Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function

Abstract

Many protein pairs that share the same fold do not have any detectable sequence similarity, providing a valuable source of information for studying sequence-structure relationship. In this study, we use a stringent data set of structurally similar, sequence-dissimilar protein pairs to characterize residues that may play a role in the determination of protein structure and/or function. For each protein in the database, we identify amino-acid positions that show residue conservation within both close and distant family members. These positions are termed "persistently conserved". We then proceed to determine the "mutually" persistently conserved (MPC) positions: those structurally aligned positions in a protein pair that are persistently conserved in both pair mates. Because of their intra- and interfamily conservation, these positions are good candidates for determining protein fold and function. We find that 45% of the persistently conserved positions are mutually conserved. A significant fraction of them are located in critical positions for secondary structure determination, they are mostly buried, and many of them form spatial clusters within their protein structures. A substitution matrix based on the subset of MPC positions shows two distinct characteristics: (i) it is different from other available matrices, even those that are derived from structural alignments; (ii) its relative entropy is high, emphasizing the special residue restrictions imposed on these positions. Such a substitution matrix should be valuable for protein design experiments.

Fig. 1.

A schematic flowchart describing the identification of mutually persistently conserved positions. See text for details.

Fig. 2.

Distribution of residue types in mutually persistently conserved (MPC) positions expressed as the log-odds ratio between the frequency of a residue in MPC positions (obs) and its frequency in the entire database of SSSD proteins (exp). All frequency differences were found to be statistically significant by a κ² test, except for Leucine, Asparagine, and Valine (marked with ‘∧’).

Fig. 3.

Amino-acid residue substitution matrices derived from (a) mutually persistently conserved positions and (b) all structurally aligned positions. Values are scaled to 1/10 bit.

Fig. 3.

Amino-acid residue substitution matrices derived from (a) mutually persistently conserved positions and (b) all structurally aligned positions. Values are scaled to 1/10 bit.

Fig. 4.

Comparison between sequence-derived and structure-derived substitution matrices. The amino-acid pair frequency distributions that were used for the derivation of the substitution matrices were compared by the Jensen-Shannon divergence. A series of BLOSUM matrices were compared with the mutually persistently conserved-derived matrix (filled squares) and with the structurally derived matrix (open circles).

Fig. 5.

Frequency of mutually persistently conserved (MPC) positions in secondary structure elements. The X-axis shows the positions in and flanking the secondary structure element (nomenclature after Aurora and Rose 1998). The flanking regions are marked with apostrophes, the in-element residues with digits, and the initial and terminal (capping) residues with a "c." The Y-axis is the logarithm of the ratio between the actual frequency of MPC residues in a position and that expected at random, based on the overall frequency of MPC positions in the data. The positions in which MPCs were found to be significantly over- or under-represented are marked with an "*." (a) α helices; (b) β strands.

Fig. 6.

Distribution of mutually persistently conserved positions (white bars) by solvent accessibility compared to all aligned residues (black bars). Residues were defined as buried when the solvent accessibility was <30% and exposed otherwise.