A script to highlight hydrophobicity and charge on protein surfaces

Abstract

The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively visualizes segments on protein surfaces that contribute to specificity in protein-protein interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a transmembrane domain. We provide YRB highlighting in form of a script that runs using the software PyMOL.

Keywords: PyMOL; amino acid properties; charge pairs; protein-protein interaction; surface hydrophobicity.

Figure 1

Highlighting at atomic level visualizes both hydrophobicity and charge. Functional groups are colored according to the YRB highlighting scheme (hydrocarbon groups without polar substitutions, yellow; negatively charged oxygens of glutamate and aspartate, red; nitrogens of positively charged functional groups of lysine and arginine, blue; all remaining atoms including the polar backbone, white).

Figure 2

The yeast Hsp90 surface highlighted in YRB. (A) Hsp90 highlighted according to the YRB highlighting scheme or, (B) displayed in cartoon. Yeast Hsp90 (A2-N676) PDB code 2cg9 (Ali et al., 2006).

Figure 3

Hydrophobic core of the Hsp90-Cdc37 interface. (A–H) Complex of yeast Hsp90-N (A2-L207) and Cdc37C (H148-K347), PDB code 1us7 (Roe et al., 2004). (C,D) Complementary views of the interfaces between Hsp90 and the mirrored co-chaperones are displayed in YRB. (B,E) Full YRB highlighting on both proteins. (A,F) The complementary interface (yellow) of Hsp90 (gray) and co-chaperones (green) are either shown in ribbon or in surface. (G,H) Hsp90-Cdc37 interface displayed in YRB stick mode. The charged pair E33 of Hsp90 and R167 of Cdc37 is visible in sticks mode.

Figure 4

Complementarity in the YRB highlighted Hsp90-p23 interface. (A–F) Complex of yeast Hsp90 (A2-N676) and Sba1 (W12-A135), PDB code 2cg9 (Ali et al., 2006). (C,D) Complementary views of the interfaces between Hsp90 and the mirrored co-chaperone p23 are displayed in YRB. The matching ion pairs K27 with D122 and D113 with K113 of the Hsp90-p23 interface are indicated by arrows. (B,E) Full YRB highlighting on both proteins. (A,F) The complementary interface (yellow) of Hsp90 (gray) and p23 (green) are either shown in ribbon or in surface in the first and last panels.

Figure 5

Complementarity in the YRB highlighted Hsp90-Aha1 interface. (A–F) Complex of yeast Hsp90-M (T273-D527) and Aha1-N (W11-D153), PDB code 1usv (Meyer et al., 2004). (C,D) Complementary views of the interfaces between the fragments of Hsp90 and the mirrored co-chaperone Aha1 are displayed in YRB. The ion pairs of the Hsp90-Aha1 interface K390 with D68, K514 with D110, and E515 with R128 are indicated by arrows. (B,E) Full YRB highlighting on both proteins. (A,F) The complementary interface (yellow) of Hsp90 (gray) and co-chaperone (green) are either shown in ribbon or in surface in the first and last panels.

Figure 6

YRB highlights specificity of the SNARE interface. (A–K) Complementary views of the interface between t-SNAREs and v-SNARE are displayed in YRB. (B,C,H) t-SNAREs, [syntaxin (S186-S259), red; SNAP25 (L11-K83/G132-G204), green], and (D–F) the v-SNARE [synaptobravin (L26-K94), blue], are displayed in YRB. (A,G) The SNARE complex is shown in ribbon representation indicating the four-helix bundle (red, green, blue; PDB code 1sfc; Sutton et al., 1998). (C–D) Matching electrostatic interactions (E41-R161, K52-D172, K59-D179, and K85-D250) between synaptobrevin and syntaxin/SNAP25 are indicated by arrows. (H–J) Zoom into the matching electrostatic interactions in the SNARE complex, indicated by circles. (K) SNARE complex colored according to electrostatic potential.

Figure 7

Hsp90-nucleotide interaction in YRB colors. The nucleotide-binding pocket in the Hsp90 N-terminal domain is displayed in YRB [human Hsp90-N (A2-E214) bound to ADP; PDB code 1am1 (Prodromou et al., 1997)]. (A) Overview of Hsp90 N-terminal domain and (B) a zoom into the nucleotide-binding pocket complexed with ADP. The interaction between Asp79 of Hsp90-N and the N-amino group of the adenine base is indicated by a circle. ADP is displayed according to CPK color scheme (carbon, green; oxygen, red; nitrogen, blue; phosphate, orange).

Figure 8

Highlighting a transmembrane protein. NADH:quinone oxidoreductase complex contains several domains (PDB code 4p6v; Weber et al., 1998). Na⁺NQR is highlighted either in (A) YRB, or (B) hydrophobic (red) to non-hydrophobic (white) gradient, or (C) according to electrostatic potential, or (D) the CPK coloring mode (carbon, green; oxygen, red; nitrogen, blue; phosphate, orange). A ring formed by positive charged head groups on the cytosolic side is marked by arrows.

Figure 9

Hsp90-p23 interfaces in hydrophobicity gradient, electrostatic potential and in CPK coloring. Complex of yeast Hsp90 (A2-N676) and Sba1 (W12-A135), PDB code 2cg9 (Ali et al., 2006). (A) Hsp90/co-chaperone interfaces are shown in a hydrophobic gradient: non-hydrophobic white to hydrophobic amino acids red (B) in electrostatic potential and (C) in CPK coloring: carbon green, oxygen red, nitrogen blue, sulfate atoms yellow.

Figure 10

YRB reveals the binding hot spot of the growth hormone receptor. The extracellular domain of the growth hormone receptor (hGHbp; E32-P234), PDB code 3hhr (de Vos et al., 1992). The binding hot spot is determined by alanine substitutions of the residues in the interface (all residues with ΔΔG > 1 kcal/mol) (Clackson and Wells, 1995).