Pages 1–5 1nar Evolutionary trace report by report maker September 12, 2010

4.3.3 DSSP 5 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 1nar): Title: Crystal structure of narbonin refined at 1.8 angstroms resolu- tion Compound: Mol id: 1; molecule: narbonin; chain: a; engineered: yes CONTENTS Organism, scientific name: Narbonensis 1nar contains a single unique chain 1narA (289 residues long). 1 Introduction 1

2 Chain 1narA 1 2.1 Q08884 overview 1 2.2 Multiple sequence alignment for 1narA 1 2.3 Residue ranking in 1narA 1 2.4 Top ranking residues in 1narA and their position on 2 CHAIN 1NARA the structure 1 2.1 Q08884 overview 2.4.1 Clustering of residues at 25% coverage. 2 From SwissProt, id Q08884, 100% identical to 1narA: 2.4.2 Possible novel functional surfaces at 25% Description: Narbonin. coverage. 2 Organism, scientific name: Vicia narbonensis (Narbonne vetch). : Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 3 Notes on using trace results 3 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3.1 Coverage 3 eudicotyledons; ; eurosids I; ; ; Papilionoi- 3.2 Known substitutions 3 deae; Vicieae; Vicia. 3.3 Surface 4 3.4 Number of contacts 4 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 1narA 4 Appendix 4 For the chain 1narA, the alignment 1narA.msf (attached) with 26 4.1 File formats 4 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 4 database, and fragments shorter than 75% of the query as well as 4.3 Credits 4 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 4 to this report, under the name of 1narA.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following:

1 Lichtarge lab 2006 Fig. 1. Residues 1-144 in 1narA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.)

Fig. 2. Residues 145-289 in 1narA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.)

Fig. 3. Residues in 1narA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 26 Total number of residues: 7032 Smallest: 231 Largest: 289 Average length: 270.5 Alignment length: 289 Average identity: 45% Most related pair: 97% Most unrelated pair: 25% Most distant seq: 34%

Furthermore, 6% of residues show as conserved in this alignment. The alignment consists of 53% eukaryotic ( 53% 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 1narA.descr. 2.3 Residue ranking in 1narA The 1narA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1narA can be found in the file called 1narA.ranks sorted in the attachment. 2.4 Top ranking residues in 1narA and their position on Fig. 4. Residues in 1narA, colored according to the cluster they belong to: the structure red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The In the following we consider residues ranking among top 25% of resi- corresponding Pymol script is attached. dues in the protein . Figure 3 shows residues in 1narA 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. 4 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.4 are composed of the residues listed in Table 1.

2 Table 1. Table 2. continued cluster size member res type substitutions(%) cvg color residues 63 F F(38)L(57)V(3) 0.16 red 70 5,7,8,9,10,18,20,21,22,33,35 95 P P(92)A(3)I(3) 0.17 36,37,39,40,41,42,52,54,58 18 L L(38)F(53).(3) 0.19 63,65,68,72,77,78,80,84,85 Y(3) 86,93,95,101,102,104,105,108 102 V V(84)I(11)L(3) 0.19 109,124,125,126,127,128,131 41 I T(38)I(61) 0.20 132,134,140,145,147,151,152 104 N N(92)K(7) 0.21 163,164,165,166,174,177,185 132 E G(7)E(92) 0.23 188,189,190,191,192,193,216 65 P P(88)L(11) 0.25 220,222,224,225,257 97 E E(38)D(7)S(46) 0.25 N(7) Table 1. Clusters of top ranking residues in 1narA. Table 2. Residues forming surface ”patch” in 1narA.

2.4.2 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1narA surface, away from (or Table 3. susbtantially larger than) other functional sites and interfaces reco- res type disruptive gnizable in PDB entry 1nar. It is shown in Fig. 5. The right panel mutations shows (in blue) the rest of the larger cluster this surface belongs to. 39 F (KE)(TQD)(SNCRG)(M) 58 W (KE)(TQD)(SNCRG)(M) 101 W (KE)(TQD)(SNCRG)(M) 108 S (KR)(FQMWH)(NYELPI)(D) 54 F (E)(K)(TQD)(SNCG) 10 G (KE)(R)(QD)(M) 20 D (R)(FWH)(K)(Y) 22 P (YR)(H)(T)(CG) 134 I (R)(TY)(KE)(SCHG) 93 F (K)(E)(Q)(D) 21 F (KE)(TQDR)(SNCG)(Y) 42 E (FWH)(R)(YVCAG)(T) 63 F (KE)(TQDR)(SNCG)(Y) 95 P (YR)(H)(T)(KE) Fig. 5. A possible active surface on the chain 1narA. The larger cluster it 18 L (R)(TK)(YE)(SCHG) belongs to is shown in blue. 102 V (YR)(KE)(H)(QD) 41 I (R)(YH)(K)(E) 104 N (Y)(FTW)(H)(SVCAG) The residues belonging to this surface ”patch” are listed in Table 132 E (FWH)(R)(Y)(VA) 2, while Table 3 suggests possible disruptive replacements for these 65 P (YR)(TH)(SKECG)(FQWD) residues (see Section 3.6). 97 E (FWH)(R)(Y)(VCAG) Table 2. res type substitutions(%) cvg Table 3. Disruptive mutations for the surface patch in 1narA. 39 F F(100) 0.06 58 W W(100) 0.06 Another group of surface residues is shown in Fig.6. The right panel 101 W W(100) 0.06 shows (in blue) the rest of the larger cluster this surface belongs to. 108 S S(100) 0.06 The residues belonging to this surface ”patch” are listed in Table 54 F F(96)H(3) 0.08 4, while Table 5 suggests possible disruptive replacements for these 10 G G(96)F(3) 0.09 residues (see Section 3.6). 20 D D(96)S(3) 0.09 22 P P(96)E(3) 0.09 Table 4. 134 I I(42)F(57) 0.10 res type substitutions(%) cvg 93 F F(88)Y(11) 0.13 151 L L(100) 0.06 21 F F(42)V(53)I(3) 0.14 152 K K(100) 0.06 42 E E(38)D(61) 0.14 72 K K(96)R(3) 0.08 continued in next column 127 I I(92)V(7) 0.12 continued in next column

