Pages 1–4 1mr4 Evolutionary trace report by report maker May 12, 2010 4.3.5 LaTex 4 4.3.6 Muscle 4 4.3.7 Pymol 4 4.4 Note about ET Viewer 4 4.5 Citing this work 4 4.6 About report maker 4 4.7 Attachments 4 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1mr4): Title: Solution structure of nad1 from nicotiana alata Compound: Mol id: 1; molecule: nicotiana alata plant defensin 1 (nad1); chain: a; fragment: residues 1-47; synonym: flower-specific gamma-thionin Organism, scientific name: Nicotiana Tabacum; 1mr4 contains a single unique chain 1mr4A (47 residues long). This is an NMR-determined structure – in this report the first model in the file was used. 2 CHAIN 1MR4A CONTENTS 2.1 Q8GTM0 overview From SwissProt, id Q8GTM0, 100% identical to 1mr4A: 1 Introduction 1 Description: Flower-specific defensin precursor (NaD1). 2 Chain 1mr4A 1 Organism, scientific name: Nicotiana alata (Winged tobacco) (Per- 2.1 Q8GTM0 overview 1 sian tobacco). 2.2 Multiple sequence alignment for 1mr4A 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.3 Residue ranking in 1mr4A 1 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 2.4 Top ranking residues in 1mr4A and their position on eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Nicotiana. the structure 2 Function: Plant defense peptide with antifungal activity against 2.4.1 Clustering of residues at 26% coverage. 2 F.oxysporum and B.cinerea. Retards the growth of the Lepidopteran insect pests H.armigera and H.punctigera. 3 Notes on using trace results 2 Biophysicochemical properties: 3.1 Coverage 2 pH dependence: Stable under extremes of pH; Temperature depen- 3.2 Known substitutions 2 dence: Stable under extremes of temperature; 3.3 Surface 2 Subcellular location: Vacuolar. 3.4 Number of contacts 3 Tissue specificity: Most abundant in the epidermal cell layers of the 3.5 Annotation 3 petals and sepals, within the connective cells of the anthers, and the 3.6 Mutation suggestions 3 cortical cells of the style. Not detected in the tapetum, pollen mother cells, the transmitting tissue, the vascular bundles of the anther and 4 Appendix 3 style or in leaves. Expressed also in ovaries, but barley detectable in 4.1 File formats 3 roots. 4.2 Color schemes used 3 Similarity: Belongs to the plant defensin family. 4.3 Credits 3 About: This Swiss-Prot entry is copyright. It is produced through a 4.3.1 Alistat 3 collaboration between the Swiss Institute of Bioinformatics and the 4.3.2 CE 3 EMBL outstation - the European Bioinformatics Institute. There are 4.3.3 DSSP 4 no restrictions on its use as long as its content is in no way modified 4.3.4 HSSP 4 and this statement is not removed. 1 Lichtarge lab 2006 Fig. 1. Residues 1-47 in 1mr4A colored by their relative importance. (See Appendix, Fig.4, for the coloring scheme.) 2.2 Multiple sequence alignment for 1mr4A For the chain 1mr4A, the alignment 1mr4A.msf (attached) with 75 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1mr4A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 75 Total number of residues: 3467 Smallest: 37 Largest: 47 Average length: 46.2 Alignment length: 47 Fig. 2. Residues in 1mr4A, colored by their relative importance. Clockwise: Average identity: 51% front, back, top and bottom views. Most related pair: 98% Most unrelated pair: 26% Most distant seq: 42% Furthermore, 12% of residues show as conserved in this alignment. The alignment consists of 54% eukaryotic ( 54% plantae) sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1mr4A.descr. 2.3 Residue ranking in 1mr4A The 1mr4A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1mr4A can be found in the file called 1mr4A.ranks sorted in the attachment. 2.4 Top ranking residues in 1mr4A and their position on the structure In the following we consider residues ranking among top 26% of resi- dues in the protein (the closest this analysis allows us to get to 25%). Figure 2 shows residues in 1mr4A colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 3. Residues in 1mr4A, colored according to the cluster they belong to: 2.4.1 Clustering of residues at 26% coverage. Fig. 3 shows the red, followed by blue and yellow are the largest clusters (see Appendix for top 26% of all residues, this time colored according to clusters they the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Table 1. Table 1. continued cluster size member cluster size member color residues color residues red 11 3,7,14,20,24,27,29,32,34,41 43 continued in next column Table 1. Clusters of top ranking residues in 1mr4A. 2 3 NOTES ON USING TRACE RESULTS 3.6 Mutation suggestions 3.1 Coverage Mutation suggestions are completely heuristic and based on