< 7^th term

Hydrophobic clusters

Last update on the 12^th of December, 2019

Here we study hydrophobic clusters in mercuric reductase (1ZK7) and dihydrolipoamide dehydrogenase (1EBD) with CluD web-server.

1ZK7 domain structure

1ZK7 consists of three putative hydrophobic cores clothed with secondary structure elements (fig. 1).

According to CATH 3 distinct domains comprise 1ZK7 which are relevant to the observable structures (fig. 2). The first domain, 1ZK7A01, is disrupted by the second domain, 1ZK7A02, in sequence. That's acceptable as CATH operates with structures, not sequences.

Fig. 2. 1ZK7 CATH domain partition. Blue: 1ZK7A01, red: 1ZK7A02, yellow: 1ZK7A03.

InterPro domain partitioning is different. (fig. 3). FAD/NAD(P) binding domain (residues 5–323, IPR023753) is split by Pyridine nucleotide-disulphide oxidoreductase active site (residues 38–48, IPR012999) thus comprising two hydrophobic cores (binding Hg²⁺, active site should remain hydrophylic). Pyridine nucleotide-disulphide oxidoreductase dimerisation domain (residues 342–450, IPR004099) gives the third hydrophobic core.

1ZK7 InterPro domains — Fig. 3. 1ZK7 InterPro domain partition. Red: IPR023753, yellow: IPR012999, blue: IPR004099, green: no InterPro domain assigned.

Therefore both InterPro and CAth domain partitioning support visual domain partitioning.

1ZK7 inner hydrophobic clusters.

Inner hydrophobic clusters of 1ZK7 were inferred with CluD. Minimal size of cluster was set to 15 in order to avoid spurious hydrophobic clusters of single residues. The optimal distance range was set from 4.4Å to 4.7Å with step 0.1Å (fig. 4).

1ZK7 hydrophobic clusters. — Fig. 4. Hydrophobic clusters in 1ZK7 at different distances.

The happy medium distance is 4.6Å: corresponding clusters reflect observable domain partitioning and one of the clusters (red in fig. 4) forming between two α-helices is not observed as a distinct structure at other distance values.

Overall, secondary structure elements coat hydrophobic cores. The active center with NAD molecule remains hydrophylic at all observed distances.

1EBD as 1ZK7 substitute for interface study.

1ZK7 is a homodimer with two identical chains (A) written as two distinct models in PDB file. Therefore CluD is unable to find any hydrophobic interactions at chain interface. To overcome the problem, a search of similar proteins was conducted with PDBeFold. The best non-mercuric reductase is 1EBD (RMSD 1.39Å, Q-score 0.74, 437/467 query residues and 437/455 target residues are aligned with more than 90% SSE aligned). 1EBD structure is almost identical to 1ZK7 structure (fig. 5).

1ZK7 and 1EBD. — Fig. 5. 1ZK7 superimposed to 1EBD with PyMol `super`.

The clusters at interface between A and B chains were inferred at the distance of 5.4Å. Multiple hydrophobic clusters of small size were found thus supporting the idea of hydrophobic nature of dimerization (fig. 6).

1EBD interface clusters. — Fig. 6. 1EBD clusters at interface between A and B chains.

However, hydrogen bonds were found to support dimerazation. Taken all together, both types of interactions stabilize homodimer.