Kevin Karplus 24 May 1998 No strong hits. Best is 1pyp+1yppA+1wqjA (fssp rep=1wqjA) At -5.35, this is TRUE FALSE bet on new domains 22 100 82% fssp 39.5 122.27 76% NOTE: secondary structure reported in submission! 25 May 1998 The alignment t56-1pyp.a2m looks fairly good for the short stretch that aligns (24 residues out of 114). We need to check whether helices align here. The global alignment extends the short region, but doesn't have as high an identity. The 1pyp-t56.a2m alignment pulls out the short region, and the global alignment extends it in a different way. The 1wgjA alignments pull out essentially the same region as the 1pyp ones. 26 May 1998 The 1pyp and 1wgjA alignments do not have helices where the submitters said there were some, so these are almost certainly bad predictions. 2mhr is a 4-helix bundle, and one helix is matched. This is probably a good secondary structure match, but not a good fold match. 2prd matches only beta strands, so is probalby not a good match. 27 May 1998 Kevin Karplus At Christian's suggestion, I tried target97 to see if we got some stronger matches, since that method searched for slightly more distant homologies. The top scores were 1ino, 1l48, 1l58, 119l and 1l92 (note the random variation between lower-case L and 1). The top-score of -2.590 is still quite weak--for target97 fssp 47.03 true 362.97 false 89% new fold Note: 1ino is represented in fssp-3-5-98 by 2prd, the other ok hits by 1l92. These two are the top two for t56-t98 also (with stronger scores) and 18th and 19th on the t56-sum98.rdb list. 10 August 1998 Christian 1l92 is an alpha+beta protein, and the alignment t56-1l92-global aligns the first few residues of t56 to beta strands. The rest of the alignment is to helix. 18 August 1998 Christian Since we are given where the helices are in this protein, I drew helical wheels for each. Helix 1: IEAEQSVLGGLM - appears to be mostly buried, but there is a face in the middle of the helix that is exposed. The exposed face is the 1st E and QS. The rest of the helical face that contains the 2nd E is all hydrophobic. Helix 2: WDDVA - the DD face of the helix is exposed, but the other side of the helix probably faces the protein core. Helix 3: HRHIFTEMARLQE - definitely an amphipathic helix. The helical face that contains I,F,M,A,L faces the protein core. The rest of the residues, asice from the first H and 2nd-to-last Q, comprise a face that is exposed. Helix 4: ITLAESLER - also a definite amphipathic helix. The helical face composed of T,E,S,E,R faces solvent, while the other residues comprise a face that faces inward. I and the last E are on the same side of the helix, but at opposite ends. So it looks like the N-terminal of that helical side is buried, whereas the C-terminal is exposed. Helix 5: AYLAELSK - a mixed bag. The last two residues are exposed. The remainder of the helix is buried, aside from the face that has the E. The Y is on the same face of the helix as the E, but since it is only polar at the end of its long hydrophobic sidechain, it is probably also buried. Helix 6: ISAYADIVRERAVVREM - this long helix look like it goes through a few different environments. Aside from the M and 2nd-to-last V, a charged face is formed by D,E,first R, and last E. The N-terminal region of the helix is probably briefly exposed on the helical face containing S, and is then mainly buried on the face formed by I,A,Y,A,I,V,I,V,A,2nd V. This stretch of the helix may be recessed into the protein a bit, as slightly more than half the circumference of the helix in this stretch is hydrophobic. The helix becomes exposed again on this face with the last two Rs. 18 August 1998 Kevin Karplus Moved all the previous results to subdirectory "old" and restarted with the latest Makefile. wu-blast finds nothing---top hits 2[ab]pk 0.74 1dyg 1.76 1mmh7 1.86 double-blast finds nothing. No PDB files in t56.t98_6. 18 August 1998 Christian Those structures that I couldn't rule out based upon secondary structure content/arrangement from SCOP or abstract have a "?". t56.t98_6 finds no strong scores: 1fsu -5.270 1auk alpha/beta ? 1ycrA -5.040 1ycqA ? 1tiiA -4.170 1lt3A alpha+beta ? 2mhr -4.090 2mhr all helical ? 1ak1 -4.060 1ak1 alpha/beta 1fji -4.060 ? theoretical model ? 