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2K7g Lichtarge Lab 2006 Pages 1–4 2k7g Evolutionary trace report by report maker May 15, 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 2k7g): Title: Solution structure of varv f Compound: Mol id: 1; molecule: varv peptide f; chain: a Organism, scientific name: Viola Arvensis; 2k7g contains a single unique chain 2k7gA (29 residues long). This is an NMR-determined structure – in this report the first model in the file was used. 2 CHAIN 2K7GA 2.1 P58451 overview From SwissProt, id P58451, 100% identical to 2k7gA: CONTENTS Description: Varv peptide F. Organism, scientific name: Viola arvensis (European field pansy) 1 Introduction 1 (Field violet). 2 Chain 2k7gA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.1 P58451 overview 1 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 2.2 Multiple sequence alignment for 2k7gA 1 eudicotyledons; rosids; eurosids I; Malpighiales; Violaceae; Viola. 2.3 Residue ranking in 2k7gA 1 Function: Probably participates in a plant defense mechanism. 2.4 Top ranking residues in 2k7gA and their position on Has cytotoxic activity against a variety of drug-resistant and drug- the structure 2 sensitive human tumor cell lines. Ptm: This is a cyclic peptide. 2.4.1 Clustering of residues at 28% coverage. 2 Mass spectrometry: MW=2856; MW ERR=3; METHOD=MALDI; 3 Notes on using trace results 2 RANGE=1-29; NOTE=Ref.1. 3.1 Coverage 2 Similarity: Belongs to the cyclotide family. Moebius subfamily. 3.2 Known substitutions 2 Caution: This peptide is cyclic, its sequence was chosen to start at 3.3 Surface 2 the position shown below by similarity to Oak1 (kalata B1) whose 3.4 Number of contacts 3 DNA sequence is known. 3.5 Annotation 3 About: This Swiss-Prot entry is copyright. It is produced through a 3.6 Mutation suggestions 3 collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are 4 Appendix 3 no restrictions on its use as long as its content is in no way modified 4.1 File formats 3 and this statement is not removed. 4.2 Color schemes used 3 4.3 Credits 3 2.2 Multiple sequence alignment for 2k7gA 4.3.1 Alistat 3 For the chain 2k7gA, the alignment 2k7gA.msf (attached) with 40 4.3.2 CE 3 sequences was used. The alignment was downloaded from the HSSP 4.3.3 DSSP 3 database, and fragments shorter than 75% of the query as well as 4.3.4 HSSP 4 duplicate sequences were removed. It can be found in the attachment 1 Lichtarge lab 2006 Fig. 1. Residues 1-29 in 2k7gA colored by their relative importance. (See Appendix, Fig.4, for the coloring scheme.) to this report, under the name of 2k7gA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 40 Total number of residues: 1131 Smallest: 22 Largest: 29 Average length: 28.3 Alignment length: 29 Average identity: 70% Most related pair: 97% Most unrelated pair: 40% Most distant seq: 60% Fig. 2. Residues in 2k7gA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, 27% of residues show as conserved in this alignment. The alignment consists of 27% eukaryotic ( 27% 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 2k7gA.descr. 2.3 Residue ranking in 2k7gA The 2k7gA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2k7gA can be found in the file called 2k7gA.ranks sorted in the attachment. 2.4 Top ranking residues in 2k7gA and their position on the structure In the following we consider residues ranking among top 28% of resi- dues in the protein (the closest this analysis allows us to get to 25%). Figure 2 shows residues in 2k7gA 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. 2.4.1 Clustering of residues at 28% coverage. Fig. 3 shows the top 28% of all residues, this time colored according to clusters they Fig. 3. Residues in 2k7gA, colored according to the cluster they belong to: belong to. The clusters in Fig.3 are composed of the residues listed red, followed by blue and yellow are the largest clusters (see Appendix for in Table 1. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 1. cluster size member color residues 3 NOTES ON USING TRACE RESULTS red 8 5,6,7,9,14,19,21,26 3.1 Coverage Table 1. Clusters of top ranking residues in 2k7gA. Trace results are commonly expressed in terms of coverage: the resi- due is important if its “coverage” is small - that is if it belongs to some small top percentage of residues [100% is all of the residues 2 in a chain], according to trace. The ET results are presented in the form of a table, usually limited to top 25% percent of residues (or to some nearby percentage), sorted by the strength of the presumed evolutionary pressure. (I.e., the smaller the coverage, the stronger the pressure on the residue.) Starting from the top of that list, mutating a COVERAGE couple of residues should affect the protein somehow, with the exact effects to be determined experimentally. V 3.2 Known substitutions 100% 50% 30% 5% One of the table columns is “substitutions” - other amino acid types seen at the same position in the alignment. These amino acid types may be interchangeable at that position in the protein, so if one wants to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has V an R at that position, it is advisable to try anything, but RVK. Conver- RELATIVE IMPORTANCE sely, when looking for substitutions which will not affect the protein, one may try replacing, R with K, or (perhaps more surprisingly), with V. The percentage of times the substitution appears in the alignment Fig. 4. Coloring scheme used to color residues by their relative importance. 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 guide - due to rounding errors these percentages often do not add up [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- to 100%. tively [KHR], or negatively [DE] charged, aromatic [WFYH], long aliphatic chain [EKRQM], OH-group possession [SDETY ], 3.3 Surface and NH2 group possession [NQRK]. The suggestions are listed To detect candidates for novel functional interfaces, first we look for according to how different they appear to be from the original amino residues that are solvent accessible (according to DSSP program) by acid, and they are grouped in round brackets if they appear equally 2 at least 10A˚ , which is roughly the area needed for one water mole- disruptive. From left to right, each bracketed group of amino acid cule to come in the contact with the residue. Furthermore, we require types resembles more strongly the original (i.e. is, presumably, less that these residues form a “cluster” of residues which have neighbor disruptive) These suggestions are tentative - they might prove disrup- within 5A˚ from any of their heavy atoms. tive to the fold rather than to the interaction. Many researcher will Note, however, that, if our picture of protein evolution is correct, choose, however, the straightforward alanine mutations, especially in the neighboring residues which are not surface accessible might be the beginning stages of their investigation. equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choo- 4 APPENDIX sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 4.1 File formats Files with extension “ranks sorted” are the actual trace results. The 3.4 Number of contacts fields in the table in this file: Another column worth noting is denoted “noc/bb”; it tells the num- • ber of contacts heavy atoms of the residue in question make across alignment# number of the position in the alignment the interface, as well as how many of them are realized through the • residue# residue number in the PDB file backbone atoms (if all or most contacts are through the backbone, • type amino acid type mutation presumably won’t have strong impact). Two heavy atoms • rank rank of the position according to older version of ET are considered to be “in contact” if their centers are closer than 5A˚ . • variability has two subfields: 3.5 Annotation 1. number of different amino acids appearing in in this column If the residue annotation is available (either from the pdb file or of the alignment from other sources), another column, with the header “annotation” 2. their type appears. Annotations carried over from PDB are the following: site • rho ET score - the smaller this value, the lesser variability of (indicating existence of related site record in PDB ), S-S (disulfide this position across the branches of the tree (and, presumably, bond forming residue), hb (hydrogen bond forming residue, jb (james the greater the importance for the protein) bond forming residue), and sb (for salt bridge forming residue).
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