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2Afp Lichtarge Lab 2006

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2Afp Lichtarge Lab 2006 Pages 1–5 2afp Evolutionary trace report by report maker November 4, 2009 4.3.3 DSSP 4 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2afp): Title: The solution structure of type ii antifreeze protein reveals a new member of the lectin family Compound: Mol id: 1; molecule: protein (sea raven type ii anti- freeze protein); chain: a; engineered: yes; other details: six amino acid his tag was added at the c- terminal end to facilitate recovery of the secreted afp from the medium using affinity chromatography. Organism, scientific name: Hemitripterus Americanus; 2afp contains a single unique chain 2afpA (129 residues long). This is an NMR-determined structure – in this report the first model CONTENTS in the file was used. 1 Introduction 1 2 CHAIN 2AFPA 2 Chain 2afpA 1 2.1 P05140 overview 2.1 P05140 overview 1 From SwissProt, id P05140, 99% identical to 2afpA: 2.2 Multiple sequence alignment for 2afpA 1 Description: Type II antifreeze protein precursor (AFP). 2.3 Residue ranking in 2afpA 1 Organism, scientific name: Hemitripterus americanus (Sea raven). 2.4 Top ranking residues in 2afpA and their position on Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; the structure 2 Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; 2.4.1 Clustering of residues at 25% coverage. 2 Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Scor- 2.4.2 Possible novel functional surfaces at 25% paeniformes; Cottoidei; Hemitripteridae; Hemitripterus. coverage. 2 Function: Antifreeze proteins lower the blood freezing point. Subcellular location: Secreted. 3 Notes on using trace results 3 Similarity: Contains 1 C-type lectin domain. 3.1 Coverage 3 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 3 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 3 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 4 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 4 and this statement is not removed. 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 2afpA 4 Appendix 4 For the chain 2afpA, the alignment 2afpA.msf (attached) with 21 4.1 File formats 4 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 4 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 4 using Muscle program. It can be found in the attachment to this 4.3.1 Alistat 4 report, under the name of 2afpA.msf. Its statistics, from the alistat 4.3.2 CE 4 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-129 in 2afpA colored by their relative importance. (See Appendix, Fig.5, for the coloring scheme.) Format: MSF Number of sequences: 21 Total number of residues: 2686 Smallest: 121 Largest: 129 Average length: 127.9 Alignment length: 129 Average identity: 39% Most related pair: 98% Most unrelated pair: 23% Most distant seq: 33% Fig. 2. Residues in 2afpA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, 7% of residues show as conserved in this alignment. The alignment consists of 95% eukaryotic ( 95% vertebrata) 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 2afpA.descr. 2.3 Residue ranking in 2afpA The 2afpA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2afpA can be found in the file called 2afpA.ranks sorted in the attachment. 2.4 Top ranking residues in 2afpA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 2 shows residues in 2afpA 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 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.3 are composed of the residues listed in Table 1. Table 1. Fig. 3. Residues in 2afpA, colored according to the cluster they belong to: cluster size member red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The color residues corresponding Pymol script is attached. red 23 7,11,18,19,27,28,31,32,35,39 41,42,44,63,65,66,77,79,80 101,117,125,126 blue 2 50,53 Table 1. continued yellow 2 88,112 cluster size member continued in next column color residues Table 1. Clusters of top ranking residues in 2afpA. 2 2.4.2 Possible novel functional surfaces at 25% coverage. One Table 2. continued group of residues is conserved on the 2afpA surface, away from (or res type substitutions(%) cvg antn susbtantially larger than) other functional sites and interfaces reco- 79 D D(90)N(4)S(4) 0.19 gnizable in PDB entry 2afp. It is shown in Fig. 4. The residues 47 S S(71)T(28) 0.20 14 L F(66)L(14)H(4) 0.22 Y(14) 80 G G(90)K(4)S(4) 0.23 114 D D(85)T(4)S(4) 0.23 N(4) 126 A K(66)E(9)S(9) 0.24 I(4)A(9) 27 T T(57)P(9)S(33) 0.25 Table 2. Residues forming surface ”patch” in 2afpA. Table 3. res type disruptive mutations 7 C (KER)(FQMWHD)(NYLPI)(SVA) 35 C (KER)(FQMWHD)(NYLPI)(SVA) 65 G (KER)(FQMWHD)(NYLPI)(SVA) 77 W (KE)(TQD)(SNCRG)(M) 101 C (KER)(FQMWHD)(NYLPI)(SVA) 112 W (KE)(TQD)(SNCRG)(M) 117 C (KER)(FQMWHD)(NYLPI)(SVA) 125 C (KER)(FQMWHD)(NYLPI)(SVA) Fig. 4. A possible active surface on the chain 2afpA. 28 W (KE)(TQD)(SNCRG)(M) 53 F (KE)(QD)(TR)(N) 88 W (KE)(TQD)(SNCRG)(M) belonging to this surface ”patch” are listed in Table 2, while Table 18 C (K)(ER)(QM)(D) 3 suggests possible disruptive replacements for these residues (see 44 S (R)(K)(H)(FYQW) Section 3.6). 11 W (KE)(QD)(TR)(N) 50 E (FWH)(R)(YVCAG)(T) Table 2. 41 H (E)(T)(MD)(SVQCAG) res type substitutions(%) cvg antn 19 I (R)(K)(TE)(Y) 7 C C(100) 0.08 S-S 32 E (FWH)(Y)(VCAG)(R) 35 C C(100) 0.08 S-S 39 G (E)(R)(K)(H) 65 G G(100) 0.08 79 D (R)(FWH)(Y)(K) 77 W W(100) 0.08 47 S (KR)(FQMWH)(NELPI)(Y) 101 C C(100) 0.08 S-S 14 L (R)(TKE)(Y)(SQCG) 112 W W(100) 0.08 80 G (FW)(ER)(H)(K) 117 C C(100) 0.08 S-S 114 D (R)(FWH)(K)(Y) 125 C C(100) 0.08 S-S 126 A (Y)(R)(H)(K) 28 W W(95)F(4) 0.10 27 T (R)(K)(H)(FQW) 53 F F(95)V(4) 0.10 88 W W(95)F(4) 0.10 18 C C(95)Y(4) 0.12 S-S Table 3. Disruptive mutations for the surface patch in 2afpA. 44 S S(90)I(9) 0.12 11 W W(95)A(4) 0.13 50 E E(90)D(9) 0.14 41 H H(85)N(14) 0.15 3 NOTES ON USING TRACE RESULTS 19 I Y(80)F(9)I(9) 0.16 3.1 Coverage 32 E E(85)Q(9)D(4) 0.18 Trace results are commonly expressed in terms of coverage: the resi- 39 G G(90)N(4)A(4) 0.19 due is important if its “coverage” is small - that is if it belongs to continued in next column 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 3 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 effects to be determined experimentally. 3.2 Known substitutions COVERAGE One of the table columns is “substitutions” - other amino acid types V seen at the same position in the alignment. These amino acid types 100% 50% 30% 5% 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 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, one may try replacing, R with K, or (perhaps more surprisingly), with V V. The percentage of times the substitution appears in the alignment RELATIVE IMPORTANCE is given in the immediately following bracket.
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