Template-based recognition of protein fold within the midnight and twilight zones of protein sequence similarity

Abstract

Most homologous pairs of proteins have no significant sequence similarity to each other and are not identified by direct sequence comparison or profile-based strategies. However, multiple sequence alignments of low similarity homologues typically reveal a limited number of positions that are well conserved despite diversity of function. It may be inferred that conservation at most of these positions is the result of the importance of the contribution of these amino acids to the folding and stability of the protein. As such, these amino acids and their relative positions may define a structural signature. We demonstrate that extraction of this fold template provides the basis for the sequence database to be searched for patterns consistent with the fold, enabling identification of homologs that are not recognized by global sequence analysis. The fold template method was developed to address the need for a tool that could comprehensively search the midnight and twilight zones of protein sequence similarity without reliance on global statistical significance. Manual implementations of the fold template method were performed on three folds--immunoglobulin, c-lectin and TIM barrel. Following proof of concept of the template method, an automated version of the approach was developed. This automated fold template method was used to develop fold templates for 10 of the more populated folds in the SCOP database. The fold template method developed three-dimensional structural motifs or signatures that were able to return a diverse collection of proteins, while maintaining a low false positive rate. Although the results of the manual fold template method were more comprehensive than the automated fold template method, the diversity of the results from the automated fold template method surpassed those of current methods that rely on statistical significance to infer evolutionary relationships among divergent proteins.

Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn‐superoxide dismutase

“…Finally, as previously reported (Pirun et al, 2005), the cupredoxin, azurin, was found to conform to a 'fold template' derived from a Psi-BLAST search based on the variable domain of human mu heavy chain (gij15777469). In fact, the match identified in Pirun et al (2005) was serendipitous resulting from a study in which an additional Cys residue was introduced into the azurin structure (van Amsterdam et al, 2002).…”

“…In fact, the match identified in Pirun et al (2005) was serendipitous resulting from a study in which an additional Cys residue was introduced into the azurin structure (van Amsterdam et al, 2002). When the regular expression was modified by replacing the requirement for the initial Cys by Asn, numerous azurin and other cupredoxin structures were obtained from the PDB database, with an apparent false positive rate on the order of 10% although the template had not been optimized for cupredoxin recognition.…”

“…Psi-BLAST (Altschul et al, 1997;Altschul and Koonin, 1998) and the related Hidden Markov Model approach (Baldi et al, 1994;Bateman et al, 1996Bateman et al, , 1997Karplus et al, 1998;Teichmann and Chothia, 2000;Edgar and Sjolander, 2004;Vilim et al, 2004) generate an amino acid usage profile to develop a representation of a search sequence that allows identification of at least some probable homologs in the 'midnight zone' (Friedberg et al, 2000;Pirun et al, 2005) of sequence comparison; that is, no statistically significant sequence identity. The term 'twilight zone' , introduced earlier by Doolittle (1986), describes sequence pairs with 20-35% sequence identity for which predictions of structure and/or function are chancy (Rost, 1999;Jaroszewski et al, 2002) although homology of such pairs can often be asserted with reasonable confidence.…”

“…However, distantly related homologs are not directly identifiable by statistical criteria and can exhibit different degrees of conformational variation, as reviewed by Grishin (2001). Perhaps examination of the sequences of putative distant homologs by the use of fold templates (Pirun et al, 2005) may reveal possible conformational changes. Nevertheless, the lack of conventional evidence of homology is not itself evidence of analogy.…”

Graph coloring: a novel heuristic based on trailing path—properties, perspective and applications in structured networks

“…In noticeable similarity, the aforementioned physico-chemical constraints in protein folding can accommodate for several alternatively designed (packed) hydrophobic protein cores [57] and hence, different amino-acid sequences. On that note, there are well-characterized 'twilight' [58] and 'midnight' [59] zones of pairs of proteins belonging to the 'low sequence identity -same fold' category. The fact that graphpartitioning based on 'coloribility' is a stable and absorptive property for structured networks (like small-world, scale-free, modular etc.)…”