comple- Trace results are commonly expressed in terms of coverage: the resi- mentarity with the substitutions found in the alignment. Note that due is important if its “coverage” is small - that is if it belongs to they are meant to be disruptive to the interaction of the protein some small top percentage of residues [100% is all of the residues with its ligand. The attempt is made to complement the following in a chain], according to trace. The ET results are presented in the properties: small [AV GSTC], medium [LPNQDEMIK], large form of a table, usually limited to top 25% percent of residues (or [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- to some nearby percentage), sorted by the strength of the presumed tively [KHR], or negatively [DE] charged, aromatic [WFYH], evolutionary pressure. (I.e., the smaller the coverage, the stronger the long aliphatic chain [EKRQM], OH-group possession [SDETY ], pressure on the residue.) Starting from the top of that list, mutating a and NH2 group possession [NQRK]. The suggestions are listed couple of residues should affect the protein somehow, with the exact according to how different they appear to be from the original amino effects to be determined experimentally. acid, and they are grouped in round brackets if they appear equally disruptive. From left to right, each bracketed group of amino acid 3.2 Known substitutions types resembles more strongly the original (i.e. is, presumably, less disruptive) These suggestions are tentative - they might prove disrup- One of the table columns is “substitutions” - other amino acid types tive to the fold rather than to the interaction. Many researcher will seen at the same position in the alignment. These amino acid types choose, however, the straightforward alanine mutations, especially in may be interchangeable at that position in the protein, so if one wants the beginning stages of their investigation. to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has 4 APPENDIX an R at that position, it is advisable to try anything, but RVK. Conver- sely, when looking for substitutions which will not affect the protein, 4.1 File formats one may try replacing, R with K, or (perhaps more surprisingly), with Files with extension “ranks sorted” are the actual trace results. The V. The percentage of times the substitution appears in the alignment fields in the table in this file: is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough • alignment# number of the position in the alignment guide - due to rounding errors these percentages often do not add up • residue# residue number in the PDB file to 100%. • type amino acid type • 3.3 Surface rank rank of the position according to older version of ET • variability To detect candidates for novel functional interfaces, first we look for has two subfields: residues that are solvent accessible (according to DSSP program) by 1. number of different amino acids appearing in in this column 2 at least 10A˚ , which is roughly the area needed for one water mole- of the alignment cule to come in the contact with the residue. Furthermore, we require 2. their type that these residues form a “cluster” of residues which have neighbor • rho ET score - the smaller this value, the lesser variability of within 5A˚ from any of their heavy atoms. this position across the branches of the tree (and, presumably, Note, however, that, if our picture of protein evolution is correct, the greater the importance for the protein) the neighboring residues which are not surface accessible might be • cvg coverage - percentage of the residues on the structure which equally important in maintaining the interaction specificity - they have this rho or smaller should not be automatically dropped from consideration when choo- • sing the set for mutagenesis. (Especially if they form a cluster with gaps percentage of gaps in this column the surface residues.) 4.2 Color schemes used 3.4 Number of contacts The following color scheme is used in figures with residues colored by cluster size: black is a single-residue cluster; clusters composed of Another column worth noting is denoted “noc/bb”; it tells the num- more than one residue colored according to this hierarchy (ordered ber of contacts heavy atoms of the residue in question make across by descending size): red, blue, yellow, green, purple, azure, tur- the interface, as well as how many of them are realized through the quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, backbone atoms (if all or most contacts are through the backbone, bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, mutation presumably won’t have strong impact).