Correction for Barth et al., Toward high-resolution prediction and design of transmembrane helical protein structures

BIOPHYSICS. For the article “Toward high-resolution prediction and design of transmembrane helical protein structures,” by P. Barth, J. Schonbrun, and D. Baker, which appeared in issue 40, October 2, 2007, of Proc Natl Acad Sci USA (104:15682–15687; first published September 28, 2007; 10.1073/pnas.0702515104), the authors note that “Renumbering the protein structure files to start at residue 1 in our calculations resulted in shifts in the residue numbering of the protein segments reported in Fig. 1 and Table 2 relative to those in the Protein Data Bank. In the Fig. 1 legend, the middle panels correspond to the helix of halorhodopsin kinked at Pro-117 rather than Pro-94, and the bottom panels correspond to bovine rhodopsin rather than halorhodopsin.” These errors do not affect the conclusions of the article. The corrected table and its legend appear below.

Table 2.

Native TMH docking tests

Protein	Docked residues	Zlrms
		Full	No weak/bif HB
Glycophorin A	All	3.26	1.02
Glycerol channel	44–60	2.56	1.89
	239–250	3.59	2.87
PsaL subunit of Photosystem I	47–57	2.22	1.82
Halorhodopsin	24–52	2.37	1.73
	227–255	1.71	1.66
Calcium ATPase	764–775	2.35	1.97
Cytochrome c oxidase	Subunit D: 76–89	2.87	2.63
Photosynthetic reaction center	Subunit L: 240–250	2.22	2.01
	Subunit M: 54–67	2.3	1.89
Mean ± SD		2.55 ± 0.55	1.95 ± 0.51

The energy gap between native, near-native (N), and nonnative (NN) docked complexes was assessed by using Z_lrms = (〈E〉_NN − 〈E〉_N)/σ _E^NN (see Materials and Methods). The contribution of the membrane-specific hydrogen bonding term to the energy gap between native and nonnative docked complexes is analyzed: full membrane potential (Full), potential without membrane-specific side-chain–backbone bifurcated and side-chain–side-chain, backbone–side-chain weak hydrogen bonds (No weak/bif HB). Successful discrimination is defined as a Z score >1.