3 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 to 100%. 3.3 Surface To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by 2 at least 10A˚ , which is roughly the area needed for one water mole- cule to come in the contact with the residue. Furthermore, we require that these residues form a “cluster” of residues which have neighbor within 5A˚ from any of their heavy atoms. Fig. 6. Another possible active surface on the chain 1narA. The larger cluster Note, however, that, if our picture of protein evolution is correct, it belongs to is shown in blue. the neighboring residues which are not surface accessible might be equally important in maintaining the interaction specificity - they Table 4. continued should not be automatically dropped from consideration when choo- res type substitutions(%) cvg sing the set for mutagenesis. (Especially if they form a cluster with 125 D D(96)E(3) 0.18 the surface residues.) 3.4 Number of contacts Table 4. Residues forming surface ”patch” in 1narA. Another column worth noting is denoted “noc/bb”; it tells the num- ber of contacts heavy atoms of the residue in question make across the interface, as well as how many of them are realized through the Table 5. backbone atoms (if all or most contacts are through the backbone, res type disruptive mutation presumably won’t have strong impact). Two heavy atoms mutations are considered to be “in contact” if their centers are closer than 5A˚ . 151 L (YR)(TH)(SKECG)(FQWD) 152 K (Y)(FTW)(SVCAG)(HD) 3.5 Annotation 72 K (Y)(T)(FW)(SVCAG) If the residue annotation is available (either from the pdb file or 127 I (YR)(H)(TKE)(SQCDG) from other sources), another column, with the header “annotation” 125 D (R)(FWH)(YVCAG)(K) appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide Table 5. Disruptive mutations for the surface patch in 1narA. bond forming residue), hb (hydrogen bond forming residue, jb (james bond forming residue), and sb (for salt bridge forming residue). 3.6 Mutation suggestions 3 NOTES ON USING TRACE RESULTS Mutation suggestions are completely heuristic and based on comple- 3.1 Coverage mentarity with the substitutions found in the alignment. Note that Trace results are commonly expressed in terms of coverage: the resi- they are meant to be disruptive to the interaction of the protein due is important if its “coverage” is small - that is if it belongs to with its ligand. The attempt is made to complement the following some small top percentage of residues [100% is all of the residues properties: small [AV GSTC], medium [LPNQDEMIK], large in a chain], according to trace. The ET results are presented in the [WFYHR], hydrophobic [LPVAMWFI], polar [GTCY ]; posi- form of a table, usually limited to top 25% percent of residues (or tively [KHR], or negatively [DE] charged, aromatic [WFYH], to some nearby percentage), sorted by the strength of the presumed long aliphatic chain [EKRQM], OH-group possession [SDETY ], evolutionary pressure. (I.e., the smaller the coverage, the stronger the and NH2 group possession [NQRK]. The suggestions are listed pressure on the residue.) Starting from the top of that list, mutating a according to how different they appear to be from the original amino couple of residues should affect the protein somehow, with the exact acid, and they are grouped in round brackets if they appear equally effects to be determined experimentally. disruptive. From left to right, each bracketed group of amino acid types resembles more strongly the original (i.e. is, presumably, less 3.2 Known substitutions disruptive) These suggestions are tentative - they might prove disrup- One of the table columns is “substitutions” - other amino acid types tive to the fold rather than to the interaction. Many researcher will seen at the same position in the alignment. These amino acid types choose, however, the straightforward alanine mutations, especially in may be interchangeable at that position in the protein, so if one wants the beginning stages of their investigation. to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has 4 APPENDIX 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, 4.1 File formats one may try replacing, R with K, or (perhaps more surprisingly), with Files with extension “ranks sorted” are the actual trace results. The V. The percentage of times the substitution appears in the alignment fields in the table in this file:

4 ”most unrelated pair” of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant seq” is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of these N COVERAGE numbers (hence, the most outlying sequence). alistat is copyrighted by HHMI/Washington University School of Medicine, 1992-2001,

V and freely distributed under the GNU General Public License. 100% 50% 30% 5% 4.3.2 CE To map ligand binding sites from different source structures, report maker uses the CE program: http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) ”Protein structure alignment by incremental combinatorial extension (CE) of the optimal path . Protein Engineering 11(9) 739-747.

