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1Kma Lichtarge Lab 2006 Pages 1–5 1kma Evolutionary trace report by report maker February 17, 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 1kma): Title: Nmr structure of the domain-i of the kazal-type thrombin inhibitor dipetalin Compound: Mol id: 1; molecule: dipetalin; chain: a; fragment: n- terminal domain-i; synonym: dipetalogastin; engineered: yes Organism, scientific name: Dipetalogaster Maximus; 1kma contains a single unique chain 1kmaA (55 residues long). This is an NMR-determined structure – in this report the first model in the file was used. CONTENTS 2 CHAIN 1KMAA 2.1 O96790 overview 1 Introduction 1 From SwissProt, id O96790, 100% identical to 1kmaA: 2 Chain 1kmaA 1 Description: Serine protease inhibitor dipetalogastin precursor 2.1 O96790 overview 1 (Dipetalin) (Fragment). 2.2 Multiple sequence alignment for 1kmaA 1 Organism, scientific name: Dipetalogaster maximus (Blood- 2.3 Residue ranking in 1kmaA 1 sucking bug). 2.4 Top ranking residues in 1kmaA and their position on Taxonomy: Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; the structure 2 Pterygota; Neoptera; Paraneoptera; Hemiptera; Euhemiptera; Hete- 2.4.1 Clustering of residues at 25% coverage. 2 roptera; Panheteroptera; Cimicomorpha; Reduviidae; Triatominae; 2.4.2 Possible novel functional surfaces at 25% Dipetalogaster. coverage. 2 Function: Thrombin inhibitor. Prevents blood clotting to allow insect to feed on blood. Also functions as an inhibitor of trypsin and 3 Notes on using trace results 3 plasmin. 3.1 Coverage 3 Subcellular location: Secreted. 3.2 Known substitutions 3 Similarity: Contains 6 Kazal-like domains. 3.3 Surface 3 About: This Swiss-Prot entry is copyright. It is produced through a 3.4 Number of contacts 3 collaboration between the Swiss Institute of Bioinformatics and the 3.5 Annotation 3 EMBL outstation - the European Bioinformatics Institute. There are 3.6 Mutation suggestions 3 no restrictions on its use as long as its content is in no way modified and this statement is not removed. 4 Appendix 3 4.1 File formats 3 2.2 Multiple sequence alignment for 1kmaA 4.2 Color schemes used 4 For the chain 1kmaA, the alignment 1kmaA.msf (attached) with 91 4.3 Credits 4 sequences was used. The alignment was downloaded from the HSSP 4.3.1 Alistat 4 database, and fragments shorter than 75% of the query as well as 4.3.2 CE 4 duplicate sequences were removed. It can be found in the attachment 1 Lichtarge lab 2006 Fig. 1. Residues 1-55 in 1kmaA colored by their relative importance. (See Appendix, Fig.5, for the coloring scheme.) to this report, under the name of 1kmaA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 91 Total number of residues: 4314 Smallest: 42 Largest: 55 Average length: 47.4 Alignment length: 55 Average identity: 37% Most related pair: 98% Most unrelated pair: 20% Fig. 2. Residues in 1kmaA, colored by their relative importance. Clockwise: Most distant seq: 42% front, back, top and bottom views. Furthermore, 3% of residues show as conserved in this alignment. The alignment consists of 46% eukaryotic ( 19% vertebrata, 14% arthropoda) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1kmaA.descr. 2.3 Residue ranking in 1kmaA The 1kmaA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1kmaA can be found in the file called 1kmaA.ranks sorted in the attachment. 2.4 Top ranking residues in 1kmaA 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 1kmaA 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 1kmaA, 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 Table 1. corresponding Pymol script is attached. cluster size member color residues red 13 8,15,16,17,19,20,22,23,25,27 2.4.2 Possible novel functional surfaces at 25% coverage. One 29,46,48 group of residues is conserved on the 1kmaA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1kma. It is shown in Fig. 4. The right panel Table 1. Clusters of top ranking residues in 1kmaA. shows (in blue) the rest of the larger cluster this surface belongs to. The residues belonging to this surface ”patch” are listed in Table 2 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 evolutionary pressure. (I.e., the smaller the coverage, the stronger the pressure on the residue.) Starting from the top of that list, mutating a couple of residues should affect the protein somehow, with the exact Fig. 4. A possible active surface on the chain 1kmaA. The larger cluster it effects to be determined experimentally. belongs to is shown in blue. 3.2 Known substitutions One of the table columns is “substitutions” - other amino acid types 2, while Table 3 suggests possible disruptive replacements for these seen at the same position in the alignment. These amino acid types residues (see Section 3.6). 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 Table 2. example if the substitutions are “RVK” and the original protein has res type substitutions(%) cvg antn an R at that position, it is advisable to try anything, but RVK. Conver- 23 Y Y(100) 0.04 sely, when looking for substitutions which will not affect the protein, 27 C C(98)G(1) 0.06 S-S one may try replacing, R with K, or (perhaps more surprisingly), with 22 T T(96)S(2)D(1) 0.07 V. The percentage of times the substitution appears in the alignment 48 C C(98)D(1) 0.11 S-S is given in the immediately following bracket. No percentage is given 8 C C(83)G(5)N(9) 0.14 S-S in the cases when it is smaller than 1%. This is meant to be a rough .(1) guide - due to rounding errors these percentages often do not add up 25 N N(80)D(14)S(4) 0.18 to 100%. T(1) 29 L L(74)F(12)M(1) 0.20 3.3 Surface A(9)R(2) To detect candidates for novel functional interfaces, first we look for 46 G Q(1)G(91)F(1) 0.22 residues that are solvent accessible (according to DSSP program) by 2 V(1)C(2)A(1) at least 10A˚ , which is roughly the area needed for one water mole- E(1)H(1) cule to come in the contact with the residue. Furthermore, we require 6 C C(64)R(4).(23) 0.24 S-S that these residues form a “cluster” of residues which have neighbor A(1)E(1)L(1) within 5A˚ from any of their heavy atoms. S(3)V(1) Note, however, that, if our picture of protein evolution is correct, the neighboring residues which are not surface accessible might be Table 2. Residues forming surface ”patch” in 1kmaA. equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choo- sing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) Table 3. res type disruptive 3.4 Number of contacts mutations Another column worth noting is denoted “noc/bb”; it tells the num- 23 Y (K)(QM)(NEVLAPIR)(D) ber of contacts heavy atoms of the residue in question make across 27 C (KER)(FQMWHD)(NYLPI)(SVA) the interface, as well as how many of them are realized through the 22 T (R)(K)(FWH)(QM) backbone atoms (if all or most contacts are through the backbone, 48 C (R)(K)(FWH)(EQM) mutation presumably won’t have strong impact). Two heavy atoms 8 C (ER)(K)(FWH)(MD) are considered to be “in contact” if their centers are closer than 5A˚ . 25 N (FYWH)(R)(TEVMA)(KCG) 29 L (Y)(R)(T)(EH) 3.5 Annotation 46 G (KER)(D)(QH)(FYMW) If the residue annotation is available (either from the pdb file or 6 C (R)(K)(E)(H) from other sources), another column, with the header “annotation” appears.
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