Table 5.

Computed versus NMR-determined pKa values for protein 1YGW

Res	pka	<pK>b	<pK>c	rmsdd	pKe	pKf
ASP 3	3.5	3.6	4.1	0.17 - 0.11	3.1	-
ASP 15	3.5	3.4	3.4	0.31 - 0.15	2.9	4.2
ASP 29	4.3	3.7	3.8	0.15 - 0.19	4.0	5.5
ASP 49	4.2	3.7	3.9	0.07 - 0.09	3.9	5.0
ASP 66	3.9	3.5	3.2	0.11 - 0.10	3.3	4.6
GLU 28	5.6	4.6	3.9	0.17 - 0.20	4.8	6.1
GLU 31	5.4	4.0	4.3	0.11 - 0.12	4.7	46
GLU 46	3.6	4.3	4.3	0.18 - 0.15	4.5	4.0
GLU 58	4.0	4.1	4.2	0.18 - 0.20	3.4	2.5
GLU 82	3.3	3.4	3.4	0.31 - 0.15	4.0	2.8
GLU 102	5.3	4.2	4.4	0.27 - 0.17	4.2	5.3
HIS 27	7.0	7.2	6.7	0.20 - 0.12	6.8	8.4
HIS 40	7.5	7.4	7.6	0.25 - 0.23	6.9	8.5
HIS 93	7.3	6.6	7.6	0.50 - 0.34	5.4	6.1

^aobserved pKa’s for each ionizable residue of protein 1YGM (Kilmbi, Gray, 2012);

^baveraged pK’s value (over 34 NMR-determined structures of 1YGW) computed by using the GB-MSR6c-pK model;

^caveraged pK’s value computed over 10 ns molecular dynamic trajectory for each of the 34 NMR-determined conformations); underlined we highlight pKa errors > 1.0 pK unit;

^dRMSD of pKa fluctuations computed from the: (i) set of 34 NMR-derived models deposited at the PDB (id 1YGW); and (ii) the MD trajectory of 10 ns of length for each of the 34 NMR-derived conformations of 1YGW;

^eaveraged pKa values obtained by using ROSETTA-pH method (Kilmbi, Gray, 2012);

^faveraged pKa values obtained by using MCCI2 method (Song, Mao, Gunner, 2009).