Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity

Abstract

Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Several interface features have been documented using known X-ray structures of protein complexes since 1975. This has improved our understanding of the interface using structural features such as interface area, binding energy, hydrophobicity, relative hydrophobicity, salt bridges and hydrogen bonds. The strength of binding between two proteins is dependent on interface size (number of residues at the interface) and thus its corresponding interface area. It is known that large interfaces have high binding energy (sum of (van der Waals) vdW, H-bonds, electrostatics). However, the selective role played by each of these energy components and more especially that of vdW is not explicitly known. Therefore, it is important to document their individual role in known protein-protein structural complexes. It is of interest to relate interface size with vdW, H-bonds and electrostatic interactions at the interfaces of protein structural complexes with known function using statistical and multiple linear regression analysis methods to identify the prominent force. We used the manually curated non-redundant dataset of 278 hetero-dimeric protein structural complexes grouped using known functions by Sowmya et al. (2015) to gain additional insight to this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck (Anshul and Sowdhamini, 2015). This dataset consists of obligatory (enzymes, regulator, biological assembly), immune and nonobligatory (enzyme and regulator inhibitors) complexes. Results show that the total binding energy is more for large interfaces. However, this is not true for its individual energy factors. Analysis shows that vdW energies contribute to about 75% ± 11% on average among all complexes and it also increases with interface size (r2 ranging from 0.67 to 0.89 with p<0.01) at 95% confidence limit irrespective of molecular function. Thus, vdW is both dominant and proportional at the interface independent of molecular function. Nevertheless, H bond energy contributes to 15% ± 6.5% on average in these complexes. It also moderately increases with interface size (r2 ranging from 0.43 to 0.61 with p<0.01) only among obligatory and immune complexes. Moreover, there is about 11.3% ± 8.7% contribution by electrostatic energy. It increases with interface size specifically among non-obligatory regulator-inhibitors (r2 = 0.44). It is implied that both H-bonds and electrostatics are neither dominant nor proportional at the interface. Nonetheless, their presence cannot be ignored in binding. Therefore, H-bonds and (or) electrostatic energy having specific role for improved stability in complexes is implied. Thus, vdW is common at the interface stabilized further with selective H-bonds and (or) electrostatic interactions at an atomic level in almost all complexes. Comparison of this observation with residue level analysis of the interface is compelling. The role by H-bonds (14.83% ± 6.5% and r2 = 0.61 with p<0.01) among obligatory and electrostatic energy (8.8% ± 4.77% and r2 = 0.63 with p <0.01) among non-obligatory complexes within interfaces (class A) having more non-polar residues than surface is influencing our inference. However, interfaces (class B) having less non-polar residues than surface show 1.5 fold more electrostatic energy on average. The interpretation of the interface using inter-atomic (vdW, H-bonds, electrostatic) interactions combined with inter-residue predominance (class A and class B) in relation to known function is the key to reveal its molecular principles with new challenges.

Keywords: PPI; electrostatics; energy; hydrogen bonds (H-bonds); interface; molecular function; van der Waals (vdW).

Figure 1

Grouping of a non-redundant dataset of 278 heterodimer protein complexes into functional groups as described elsewhere [23]. These include obligatory (208), immune (18) and non-obligatory (52). The obligatory protein complexes are further classified into enzyme (40), regulator (144) and biological assembly (24) and the non-obligatory protein complexes into enzyme inhibitor (25) and regulator inhibitor (27).

Figure 2

Protein-protein complexes among different categories are shown using Discovery studio™ [28] with backbone structures displayed in Ca stick style and interface regions depicted using CPK (Corey Pauling Koltun) representation. The interface residues of chain A and B are colorized in green and red, respectively. (A) An enzyme complex (PDB ID 2O2V) between MAP2K5-PHOX / MAP3K3B-PHOX, (B) A regulator complex (PDB ID 3OUN) between FhaA FHA protein/Rv3910, (C) A protein assembly complex (PDB ID 4F48) formed between FimXEAL / type II PilZ, (D) An enzyme-inhibitor complex (PDB ID 4DRI) between Peptidyl-prolyl cistrans isomerase FKBP5 / Serine-Threonine-protein kinase MTOR, (E) A regulator inhibitor complex (PDB ID 4GVB) between KP6α/ KP6β and (F) An immune complex (PDB ID 2P45) between Ribonuclease RNASE A / Ab CAB-RN05. The interface residues were identified using change in Accessible Surface Area (ASA) [29] upon complex formation as described elsewhere [8, 13].

Figure 3

Correlation between interface size and energy (total, van der Waals, hydrogen bond and electrostatic) is shown. The correlation of determination r2 was calculated for energy and interface size among obligatory (compulsory), non-obligatory and immune complexes.

Figure 4

Correlation between interface size and energy (total, van der Waals, hydrogen bond and electrostatic) is shown. The correlation of determination r2 was calculated for energy and interface size among enzymes, regulators and biological assemblies.

Figure 5

Correlation between interface size and energy (total, van der Waals, hydrogen bond and electrostatic) is shown. The correlation of determination r2 was calculated for energy and interface size among enzyme inhibitors and regulator inhibitors.

Figure 6

Grouping of 278 hetero-dimer non-redundant dataset protein complexes into class A (interface non-polar residues is more than surface) and class B (interface non-polar residues less than surface and core) [21, 22]. Class A (165) protein complexes are further grouped into functional groups such as obligatory (132), immune (4) and non-obligatory (29). The obligatory protein complexes are further classified into enzyme (29), regulator (88) and biological assembly (15) and the non-obligatory protein complexes into enzyme inhibitor (15) and regulator inhibitor (14). Simultaneously class B (113) is grouped into obligatory (76), immune (14) and non-obligatory (23). The obligatory protein complexes are further classified into enzyme (11), regulator (56) and biological assembly (9) and the nonobligatory protein complexes into enzyme inhibitor (10) and regulator inhibitor (13).

Figure 7

Correlation between interface size and energy (total, van der Waals, hydrogen bond and electrostatic) is shown. The correlation of determination r2 was calculated for energy and interface size among class A (interface non-polar residues is more than surface) and class B (interface non-polar residues less than surface) [21].