Authors

<html> Evolu-sec package forms part of a research project, reported in “Evolutionary model of protein secondary structure capable of revealing new biological relationships”.<o:p></o:p><a href="https://doi.org/10.1002/prot.25898">http://dx.doi.org/10.1101/563452</a> Evolu-sec package contains phylogenetic analysis tools based on an evolutionary model of secondary structure [centre, Table 1]. The analysis focuses on phylogenetic tree inference [left], evolutionary distance estimation [top], and ancestral secondary structure reconstruction. [bottom and right]. </html>

The research project abstract is provided in the next section. The dataset (140.9MB) for the model development and the software can be accessed in the “Supplementary Data” section.

Evolutionary model of protein secondary structure capable of revealing new biological relationships
Jhih-Siang Lai, Burkhard Rost , Bostjan Kobe and Mikael Bodén
School of Chemistry and Molecular Biosciences, The University of Queensland
Contact: Jhih-Siang Lai

Abstract
<html> <a name="_GoBack"></a>Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, attempts to reconstruct ancient proteins and phylogenetic analyses of remote homologues must handle extreme amino-acid sequence diversity resulting from extended periods of evolutionary change [2]. We exploited the wealth of protein structures in the Protein Data Bank (PDB) to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesised in their immediate ancestors [1]. Based on this new evolutionary model, we implemented maximum likelihood-based phylogenetic inference tools to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of structure comparative modelling and sequence-based prediction methods; the reconstruction extracts information not available from modern structures or the ancestral protein sequences alone [3,4,5]. Based on a phylogenetic analysis of a sequence-diverse protein family, we showed that the model has the capacity to highlight relationships that are evolutionarily rooted in structure and not evident in sequence-based phylogenetic analysis. </html>

Supplementary data for "Evolutionary model of protein secondary structure capable of revealing new biological relationships" can be downloaded from
Dataset (140.3 MB) or Software (617 KB), separately.

Package may be downloaded as a single archive from
Full package download (140.9 MB).

(Ancestral secondary structure reconstruction) ASSR needs version MATLAB 8.2 (R2013b) or later.
Please send feedback and questions to author.

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<![if !supportLists]>1.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Dayhoff M, Schwartz R and Orcutt B (1978), "A Model of Evolutionary Change in Proteins", In Atlas of protein sequence and structure. Vol. 5, pp. 345-352. National Biomedical Research Foundation Silver Spring, MD.<o:p></o:p>

<![if !supportLists]>2.     <![endif]>Ve<span lang=EN-US style='font-size: 10.0pt;font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'> T, Williams SJ and Kobe B (2015), "Structure and function of Toll/interleukin-1 receptor/resistance protein (TIR) domains", Apoptosis. Vol. 20(2), pp. 250-261.<o:p></o:p>

<![if !supportLists]>3.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Clifton BE and Jackson CJ (2016), "Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins", Cell Chem Biol. Vol. 23(2), pp. 236-245.<o:p></o:p>

<![if !supportLists]>4.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ and Ortlund EA (2016), "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space", Proc Natl Acad Sci U S A. Vol. 113(2), pp. 326-331.<o:p></o:p>

<![if !supportLists]>5.     <![endif]><span lang=EN-US style='font-size:10.0pt; font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language: EN-US'>Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL and Kern D (2015), "Using ancient protein kinases to unravel a modern cancer drug's mechanism", Science. Vol. 347(6224), pp. 882-886.<o:p></o:p>

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The Evolu-sec was applied for analysing the structural divergence of Toll/interleukin-1 receptor domains further including plant RUN1 TIR domain and human SARM1 TIR domain, published in <html> <head> <meta http-equiv=Content-Type content="text/html; charset=utf-8"> <style> <!– @font-face

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<a name="_GoBack"></a>"NAD⁺ cleavage activity by animal and plant TIR domains in cell death pathways, Science, 365, 6455, 2019."

<a href="http://www.doi.org/10.1126/science.aax1911">http://www.doi.org/10.1126/science.aax1911</a>

</div> </body> </html> This wiki page provides images of better resolution, which have been included in the supplementary dataset of "NAD+ cleavage activity by animal and plant TIR domains in cell death pathways".

Figure 1. Unrooted phylogenetic tree of proteins containing TIR domains and structurally related domains. The phylogenetic tree includes 114 proteins from the intersection of DALI searches on human SARM1 TIR and plant RUN1 TIR. Only non-redundant proteins with structures at 4Å resolution or better and superpositions covering 125 residues or more in length were used. Numbers on branches are standard bootstrap values by resampling 100 times. Sub-trees are coloured to indicate kingdom and broad function and annotated with Gene Ontology terms that are statistically enriched for the group of proteins at the leaves. Each leaf specifies PDB and UniProt identifiers, protein and gene names; in addition, the absolute number of mutated amino acids and the ratio of missing residues in the structure relative to the protein sequence are provided.

Figure 2. The alternative tree visualisation of Figure 1. Tips in red, brown, green, blue, purple are mammalian TIR domains, bacterial TIR domains, plant TIR domains, enzymes, and response regulatory domains, respectively. The star and the circle highlight the plant RUN1 TIR and human SARM1 TIR structures, respectively.