Volume 78, Issue 3, Pages 1126-1144 (March 2000) Backbone Dipoles Generate Positive Potentials in all Proteins: Origins and Implications of the Effect  M.R. Gunner, Mohammad A. Saleh, Elizabeth Cross, Asif ud-Doula, Michael Wise  Biophysical Journal  Volume 78, Issue 3, Pages 1126-1144 (March 2000) DOI: 10.1016/S0006-3495(00)76671-9 Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 1 Space filling representation of an amide group. The amine HN (r=1.0Å) is substantially smaller than the carbonyl oxygen (r=1.6Å). The first atom of the two side chains (CB) adjacent to the amide are oriented as they would be in an α-helix. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 2 Each non-terminal side chain lies between 2 amides, one toward the N-terminal and the other toward the C-terminal. (A) The amides toward the N-terminal (amide(n)) and C-terminal (amide(c)) of the side chain of residue i. (B) One amide is amide(c) for one side chain (i) and is amide(n) for the next side chain (i+1) in the protein. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 3 Electrostatic potential at a slice through four proteins with different folds. Potentials calculated and displayed with the program grasp (Nicholls et al., 1991). Blue regions are at positive and red at negative potential; charmm charges, ϵprotein=4; ϵsolvent=80. (A) α motif: Met-hemerythrin from sipunculid worm (Themiste dyscrita) (2hmq chain A) (Holmes and Stenkamp, 1991). A 104 residue iron-binding protein in a four-helical up-and-down bundle with a left-handed twist (Motif descriptions from the scop data base (Murzin et al., 1995)). (B) β motif: human lipid binding protein (1hmr) (Zanotti et al., 1992). A 129 residue 10-stranded meander β-sheet folded upon itself. (C) α/β motif: triose phosphate isomerase from Trypanosoma brucie brucei (1tpf) (Kishan et al., 1994); a 247 residue α/β barrel which has 8 alternating α and β segments forming an internal, parallel β-sheet barrel; and (D) α+β motif: bovine ribonuclease A (7rsa) (Wlodawer et al., 1988); A 124 residue protein with a long curved β-sheet and 3 α-helices. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 4 The number of proteins with different values of the average electrostatic potential at the side chain heavy atoms (VP). VP was calculated with Eq. 3a for 305 proteins. The patterns for different scop protein motifs: α, black; β, horizontal; α+β, diagonal; α/β, cross-hatch; others, white. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 5 Comparison of the average potential at side chain heavy atoms (VP) for proteins with different charges on the backbone. VP was calculated with Eq. 3a. Charges from Table 1: (○), amine (HN, N, CA) charges; (●), carbonyl (C, O) charges. The straight lines are described by: 11.91+0.77x (r2=0.96) and −11.2+0.22x (r2=0.71) Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 6 Comparison of the contribution of the neighbor and distal amides to the average potential for 51 proteins. Each residue is charged in turn in each protein and the potential collected at the two neighboring side chains and at the distal side chains. Different protein motifs: α, ■; β, □; α+β, ▴; α/β, ○; others, △. The straight lines are described by neighboring amides, 86.91+0.18x (r2=0.56); and distal amides, −86.9+0.82x (r2=0.96) Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 7 Each amide forms the junction between two residues (Fig. 2 B). One amide is amide(c) for residue (i), with an orientation between side chain and amide determined by the psi angle. The same amide is amide(n) for the next side chain (i+1) and their orientation is described by the phi angle. grasp (Nicholls et al., 1991) pictures showing the two CBs (green) neighboring one amide in (A) α-helix (ϕ=−52, ψ=−53); (B) β-strand (ϕ=−123, ψ=143). The five atoms assigned charge are labeled, colored red (negative) or blue (positive), and given a radius that is proportional to the partial charge. The isopotential contours at +0.85kcal/e (blue) and −0.85kcal/e (red) calculated with (C, D) ϵpeptide=ϵsolv=4; and (E, F) ϵpeptide=4, ϵsolv=80. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 8 The potential at the middle CB in an Ala tripeptide from (A) amide(n) as a function of the phi angle and (B) amide(c) as a function of the psi angle (see Fig. 7 A). The potential was calculated with (bold line) ϵpeptide=ϵsolv=4; (flatter, light line) ϵpeptide=4, ϵsolv=80. The relative occurrence of residues with different phi (C) and psi (D) angles in the 305 proteins considered in this study were determined with the program dssp (Kabsch and Sander, 1983): Solid line, α-helix; heavy dotted line, β-sheet; light line, other. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 9 The dependence of the average potential at the side chain (VS) on the length of the side chain. The average potential (VS), ●; the contribution from the neighboring amides, △; the contribution of the distal amides, ■. Data from Table 8. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 10 The difference in the exposure of the HN and O vs. the contribution of that amide to the average potential within the four-helix bundle 2hmq, the β-barrel 1hmr, the α/β barrel 1tpf, and the α+β protein 7rsa. Residues in α-helices (■), in β-sheets (▴), and in loops (○). The structures were modified as described in the Methods section to equalize the length and size of the HN-N and C-O dipoles. The potential was calculated with ϵprotein=4, ϵsolv=80. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 11 The distribution of acidic and basic side chains with different values of ΔGrxn and ΔGbkn in 305 proteins with different motifs. charmm charges were used for side chains and amides. The net charges in each run were +1 on the bases or −1 on the acids. ϵprotein=4, ϵsolv=80. Acids: ●, Asp; ○, Glu. Bases: ■, Arg; □, Lys. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions

Figure 12 The relationship between ΔGbkn and ΔGrxn for the acidic and basic amino acids in 305 proteins. The bold line is for −ΔGbkn=ΔGrxn. The dashed line shows the maximum value for ΔGxn, when Grxn=0 and ΔGrxn=−Grxn in soln (Table 2). The ±1.5kcal/mol has been removed. Biophysical Journal 2000 78, 1126-1144DOI: (10.1016/S0006-3495(00)76671-9) Copyright © 2000 The Biophysical Society Terms and Conditions