On the molecular discrimination between adenine and guanine by proteins

Abstract

The molecular recognition and discrimination of adenine and guanine ligand moieties in complexes with proteins have been studied using empirical observations on carefully selected crystal structures. The distribution of protein folds that bind these purines has been found to differ significantly from that across the whole PDB, but the most populated architectures and folds are also the most common in three genomes from the three different domains of life. The protein environments around the two nucleic acid bases were significantly different, in terms of the propensities of amino acid residues to be in the binding site, as well as their propensities to form hydrogen bonds to the bases. Plots of the distribution of protein atoms around the two purines clearly show different clustering of hydrogen bond donors and acceptors opposite complimentary acceptors and donors in the rings, with hydrophobic areas below and above the rings. However, the clustering pattern is fuzzy, reflecting the variety of ways that proteins have evolved to recognise the same molecular moiety. Furthermore, an analysis of the conservation of residues in the protein chains binding guanine shows that residues in contact with the base are in general better conserved than the rest of the chain.

Figure 1

Schematic diagrams of adenine (A) and guanine (B). Hydrogens connected to carbon atoms have been omitted for clarity. The arrows show the positions of hydrogen bond donors and acceptors. The direction of the arrow indicates a donor (away from the ring atom) or an acceptor (towards the ring atom).

Figure 2

The distribution of functions across the adenine (A) and guanine (B) datasets. In this plot the first class of the enzyme classification (first E.C. number) has been used to categorise the proteins to the six known enzyme classes (oxidoreductases, E.C.1; transferases, E.C.2; hydrolases, E.C.3; lyases, E.C.4; isomerases, E.C.5; ligases, E.C.6). The ‘no E.C.’ category represents protein chains that are known to have enzymatic activity but there is no E.C. number assigned to them in SWISS-PROT. The ‘non-enzymes’ category represents proteins that either do not have any enzymatic activity, or they have some activity but their main biological role is not enzymatic.

Figure 2

The distribution of functions across the adenine (A) and guanine (B) datasets. In this plot the first class of the enzyme classification (first E.C. number) has been used to categorise the proteins to the six known enzyme classes (oxidoreductases, E.C.1; transferases, E.C.2; hydrolases, E.C.3; lyases, E.C.4; isomerases, E.C.5; ligases, E.C.6). The ‘no E.C.’ category represents protein chains that are known to have enzymatic activity but there is no E.C. number assigned to them in SWISS-PROT. The ‘non-enzymes’ category represents proteins that either do not have any enzymatic activity, or they have some activity but their main biological role is not enzymatic.

Figure 3

Percentage burial of adenine (A) and guanine (B) moieties in their corresponding complexes. The line drawn through the individual data points is of no significance and is only added for clarity.

Figure 3

Percentage burial of adenine (A) and guanine (B) moieties in their corresponding complexes. The line drawn through the individual data points is of no significance and is only added for clarity.

Figure 4

Classification of neighbours and hydrogen-bond partners of adenine and guanine moieties into protein atoms (main-chain and side-chain) and small molecule atoms (water or other hetero-group). (A) Adenine neighbours, (B) guanine neighbours, (C) adenine hydrogen-bond partners, (D) guanine hydrogen-bond partners.

Figure 4

Classification of neighbours and hydrogen-bond partners of adenine and guanine moieties into protein atoms (main-chain and side-chain) and small molecule atoms (water or other hetero-group). (A) Adenine neighbours, (B) guanine neighbours, (C) adenine hydrogen-bond partners, (D) guanine hydrogen-bond partners.

Figure 4

Classification of neighbours and hydrogen-bond partners of adenine and guanine moieties into protein atoms (main-chain and side-chain) and small molecule atoms (water or other hetero-group). (A) Adenine neighbours, (B) guanine neighbours, (C) adenine hydrogen-bond partners, (D) guanine hydrogen-bond partners.

Figure 4

Classification of neighbours and hydrogen-bond partners of adenine and guanine moieties into protein atoms (main-chain and side-chain) and small molecule atoms (water or other hetero-group). (A) Adenine neighbours, (B) guanine neighbours, (C) adenine hydrogen-bond partners, (D) guanine hydrogen-bond partners.

