Evolutionary tracing

In the particular case of GPCRs, the application of CMA techniques, including the evolutionary trace method (181-183), has been aimed at the prediction of putative functionally important residues involved in GPCR-G protein interactions (170-175), GPCR-GPCR interactions (151,152,175,184-189), ligand-protein interactions (23,190,191), as well as signal transduction (170,192,193). 

Although the evolutionary trace method applied to GPCRs (175,185) fails to detect any residues responsible for the subtype-specific heterodimerizafion that has recently been demonstrated for opioid (96), somatostatin (106), and chemokine (98) receptors, correlated mutation analysis had already been demonstrated to be able to identify useful details of molecular specificity (184). Thus, the molecular basis of specificity was hypothesized to reside in outward (i.e., lipid) facing residues of TM5 and TM6 that exhibited evolutionarily correlated mutations and differed between receptor subtypes (184) in the case of dimerization. In the case of oligomers, the key interface between different subtypes was suggested to be the 2,3-interface (152) rather than the 5,6-interface. 

Lichtarge, O., Sowa, M. E., and Philippi, A. (2002) Evolutionary traces of functional surfaces along G protein signaling pathway. Methods Enzymol. 344, 536-556. 

Lichtarge, O., Bourne, H. R., and Cohen, F. E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257, 342-358. 

Gkoutos, G. V., Higgs, C., Bywater, R. P Gouldson, P. R., and Reynolds, C. A. (1999) Evidence for dimerization in the p2-adrenergic receptor from the evolutionary trace method. Inti. J. Quantum. Chem. Biophys. Q. 74,371-379. 

Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O (2004) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J. Biol. Chem. 279(9) 8126-8132... 

A method for detecting conserved residues, called evolutionary tracing (ET), was developed by lichtarge et al. [45], Several groups have embarked on developing methods for detecting functional sites based on ET and related methods (see... 

Sequence analysis has become a powerful tool in identifying functional domains in proteins. One such tool is the Evolutionary Trace (ET) method as developed and implemented by Lichtarge et One such study was on the... 

Figure 9. The residues identified by the Evolutionary Trace (ET) method on the external face of the receptor. In each orientation the helix/helices in focus are coloured mid grey while the ET residues in focus are coloured light grey. The remaining residues are dark grey, a) helices 5 and 6, b) helix 4, c) helices 2 and 3 d) helix7.

R. Landgraf, D. Fischer, D. Eisenberg. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 1999, 12, 943-951. 

When structural alignments do not reveal structural similarities that allow annotation transfer, other approaches can be used to obtain information about the function of the target protein. The analysis of the conservation of 3D patterns of functionally relevant residues and evolutionary trace analysis (described in section 2.3.3) are examples of these methodologies. Structural patterns consist of coordinate files in PDB format containing the spatial positions of functionally important residues without considering their positions on the primary or secondary structure. In fact, these patterns can correspond to functional sites present in proteins with completely different folds. The program PINTS (Patterns In Non-homologous Tertiary Structures)... 

Madabushi, S., H. Yao, M. Marsh, D. M. Kristensen, A. Philippi, M. E. Sowa, and O. Lichtarge. 2002. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 316 139-54. 

E Joachimiak, M., and F. E. Cohen. 2002. JEvTrace Refinement and variations of the evolutionary trace in JAVA. Genome Biol 3 research0077. 

Fortunately, in the past 10 years this approach has been developed to yield a number of automatic methods for predicting functional sites. The pioneer Evolutionary Trace method [35] (http //www-cryst.bioc.cam.ac.uk/ jiye/evoltrace/evol-trace.html) maps phylogenetic information onto structures and often reveals accurate information about functional regions. Many similar approaches have since been devised and applied in various contexts [36,37], and several are available over the Internet (e.g., JEvTrace [38], http //www.cmpharm.ucsf.edu/ marcinj/JEvTrace/). See Campbell et al. [39] for a timely review. 

When co-crystal structures are not available, Ortiz et al. have suggested using functional residue prediction methods to identify selectivity residues [35]. The most popular of fhese mefhods are Evolutionary Trace [36] and ConSurf [37], which use phylogenetic trees to predict biologically-relevant residues that are then mapped onto a representative crystal structure. 

E. coli = Escherichia coli ET = evolutionary trace analysis MLE = muconate lactonizing enzyme MR = mandelate racemase ORF = open reading frame PAM = number of accepted point mutations per 100 residues separating two sequences PEP = phosphoenolpyruvate. 

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