Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Moroni, Elisabetta; Caselle, Michele; Fogolari, Federico

doi:10.1186/1472-6807-7-61

Table 5 Components of the free energies (in kcal/rnol) calculated according to the MM/GBSA model. The constant term x_constis 13.699 kcal/mol

From: Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Original base	Mutated	ΔG_exp	ΔG_calc	Coul	vdW	GB	P	H	HB
T3-A39	C-G	0.400	0.115	-79.691	-33.547	50.408	30.607	37.296	-18.658
	G-C	0.600	0.525	-79.292	-33.467	50.226	30.690	37.327	-18.658
	A-T	0.400	1.165	-78.394	-33.432	49.648	30.588	37.181	-18.125
A4-T38	C-G	1.000	0.777	-81.129	-33.803	51.302	30.367	37.934	-17.592
	T-A	1.400	1.036	-81.246	-33.723	51.482	30.201	38.215	-17.592
	G-C	1.100	1.613	-79.949	-33.852	50.681	30.609	38.017	-17.592
C5-G37	T-A	0.800	2.136	-80.893	-33.864	51.109	30.552	39.125	-17.592
	A-T	0.600	0.996	-79.955	-33.842	50.645	30.484	38.090	-18.125
	G-C	0.700	0.377	-81.302	-33.810	51.382	30.589	37.944	-18.125
C6-G36	T-A	0.900.	1.362	-80.476	-33.730	50.877	30.661	38.456	-18.125
	A-T	1.000	0.622	-79.641	-33.667	50.411	30.314	38.163	-18.658
	G-C	0.600	1.110	-80.186	-33.579	50.678	30.491	38.132	-18.125
T7-A35	G-C	0.400	-0.082	-80.781	-33.792	51.084	30.579	37.254	-18.125
	A-T	-0.200	0.318	-80.382	-33.960	50.847	30.200	38.038	-18.125
	C-G	0.900	1.146	-80.387	-33.817	50.873	30.729	37.641	-17.592
C8-G34	T-A	0.500	1.350	-80.849	-33.862	51.113	30.593	38.247	-17.592
	A-T	3.600	3.360	-77.402	-33.305	49.165	30.110	38.152	-17.059
	G-C	3.400	2.435	-78.703	-33.834	49.920	30.582	37.829	-17.059
T9-A33	A-T	2.800	2.732	-78.808	-33.818	50.131	30.297	38.289	-17.059
	G-C	1.000	1.489	-79.210	-34.213	50.394	30.812	37.599	-17.592
	C-G	0.300	0.714	-80.866	-33.839	51.216	30.778	37.851	-18.125
G10-C32	A-T	0.400	1.868	-79.605	-33.008	50.347	30.450	38.110	-18.125
	T-A	0.500	1.034	-80.384	-34.230	50.938	30.722	38.414	-18.125
	C-G	0.200	-0.182	-81.436	-34.074	51.523	30.789	37.975	-18.658
G11-C31	C-G	1.400	1.533	-78.037	-33.806	49.387	30.408	38.007	-18.125
	A-T	1.100	1.009	-79.919	-33.894	50.529	30.555	38.163	-18.125
	T-A	2.300	0.731	-78.332	-33.617	49.511	30.299	38.362	-19.191
C12-G30	G-C	2.500	3.881	-78.666	-33.416	50.051	30.575	38.163	-16.526
	A-T	2.500	2.061	-78.455	-33.360	49.873	30.306	37.588	-17.592
	T-A	2.700	2.656	-78.889	-33.693	50.116	30.223	38.257	-17.059
G13-C29	A-T	2.900	1.744	-79.600	-33.700	50.381	30.624	37.933	-17.592
	C-G	3.400	1.941	-80.240	-33.646	50.825	30.805	38.090	-17.592
	T-A	3.200	2.131	-79.467	-33.720	50.343	30.737	38.665	-18.125
G14-G28	C-G	3.700	3.688	-78.059	-33.822	49.562	30.408	38.425	-16.526
	T-A	3.700	2.495	-78.334	-33.204	49.700	30.231	37.996	-17.592
	A-T	3.100	1.703	-80.426	-33.916	50.878	30.593	38.467	-17.592
T15-A27	G-C	2.900	1.755	-79.475	-33.371	50.375	30.884	37.766	-18.125
	A-T	2.000	1.946	-79.417	-33.359	50.311	30.820	37.484	-17.592
	C-G	2.500	1.088	-80.371	-33.422	50.848	30.775	37.683	-18.125
G16-C26	C-G	0.900	1.507	-79.347	-33.801	50.310	30.514	37.724	-17.592
	T-A	1.000	1.411	-79.452	-33.016	50.268	30.302	37.735	-18.125
	A-T	0.600	1.490	-79.733	-33.915	50.492	30.521	38.550	-18.125
A17-T25	C-G	0.200	0.100	-81.783	-33.375	51.717	30.952	37.014	-18.125
	T-A	-0.100	0.258	-81.595	-33.370	51.621	30.858	37.171	-18.125
	G-C	-0.200	0.741	-79.839	-33.332	50.528	30.608	37.202	-18.125
T18-A24	C-G	2.000	1.549	-81.158	-33.893	51.430	30.971	38.090	-17.592
	A-T	2.800	1.747	-81.528	-33.712	51.592	30.487	37.735	-16.526
	G-C	1.100	1.382	-80.583	-33.977	51.012	30.627	38.195	-17.592
A19-T23	T-A	0.400	1.602	-78.329	-33.474	49.625	30.680	37.526	-18.125
	C-G	0.500	0.917	-79.871	-33.472	50.549	30.684	37.453	-18.125
	G-C	0.400	0.878	-80.353	-33.573	50.784	30.669	37.777	-18.125
wild- type	--	0.000	1.120	-79.937	-33.811	50.610	30.593	38.090	-18.125

Back to article page