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1Pe4 Lichtarge Lab 2006 Pages 1–5 1pe4 Evolutionary trace report by report maker June 24, 2010 4.3.3 DSSP 4 4.3.4 HSSP 4 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 5 4.7 Attachments 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1pe4): Title: Solution structure of toxin cn12 from centruroides noxius alfa scorpion toxin acting on sodium channels. nmr structure Compound: Mol id: 1; molecule: neurotoxin cn11; chain: a; synonym: cn12 Organism, scientific name: Centruroides Noxius; 1pe4 contains a single unique chain 1pe4A (67 residues long). This is an NMR-determined structure – in this report the first model in the file was used. CONTENTS 2 CHAIN 1PE4A 2.1 P63019 overview 1 Introduction 1 From SwissProt, id P63019, 100% identical to 1pe4A: 2 Chain 1pe4A 1 Description: Neurotoxin Cn12. 2.1 P63019 overview 1 Organism, scientific name: Centruroides noxius (Mexican scor- 2.2 Multiple sequence alignment for 1pe4A 1 pion). 2.3 Residue ranking in 1pe4A 1 Taxonomy: Eukaryota; Metazoa; Arthropoda; Chelicerata; Arach- 2.4 Top ranking residues in 1pe4A and their position on nida; Scorpiones; Buthida; Buthoidea; Buthidae; Centruroides. the structure 2 Function: Binds, in vitro, to sodium channels and inhibits the inac- 2.4.1 Clustering of residues at 25% coverage. 2 tivation of the activated channels. Seems not toxic to mice, crickets 2.4.2 Possible novel functional surfaces at 25% and sweet-water shrimps. coverage. 2 Subcellular location: Secreted. Tissue specificity: Expressed by the venom gland. 3 Notes on using trace results 3 Mass spectrometry: MW=7139.5; METHOD=Unknown; 3.1 Coverage 3 RANGE=1-67; NOTE=Ref.1. 3.2 Known substitutions 3 Similarity: Belongs to the alpha/beta-scorpion toxin family. Beta- 3.3 Surface 3 toxin subfamily. 3.4 Number of contacts 3 About: This Swiss-Prot entry is copyright. It is produced through a 3.5 Annotation 3 collaboration between the Swiss Institute of Bioinformatics and the 3.6 Mutation suggestions 3 EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified 4 Appendix 3 and this statement is not removed. 4.1 File formats 3 4.2 Color schemes used 4 2.2 Multiple sequence alignment for 1pe4A 4.3 Credits 4 For the chain 1pe4A, the alignment 1pe4A.msf (attached) with 131 4.3.1 Alistat 4 sequences was used. The alignment was downloaded from the HSSP 4.3.2 CE 4 database, and fragments shorter than 75% of the query as well as 1 Lichtarge lab 2006 Fig. 1. Residues 1-67 in 1pe4A colored by their relative importance. (See Appendix, Fig.5, for the coloring scheme.) duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1pe4A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 131 Total number of residues: 7702 Smallest: 55 Largest: 67 Average length: 58.8 Alignment length: 67 Average identity: 41% Most related pair: 98% Fig. 2. Residues in 1pe4A, colored by their relative importance. Clockwise: Most unrelated pair: 18% front, back, top and bottom views. Most distant seq: 45% Furthermore, 4% of residues show as conserved in this alignment. The alignment consists of 66% eukaryotic ( 66% arthropoda) 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 1pe4A.descr. 2.3 Residue ranking in 1pe4A The 1pe4A sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1pe4A can be found in the file called 1pe4A.ranks sorted in the attachment. 2.4 Top ranking residues in 1pe4A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 1pe4A colored by their importance: bright red and yellow indicate more conser- ved/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 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they Fig. 3. Residues in 1pe4A, 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 red 17 3,4,10,11,12,15,25,29,34,38 Table 1. continued 39,40,45,46,47,50,51 cluster size member continued in next column color residues Table 1. Clusters of top ranking residues in 1pe4A. 2 2.4.2 Possible novel functional surfaces at 25% coverage. One Table 3. continued group of residues is conserved on the 1pe4A surface, away from (or res type disruptive susbtantially larger than) other functional sites and interfaces reco- mutations gnizable in PDB entry 1pe4. It is shown in Fig. 4. The right panel 34 G (R)(K)(E)(FWH) shows (in blue) the rest of the larger cluster this surface belongs to. 29 C (E)(KR)(D)(FW) Table 3. Disruptive mutations for the surface patch in 1pe4A. 3 NOTES ON USING TRACE RESULTS 3.1 Coverage 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 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 Fig. 4. A possible active surface on the chain 1pe4A. The larger cluster it evolutionary pressure. (I.e., the smaller the coverage, the stronger the belongs to is shown in blue. pressure on the residue.) Starting from the top of that list, mutating a couple of residues should affect the protein somehow, with the exact effects to be determined experimentally. The residues belonging to this surface ”patch” are listed in Table 2, while Table 3 suggests possible disruptive replacements for these 3.2 Known substitutions residues (see Section 3.6). One of the table columns is “substitutions” - other amino acid types Table 2. seen at the same position in the alignment. These amino acid types res type substitutions(%) cvg antn may be interchangeable at that position in the protein, so if one wants 4 Y Y(100) 0.04 to affect the protein by a point mutation, they should be avoided. For 15 C C(100) 0.04 S-S example if the substitutions are “RVK” and the original protein has 45 C C(98)L(1) 0.06 S-S an R at that position, it is advisable to try anything, but RVK. Conver- 39 Y Y(96)CIHE 0.09 sely, when looking for substitutions which will not affect the protein, 38 G G(96)YC(3) 0.10 one may try replacing, R with K, or (perhaps more surprisingly), with 40 C C(96)AFW(2) 0.12 S-S V. The percentage of times the substitution appears in the alignment 46 Y W(63)Y(35)A(1) 0.18 is given in the immediately following bracket. No percentage is given 25 C .C(65)D(15)L(9) 0.21 S-S in the cases when it is smaller than 1%. This is meant to be a rough N(5)I(2)KT guide - due to rounding errors these percentages often do not add up 34 G G(79)NK(14)AY 0.24 to 100%. D(2).S 3.3 Surface 29 C IC(64).(6)K(25) 0.25 S-S R(2)Y To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by at least A˚ 2, which is roughly the area needed for one water mole- Table 2. Residues forming surface ”patch” in 1pe4A. 10 cule to come in the contact with the residue. Furthermore, we require that these residues form a “cluster” of residues which have neighbor Table 3. within 5A˚ from any of their heavy atoms. res type disruptive Note, however, that, if our picture of protein evolution is correct, mutations the neighboring residues which are not surface accessible might be 4 Y (K)(QM)(NEVLAPIR)(D) equally important in maintaining the interaction specificity - they 15 C (KER)(FQMWHD)(NYLPI)(SVA) should not be automatically dropped from consideration when choo- 45 C (R)(KE)(H)(FYQWD) sing the set for mutagenesis. (Especially if they form a cluster with 39 Y (K)(Q)(MR)(E) the surface residues.) 38 G (K)(ER)(M)(Q) 3.4 Number of contacts 40 C (KE)(R)(QD)(M) Another column worth noting is denoted “noc/bb”; it tells the num- 46 Y (K)(Q)(E)(R) ber of contacts heavy atoms of the residue in question make across 25 C (R)(H)(FKEW)(Y) the interface, as well as how many of them are realized through the continued in next column backbone atoms (if all or most contacts are through the backbone, mutation presumably won’t have strong impact).
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