Pages 1–7 1hfo Evolutionary trace report by report maker July 28, 2010 4.3.1 Alistat 6 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 7 4.4 Note about ET Viewer 7 4.5 Citing this work 7 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1hfo): Title: The structure of the macrophage migration inhibitory factor from trichinella spiralis. CONTENTS Compound: Mol id: 1; molecule: migration inhibitory factor; chain: a, b, c, d, e, f; engineered: yes 1 Introduction 1 Organism, scientific name: Trichinella Spiralis; 1hfo contains a single unique chain 1hfoA (113 residues long) and 2 Chain 1hfoA 1 its homologues 1hfoF, 1hfoD, 1hfoC, 1hfoE, and 1hfoB. 2.1 Q9Y063 overview 1 2.2 Multiple sequence alignment for 1hfoA 1 2.3 Residue ranking in 1hfoA 1 2.4 Top ranking residues in 1hfoA and their position on the structure 1 2.4.1 Clustering of residues at 25% coverage. 1 2 CHAIN 1HFOA 2.4.2 Overlap with known functional surfaces at 2.1 Q9Y063 overview 25% coverage. 2 2.4.3 Possible novel functional surfaces at 25% From SwissProt, id Q9Y063, 98% identical to 1hfoA: coverage. 4 Description: Macrophage migration inhibitory factor like protein. Organism, scientific name: Trichinella spiralis (Trichina worm). 3 Notes on using trace results 5 Taxonomy: Eukaryota; Metazoa; Nematoda; Enoplea; Trichocepha- 3.1 Coverage 5 lida; Trichinellidae; Trichinella. 3.2 Known substitutions 5 3.3 Surface 5 3.4 Number of contacts 6 3.5 Annotation 6 2.2 Multiple sequence alignment for 1hfoA 3.6 Mutation suggestions 6 For the chain 1hfoA, the alignment 1hfoA.msf (attached) with 117 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 6 database, and fragments shorter than 75% of the query as well as 4.1 File formats 6 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 6 to this report, under the name of 1hfoA.msf. Its statistics, from the 4.3 Credits 6 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-113 in 1hfoA colored by their relative importance. (See Appendix, Fig.8, for the coloring scheme.) Format: MSF Number of sequences: 117 Total number of residues: 13047 Smallest: 95 Largest: 113 Average length: 111.5 Alignment length: 113 Average identity: 36% Most related pair: 99% Most unrelated pair: 17% Most distant seq: 35% Fig. 2. Residues in 1hfoA, colored by their relative importance. Clockwise: front, back, top and bottom views. Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 33% eukaryotic ( 14% vertebrata, <1% arthropoda, 3% plantae), and 3% prokaryotic sequences. (Des- criptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1hfoA.descr. 2.3 Residue ranking in 1hfoA The 1hfoA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 1hfoA can be found in the file called 1hfoA.ranks sorted in the attachment. 2.4 Top ranking residues in 1hfoA 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 1hfoA 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 Fig. 3. Residues in 1hfoA, colored according to the cluster they belong to: 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 15 1,3,23,27,30,32,33,36,37,39 Table 1. continued 63,64,65,112,113 cluster size member blue 7 7,8,49,51,55,93,95 color residues continued in next column yellow 4 72,76,79,98 Table 1. Clusters of top ranking residues in 1hfoA. 2 2.4.2 Overlap with known functional surfaces at 25% coverage. Table 3. continued The name of the ligand is composed of the source PDB identifier res type disruptive and the heteroatom name used in that file. mutations Interface with 1hfoC.Table 2 lists the top 25% of residues at the 107 G (KR)(E)(QH)(FMWD) interface with 1hfoC. The following table (Table 3) suggests possible 37 V (R)(Y)(KE)(H) disruptive replacements for these residues (see Section 3.6). 113 F (TKE)(D)(SQCRG)(N) 112 T (R)(K)(H)(Q) Table 2. 23 S (R)(K)(H)(Q) res type subst’s cvg noc/ dist antn 39 V (R)(K)(Y)(E) (%) bb (A˚ ) 1 P P(97) 0.04 10/9 3.77 site Table 3. List of disruptive mutations for the top 25% of residues in .(2) 1hfoA, that are at the interface with 1hfoC. 36 Y Y(84) 0.04 22/15 2.58 R(12)FC W 107 G G(78) 0.09 52/52 2.75 A(16)S .(4) 37 V V(64) 0.12 20/20 2.91 I(29) L(1) M(2)C 113 F F(77) 0.16 8/4 4.04 .(8) M(9) L(4) 112 T T(82) 0.17 51/20 2.98 .(5)I V(6) P(1) L(2) 23 S T(32) 0.23 7/0 3.55 S(49) C(7) A(1) E(3)GI H(1).P 39 V V(57) 0.25 44/38 2.78 Fig. 4. Residues in 1hfoA, at the interface with 1hfoC, colored by their rela- I(15) tive importance. 1hfoC is shown in backbone representation (See Appendix T(19) for the coloring scheme for the protein chain 1hfoA.) A(3) S(2) L(1) Figure 4 shows residues in 1hfoA colored by their importance, at the interface with 1hfoC. Interface with 1hfoB.Table 4 lists the top 25% of residues at the Table 2. The top 25% of residues in 1hfoA at the interface with 1hfoC. interface with 1hfoB. The following table (Table 5) suggests possible (Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type disruptive replacements for these residues (see Section 3.6). in the bracket; noc/bb: number of contacts with the ligand, with the number of Table 4. contacts realized through backbone atoms given in the bracket; dist: distance res type subst’s cvg noc/ dist of closest apporach to the ligand. ) (%) bb (A˚ ) 93 R R(94)HY 0.06 2/2 4.39 Table 3. K(3) res type disruptive 72 N N(70) 0.08 23/7 3.11 mutations M(2) 1 P (YR)(TH)(SCG)(KE) T(16) 36 Y (K)(Q)(E)(M) .(6) continued in next column continued in next column 3 Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) K(2)A 51 G G(89) 0.13 5/5 4.03 D(2)T A(4) K(1)N 98 F F(87)L 0.18 41/17 2.84 Y(9)VS. 76 S S(78) 0.19 34/10 2.89 A(9) T(9)RIN 95 Y Y(80)P 0.20 80/6 2.78 L(3) F(5)M I(3) V(4)H 49 F F(78) 0.21 28/10 3.49 L(3) V(4) Y(3) H(4)R Fig. 5. Residues in 1hfoA, at the interface with 1hfoB, colored by their rela- W(3) tive importance. 1hfoB is shown in backbone representation (See Appendix M(1) for the coloring scheme for the protein chain 1hfoA.) Table 4. The top 25% of residues in 1hfoA at the interface with 1hfoB. (Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 5. res type disruptive mutations 93 R (TD)(EVA)(SCLPIG)(YM) 72 N (Y)(H)(FW)(T) 51 G (R)(FWH)(KE)(Y) 98 F (K)(E)(Q)(DR) 76 S (R)(K)(H)(FW) 95 Y (K)(QR)(E)(M) 49 F (E)(K)(TD)(Q) Table 5. List of disruptive mutations for the top 25% of residues in 1hfoA, that are at the interface with 1hfoB. Fig. 6. A possible active surface on the chain 1hfoA. Figure 5 shows residues in 1hfoA colored by their importance, at the interface with 1hfoB. 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1hfoA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1hfo. It is shown in Fig. 6. The residues belonging to this surface ”patch” are listed in Table 6, while Table 7 suggests possible disruptive replacements for these residues (see Section 3.6).