1xyz[AB] -4.050 1xyzA TIM barrel (none of these are structural homologs of each other.) fssp library models find 2mprA T0056 -6.040 all beta 1wgjA T0056 -4.910 mainly beta 1l92 T0056 -4.880 alpha+beta, doubtful 1af9 T0056 -4.830 essentially all beta 1theA T0056 -4.320 mainly beta 1fosE T0056 -4.310 all helical, but leucine zipper 1phd T0056 -4.110 all helical ? 1afrA T0056 -4.030 all helical ? 2prd T0056 -3.000 all beta target98-mixed library models with w0.5 find 1auk T0056 -4.020 alpha/beta fold 1l58 T0056 -3.980 alpha+beta, doubtful 1l92 T0056 -3.970 alpha+beta, doubtful 119l T0056 -3.960 alpha+beta, doubtful 2prd T0056 -3.780 all beta 1dkgA T0056 -3.110 coiled-coil target98 with viterbi scoring finds 1hqi T0056 -5.590 two sheets and loosely-packed helices 1l58 T0056 -5.470 alpha+beta, doubtful 119l T0056 -5.450 alpha+beta, doubtful 1pyp T0056 -5.420 all beta 1yppA T0056 -5.360 all beta 1l92 T0056 -5.150 alpha+beta, doubtful 2prd T0056 -5.130 all beta 1gd1O_2 T0056 -4.930 alpha+beta ? 1wgjA T0056 -4.890 mainly beta 1gd1O T0056 -4.880 alpha+beta 1dpgA_2 T0056 -4.420 alpha/beta ? 3rubL_1 T0056 -4.400 alpha/beta barrel 1auk T0056 -4.250 alpha/beta fold 1berA T0056 -3.310 alpha/beta Target98 library models find 1l92 T0056 -3.850 nothing new here 1l58 T0056 -3.810 119l T0056 -3.760 1yppA T0056 -3.630 1pyp T0056 -3.610 2prd T0056 -3.600 1wgjA T0056 -3.460 1auk T0056 -3.440 1hqi T0056 -2.940 1gd1O_2 T0056 -2.850 1pii_1 T0056 -2.810 1berA T0056 -2.700 19 August 1998 Kevin Summing both ways pulls up 1pyp 1pyp -6.39 1wgjA 1ycrA -6.13 1ycqA 1yppA -6.04 1wgjA 1wgjA -5.84 1wgjA 1fsu -5.270 1auk 2mhr -5.2 2mhr 1xyzA -5.14 1xyzA 2prd -4.87 2prd 19 August 1998 Christian The most interesting alignments from the above are: 1l92/1l92-t56-vit.pw.dist:T0056 114 -5.56 -5.16 1pyp/1pyp-t56-vit.pw.dist:T0056 114 -4.63 -4.58 1pyp/t56-1pyp-vit.pw.dist:1pyp 280 -3.41 -4.48 1tiiA/t56-1tiiA-vit.pw.dist:1tiiA 186 -6.95 -7.41 1tiiA/t56-1tiiA-global.pw.dist:1tiiA 186 -2.54 -6.31 1wgjA/1wgjA-t56-vit.pw.dist:T0056 114 -4.59 -4.81 1wgjA/t56-1wgjA-vit.pw.dist:1wgjA 282 -3.04 -4.11 1ycrA/t56-1ycrA-vit.pw.dist:1ycrA 85 -7.26 -7.15 2mhr/t56-2mhr-global.pw.dist:2mhr 118 -7.15 -8.11 2mhr/t56-2mhr-post.pw.dist:2mhr 118 -7.15 -8.11 2prd/2prd-t56-vit.pw.dist:T0056 114 -5.57 -5.13 Still need to check out 1gd1O_2; the make failed. 1wgjA, 2prd, 1pyp, and 1tiiA have beta cores with some scattered helices. 1l92 is the closest thing to a possibility that I have seen yet. My alignment, constrained by hydrophobicity on the pieces of t56 that we know to be helix, is 1l92-t56.cbarrett1.a2m. [Note: only 10 residues conserved.] 2mhr is a 4-helix bundle. It's probably possible to fit part of the target onto it. Unless we find something more promising by digging further into the noise, I'm thinking new fold. Wed Aug 19 14:52:25 PDT 1998 Kevin Karplus The top-scoring alignments are 2mhr/t56-2mhr-global 2mhr 118 -7.15 -8.11 2mhr/t56-2mhr-post 2mhr 118 -7.15 -8.11 1tiiA/t56-1tiiA-vit 1tiiA 186 -6.95 -7.41 1ycrA/t56-1ycrA-vit 1ycrA 85 -7.26 -7.15 1tiiA/t56-1tiiA-global 1tiiA 186 -2.54 -6.31 1tiiA/t56-1tiiA-post 1tiiA 186 -2.54 -6.31 2mhr/t56-2mhr-vit 2mhr 118 -5.15 -5.84 1l92/1l92-t56-vit T0056 114 -5.56 -5.16 2prd/2prd-t56-vit T0056 114 -5.57 -5.13 1gd1O/1gd1O-t56-vit T0056 114 -4.15 -4.85 1wgjA/1wgjA-t56-vit T0056 114 -4.59 -4.81 1pyp/1pyp-t56-vit T0056 114 -4.63 -4.58 1pyp/t56-1pyp-vit 1pyp 280 -3.41 -4.48 2prd/2prd-t56-const-global T0056 114 0.04 -4.43 2prd/2prd-t56-global T0056 114 -0.26 -4.43 2prd/2prd-t56-post T0056 114 -0.26 -4.43 1wgjA/t56-1wgjA-vit 1wgjA 282 -3.04 -4.11 2prd/t56-2prd-global 2prd 174 -1.11 -3.80 2prd/t56-2prd-post 2prd 174 -1.11 -3.80 2prd/2prd-t56-fssp-global T0056 114 0.53 -3.54 I modified the t56-2mhr-global to create 2t56-2mhr-hand1, which has 17 conserved residues and an excellent match to secondary structure. The t56-1tiaa-vit match is a tiny piece that doesn't match on 2secondary structure. Thu Aug 20 10:09:50 PDT 1998 The t56-1ycrA-vit match is an excellent match of the final helix of 1ycrA to the 3rd helix of t56---extending the alignment earlier does not help. The t56-1tiiA-global alignment just makes a worse mess than the t56-1tiiA-vit one. The 1l92/1l92-t56-vit alignment matches a helix-turn-helix at LMLDNERWD, but continues into a longer helix than is reported. The alignment can't be extended to a complete one (not enough helices in 1l92 after the matching one).