Figure 5

Calculated Π values for the 20 most common amino acids, representing the propensity of an amino acid to be within a 4.0 Å cut-off from an adenine or guanine atom in the complexes studied. The y-error bars have lengths of four standard deviations, calculated for each amino acid from the entire population of Π values, obtained using a jack-knife method on the dataset of complexes.

Figure 6

Amino acid propensity-based scores for the guanine binding sites in 28 protein–guanine complexes. White columns, calculated from all guanine-binding complexes except the one being scored; grey columns, the mean of 97 scores for each complex, each calculated from the adenine dataset propensities using a jack-knife method. The y-error bars are four standard deviations long.

Figure 7

The distribution in space of protein atoms around guanine and adenine ligand fragments. Only the shortest contact from each residue is shown. Each atom is categorised as hydrogen bond donor (blue), hydrogen bond acceptor (green) or simple contact (no hydrogen bond involved, grey). (A) View along the plane of the guanine ring, (B) view from the top of the guanine ring, (C) view along the plane of the adenine ring, (D) view from the top of the adenine ring. In plots (B) and (D) the carbon atoms have been removed for clarity.

Figure 7

The distribution in space of protein atoms around guanine and adenine ligand fragments. Only the shortest contact from each residue is shown. Each atom is categorised as hydrogen bond donor (blue), hydrogen bond acceptor (green) or simple contact (no hydrogen bond involved, grey). (A) View along the plane of the guanine ring, (B) view from the top of the guanine ring, (C) view along the plane of the adenine ring, (D) view from the top of the adenine ring. In plots (B) and (D) the carbon atoms have been removed for clarity.

Figure 7

The distribution in space of protein atoms around guanine and adenine ligand fragments. Only the shortest contact from each residue is shown. Each atom is categorised as hydrogen bond donor (blue), hydrogen bond acceptor (green) or simple contact (no hydrogen bond involved, grey). (A) View along the plane of the guanine ring, (B) view from the top of the guanine ring, (C) view along the plane of the adenine ring, (D) view from the top of the adenine ring. In plots (B) and (D) the carbon atoms have been removed for clarity.

Figure 7

The distribution in space of protein atoms around guanine and adenine ligand fragments. Only the shortest contact from each residue is shown. Each atom is categorised as hydrogen bond donor (blue), hydrogen bond acceptor (green) or simple contact (no hydrogen bond involved, grey). (A) View along the plane of the guanine ring, (B) view from the top of the guanine ring, (C) view along the plane of the adenine ring, (D) view from the top of the adenine ring. In plots (B) and (D) the carbon atoms have been removed for clarity.

Figure 8

Calculated Π values for the 20 most common amino acids, representing the propensity of an amino acid to form hydrogen bonds to an adenine (grey) or guanine (white) atom in the complexes studied.

Figure 9

Ratio of observed number of hydrogen bonds over the theoretically possible maximum for four adenine (grey) and five guanine (white) atoms, as well as for the sum of all hydrogen bonds in the complexes studied.

Figure 10

Difference in BLEEP scores calculated for the original complex and for the hypothetically constructed complex where one purine replaces the other. (A) 97 complexes where guanine was substituted for adenine, (B) 28 complexes where adenine was substituted for guanine.

Figure 10

Difference in BLEEP scores calculated for the original complex and for the hypothetically constructed complex where one purine replaces the other. (A) 97 complexes where guanine was substituted for adenine, (B) 28 complexes where adenine was substituted for guanine.

Figure 11

Plot of conservation difference scores, ΔC, for 26 protein-chains in contact with guanine, where ΔC is defined as: ΔC = C_gua – C_chain. C_gua is the average conservation score for residues in contact with guanine atoms and C_chain is the average conservation score for the whole chain. Black, difference scores calculated using the average score from residues in contact with O6, N1 or N2 only; white, difference scores calculated using the average score from residues in contact with all other atoms.