Correlating structure and function during the evolution of fibrinogen-related domains

Abstract

Fibrinogen-related domains (FReDs) are found in a variety of animal proteins with widely different functions, ranging from non-self recognition to clot formation. All appear to have a common surface where binding of one sort or other occurs. An examination of 19 completed animal genomes--including a sponge and sea anemone, six protostomes, and 11 deuterostomes--has allowed phylogenies to be constructed that show where various types of FReP (proteins containing FReDs) first made their appearance. Comparisons of sequences and structures also reveal particular features that correlate with function, including the influence of neighbor-domains. A particular set of insertions in the carboxyl-terminal subdomain was involved in the transition from structures known to bind sugars to those known to bind amino-terminal peptides. Perhaps not unexpectedly, FReDs with different functions have changed at different rates, with ficolins by far the fastest changing group. Significantly, the greatest amount of change in ficolin FReDs occurs in the third subdomain ("P domain"), the very opposite of the situation in most other vertebrate FReDs. The unbalanced style of change was also observed in FReDs from non-chordates, many of which have been implicated in innate immunity.

Figure 1

Backbone structure of a typical FReD (human H ficolin, PDB 2J5Z) showing three subdomains (A, violet; B, brown; P, blue). The amino-terminal (N) is usually preceded by one of a variety of connecting domains of various sorts. Interactions usually occur on the outer face of the third subdomain (“P domain”). Note how the central strand of the main sheet (green) is provided by a sequence segment that occurs after the third subdomain.

Figure 2

Phylogenetic tree (unrooted) constructed from 23 FReD sequences found in human genome. Designations are those used by the NCBI.

Figure 3

Phylogenetic tree of 23 FReDs from human and 23 from chicken. Those cases in which the chicken does not have an ortholog of the human type (e.g., MFAgp) are denoted with asterisks (*), and in those instances where the inverse is true are marked with arrows (←) (e.g., chicken has two hepassocins).

Figure 4

Different vertebrate FReD types change at different rates. The pairs chosen for time points are: rodent-human (70 mya); human-opossum (110 mya); and human-platypus (130 mya).

Figure 5

The evolution of a transcription factor in the ascidian lineage (shown here as a region from the sea squirt (Ciona intestinalis genome) resulted from the duplication of a ficolin gene downstream from a histone-2A gene. The duplication led to an unusual alternative splice in which a histone exon connects to a FReD in the duplicated gene, omitting the collagen segment (violet). In the NCBI versions, the exons X₁ and X₂ (light green) have the same DNA sequence but are read in different frames, a happenstance that would befuddle further splicing in the correct frame. The problem would be solved if a putative exon (yellow) in the histone region was used to put the reading frames in register.

Figure 6

Chordate FReDs (top) occur in two general classes (I and II) that can be distinguished simply by the number of intervening residues between the two essential disulfide bonds. Non-chordate FReDs (lower) are predominantly Class I, an anomalous cluster found in C. elegans (denoted by W) notwithstanding.

Figure 7

Alignment of key interfacial region (third subdomain) from a series of FReDs. Residues known to be involved in ligand contacts on the basis of X-ray crystallography (sequences marked with have X-ray structures) are shaded red; otherwise conserved residues are green. Note that matches with all the shaded residues from human ficolins and the horseshoe crab tachylectin occur in several sponge and sea anemone FReDs, as well as with FIBCD1 and MFAgp. Tenascin FReDs have suffered a deletion in a region thought to be essential for binding acetylated sugars.

Figure 8

Class I and II FReDs are structurally distinct at their principal interaction sites. The upper panel is a stereo-depiction of the angiopoietin-2/Tie-2 receptor complex (PDB 2GY7) with two other class I FReDs (human ficolin 1, PDB 2J5Z, blue, and horseshoe crab tachylectin, PDB 1JC9, red) structurally aligned on the angiopoietin (green). In the lower panel two class II FReDs (the βC (brown) and γC (magenta) domains from human fibrinogen, PDB 1FZC) structurally aligned with angiopoietin in the same way. Unlike the ficolin and tachylectin, the class II FReDs clearly clash with the appropriately positioned angiopoietin-2/Tie-2 receptor (cyan).