V 4.3.3 DSSP In this work a residue is considered solvent accessi- 2 RELATIVE IMPORTANCE ble if the DSSP program finds it exposed to water by at least 10A˚ , which is roughly the area needed for one water molecule to come in the contact with the residue. DSSP is copyrighted by W. Kabsch, C. Fig. 7. Coloring scheme used to color residues by their relative importance. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version by [email protected] November 18,2002,

• alignment# number of the position in the alignment http://www.cmbi.kun.nl/gv/dssp/descrip.html. • residue# residue number in the PDB file 4.3.4 HSSP Whenever available, report maker uses HSSP ali- • type amino acid type gnment as a starting point for the analysis (sequences shorter than 75% of the query are taken out, however); R. Schneider, A. de • rank rank of the position according to older version of ET Daruvar, and C. Sander. ”The HSSP database of protein structure- • variability has two subfields: sequence alignments.” Nucleic Acids Res., 25:226–230, 1997. 1. number of different amino acids appearing in in this column of the alignment http://swift.cmbi.kun.nl/swift/hssp/ 2. their type 4.3.5 LaTex The text for this report was processed using LATEX; • rho ET score - the smaller this value, the lesser variability of Leslie Lamport, “LaTeX: A Document Preparation System Addison- this position across the branches of the tree (and, presumably, Wesley,” Reading, Mass. (1986). the greater the importance for the protein) 4.3.6 Muscle When making alignments “from scratch”, report • cvg coverage - percentage of the residues on the structure which maker uses Muscle alignment program: Edgar, Robert C. (2004), have this rho or smaller ”MUSCLE: multiple sequence alignment with high accuracy and • gaps percentage of gaps in this column high throughput.” Nucleic Acids Research 32(5), 1792-97. 4.2 Color schemes used http://www.drive5.com/muscle/ The following color scheme is used in figures with residues colored 4.3.7 Pymol The figures in this report were produced using by cluster size: black is a single-residue cluster; clusters composed of Pymol. The scripts can be found in the attachment. Pymol more than one residue colored according to this hierarchy (ordered is an open-source application copyrighted by DeLano Scien- by descending size): red, blue, yellow, green, purple, azure, tur- tific LLC (2005). For more information about Pymol see quoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, http://pymol.sourceforge.net/. (Note for Windows bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, users: the attached package needs to be unzipped for Pymol to read DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, the scripts and launch the viewer.) tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. The colors used to distinguish the residues by the estimated 4.4 Note about ET Viewer evolutionary pressure they experience can be seen in Fig. 7. Dan Morgan from the Lichtarge lab has developed a visualization tool specifically for viewing trace results. If you are interested, please 4.3 Credits visit: 4.3.1 Alistat alistat reads a multiple sequence alignment from the http://mammoth.bcm.tmc.edu/traceview/ file and shows a number of simple statistics about it. These stati- stics include the format, the number of sequences, the total number The viewer is self-unpacking and self-installing. Input files to be used of residues, the average and range of the sequence lengths, and the with ETV (extension .etvx) can be found in the attachment to the alignment length (e.g. including gap characters). Also shown are main report. some percent identities. A percent pairwise alignment identity is defi- ned as (idents / MIN(len1, len2)) where idents is the number of 4.5 Citing this work exact identities and len1, len2 are the unaligned lengths of the two The method used to rank residues and make predictions in this report sequences. The ”average percent identity”, ”most related pair”, and can be found in Mihalek, I., I. Res,ˇ O. Lichtarge. (2004). ”A Family of

5 Evolution-Entropy Hybrid Methods for Ranking of Protein Residues • 1narA.complex.pdb - coordinates of 1narA with all of its inter- by Importance” J. Mol. Bio. 336: 1265-82. For the original version acting partners of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolu- • 1narA.etvx - ET viewer input file for 1narA tionary Trace Method Defines Binding Surfaces Common to Protein • 1narA.cluster report.summary - Cluster report summary for Families” J. Mol. Bio. 257: 342-358. 1narA report maker itself is described in Mihalek I., I. Res and O. Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type • 1narA.ranks - Ranks file in sequence order for 1narA of service for comparative analysis of proteins.” Bioinformatics • 1narA.clusters - Cluster descriptions for 1narA 22:1656-7. • 1narA.msf - the multiple sequence alignment used for the chain 4.6 About report maker 1narA report maker was written in 2006 by Ivana Mihalek. The 1D ran- • 1narA.descr - description of sequences used in 1narA msf king visualization program was written by Ivica Res.ˇ report maker • 1narA.ranks sorted - full listing of residues and their ranking for is copyrighted by Lichtarge Lab, Baylor College of Medicine, 1narA Houston. 4.7 Attachments The following files should accompany this report:

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