. Author manuscript; available in PMC: 2008 May 29.

Published in final edited form as: Protein Eng Des Sel. 2008 Mar;21(3):215–222. doi: 10.1093/protein/gzm092

Table I.

Structural properties of the TS ensembles determined for the five proteins considered in this work

Protein	MD type	N_Φ^a	RMSD^b (Å)	R_g^c (Å)	ΔR_g^c (%)	S^d (Å²)	ΔS^d (%)	<Φ^cal>^e	<Φ^exp>^f
CspB	‘specific’	17	5.8±0.7	11.6±0.4	+6	4700±400	+11	0.37	0.43^g
CspB	‘classes’	17	6.3±1.1	11.8±0.4	+7	4900±300	+15	0.36	0.43^g
CspB	‘classes^21-70’^h	17	5.2±1.2	11.9±0.5	+8	4900±300	+15	0.35	0.43^g
CspB	‘classes^30-60’ⁱ	17	5.3±1.0	11.8±0.4	+7	4900±300	+15	0.36	0.43^g
CspB	‘specific’ ΔG^j	17	6.8±1.5	12.0±1.0	+9	5000±700	+17	0.36	0.43^g
mAcP	‘specific’	22	7.3±2.4	13.7±0.5	+4	6800±400	+19	0.27	0.30^k
mAcP	‘classes’	22	5.9±1.1	13.8±0.4	+5	6900±400	+21	0.26	0.30^k
mAcP	‘classes’	3^l	7.4±1.4	14.2±0.4	+7	7200±400	26%	0.24	0.30^k
CI2	‘specific’	34	10.1±2.4	14.7±1.2	+30	6600±500	+51	0.19	0.24^m
CI2	‘classes’	34	10.6±2.0	14.4±1.1	+28	6300±400	+44	0.19	0.24^m
TI I27	‘specific’	22	3.7±0.8	12.9±0.2	+0	5500±200	+8	0.50	0.57ⁿ
TI I27	‘classes’	22	3.5±0.6	12.8±0.2	-1	5400±300	+6	0.51	0.57ⁿ
TNfn3	‘specific’	25	6.9±2.0	13.7±0.6	+5	6500±500	+26	0.24	0.28^o
TNfn3	‘classes’	25	5.9±2.4	13.6±0.8	+5	6300±400	+22	0.25	0.28^o

Reported errors correspond to one standard deviation.

Number of experimental Φ-values used as restraints.

Root mean square distance from the native conformation.

Average radius of gyration; difference in R_g between the TS and the native state.

Solvent accessible surface area; difference in S between the TS and the native state.

Average calculated Φ-value computed from all the residues that have non-zero number of side-chain native contacts.

Average experimental Φ-value.

λ₁ and λ₂ in Eq. (3) were set to 0.21 and 0.70, respectively.

ⁱ

λ₁ and λ₂ in Eq. (3) were set to 0.30 and 0.60, respectively.

The generated structures are selected as defined by Eq. (9).

Simulation restrained using only the key residues Tyr11, Pro54 and Phe94.

ⁿ