3.01	-	-	(Gly²⁸)
	Arg²⁸-O32			22.7	3.14	(Gly²⁸)
	Arg²⁸-O33	12.2	3.03	55.9	3.05	(Gly²⁸)

For each hydrogen bond, the percentage of occurrence is followed by the average distance between heavy atoms (in Å). Only hydrogen bonds that occur more than 5% of the time are reported using 3.5 Å and 120° as distance and angle cut-offs, respectively. Bold numbers indicate the highest percentages in each row. Nx and Ox refer to the amide and carbonyl groups of residue x, respectively. When side-chains are involved, the residue is indicated using the three letter code.

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