Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family

Abstract

The PAAD/DAPIN/pyrin domain is the fourth member of the death domain superfamily, but unlike other members of this family, it is involved not only in apoptosis but also in innate immunity and several other processes. We have identified 40 PAAD domain-containing proteins by extensively searching the genomes of higher eukaryotes and viruses. Phylogenetic analyses suggest that there are five categories of PAAD domains that correlate with the domain architecture of the entire proteins. Homology models built on CARD and DD structures identified functionally important residues by studying conservation patterns on the surface of the models. Surface maps of each subfamily show different distributions of these residues, suggesting that domains from different subfamilies do not interact with each other, forming independent regulatory networks. Helix3 of PAAD is predicted to be critical for dimerization. Multiple alignment analysis and modeling suggest that it may be partly disordered, following a new paradigm for interaction proteins that are stabilized by protein-protein interactions.

Figure 1.

Multiple alignment of 40 PAAD sequences. Yellow background indicates similarities between AIM and PYR/PAN group (as well as specific residues for AIM). Pink background shows differences/similarities between IFI and AIM groups. Red background shows similarities/differences between PAN5/PAN3 and PYR group, and cyan background shows similarities of PYR/AF427627 with the PYR members. Accession numbers for (1) PYR group: MEFV human gi|8928170, MEFV mouse gi|9506893, MEFV rat gi|13928876, ASC human gi|11096299, ASC pending mouse gi|12963605, ASC1 zebrafish 18858287, caspase zebrafish gi|7673640, PYC1 human gi|25024272, cryopyrin/AF427617 gi|17026378. For Fugu sequences, Genscan assembling was performed (http://genes.mit.edu/GENSCAN.html), then gi|CAAB01003190 fugu (Genscan predicted peptide 1 of 132 aa) and gi|CAAB01007457 (Genscan predicted peptide 2 of 195 aa). (2) PAN group: PAN1 human gi|8923473, PAN2 human gi|19031214, PAN3 human gi|19387136, PAN4 human gi|17483019, PAN5 human gi|17472937, PAN6 human gi|21711821, PAN7 human gi|18448933, PAN8 human gi|17461450, PAN10 human gi|21450725, PAN11 human gi|19882273. (3) AIM group: AIM2 human gi|4757734, AIM2 mouse gi|20830743, AIM2 rat gi|27678602. (4) IFI group: IFI203 mouse gi|6680355, IFI204 mouse gi|6680357, IFI205 mouse gi|20831393, MNDA human gi|730038, IFI16 human gi|5031779, IFI16 mouse gi|20830748, LOC226690 mouse gi|20830168, similar to IFI16 mouse gi|20920143, similar to IFI16 mouse gi|20830753. (5) Viral group: 18L Yaba-like gi|12085001, SPV014 Swinepox gi|18640100, GP013L rabbit fibroma virus gi|9633972, M)13L Myxoma gi|9633972. 1E41 (the top sequence) is the template selected for homology modeling. Pairwise alignments used for modeling can be obtained from the multiple alignment by reading appropriate lines: one for the target, one for the template.

Figure 2.

Unrooted tree for PAAD sequences. This is a consensus tree after screening 9701 trees. Numbers are clade confidence values; only values higher than 80% are shown.

Figure 3.

The homology model of PAAD domain. The model of MEFV_Mouse was chosen as the representation. (A) The ribbon diagram of MEFV_Mouse. (B) The conserved hydrophobic core of MEFV_Mouse. The conserved hydrophobic residues are shown in ball and stick. (A) and (B) are in the same orientation. (C) The ribbon diagram of template. For comparison, the residues that were aligned to the residues highlighted in (B) are shown.

Figure 4.

Multiple sequence alignments of the PAAD family. Black background denotes conserved external residues, gray background denotes functional important residues. The "Sec_str" line shows the secondary structure of the reference sequences in each subfamily, namely MEFV_Mouse, PAN2_Human, AIM2_Human, IFI204_Mouse and 18L_Yaba-Like_Disease. The secondary structure was identified from the homology model. The Accession numbers for sequences are the same as Figure 1 ▶.

Figure 5.

Surface representation of PAAD family. (A1, A2) The electrostatic potential of the model of the MEFV_Mouse PAAD domain, with a color scale that varies from blue to red, representing positive and negative potential, respectively. The conserved external hydrophobic residues are colored in cyan. The same color scheme is used in all subsequent figures. (A1) and (A2) are related by a 180° rotation around the indicated axis. (B) Surface representation of the model of the PAN2_Homo PAAD domain. (C1, C2) The electrostatic potential of the model of the IFI204_Mouse PAAD domain. Two views are related by a 90° rotation around the indicated axis. (D1, D2) The electrostatic potential of the model of the AIM2_Human PAAD domain. Two views are related by a 180° rotation around the indicated axis. (E1, E2) The electrostatic potential of the model of the 18L_Yaba-like_disease PAAD domain. Two views are related by a 180° rotation around the indicated axis.