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1、Properties of TFIIIA Protein,Problem-Oriented Learning (II),Standard Analysis of A Cloned Gene,Database Search,Pattern Recognition,Protein Analysis,Find Similar Sequence?,Publication,Gene Searching,Consistent?,Fragment Assembly,Multiple Sequence Alignment,Profile Analysis,Find Consensus?,Phylogeneti
2、c Analysis,Yes,Yes,Yes,No,No,No,Pattern Recognition,Jargon,“Motifs” in bioinformatics a particular cluster of residue types as identification of an important function “Motifs” in protein structures supersecondary structures including a few secondary structure elements such as helix and sheet e.g. Gr
3、eek key, hairpin,Motifs Can Provide Insights on Possible Protein Functions,Part of prosite.seqcat: Atp_Gtp_A ATP/GTP-binding site motif A (P-loop). 11/19 (0017.pdoc) (A,G)x4GK(S,T) Atpase_Na_K_Beta_1 Sodium and potassium ATPases beta subunits signature 1. 11/19 (0328.pdoc) (F,Y,W) Atpase_Na_K_Beta_2
4、 Sodium and potassium ATPases beta subunits signature 2. 11/19 (0328.pdoc) (R,K)x2,Two Ways to Recognize Protein Patterns,“Motifs” looks for PROSITE patterns in a sequence “FindPatterns” identifies sequences that contain given patterns,Seq1,Seq2,Seq3,Seq4,Seq5,Pattern 1,Pattern 2,Pattern 3,Pattern 4
5、,Demo 1,Examine the known motifs on TFIIIA protein sequence,Conventions to Express Patterns in Prosite,Pattern of Zinc_Finger_C2H2: Cx2,4Cx3(L,I,V,M,F,Y,W,C)x8Hx3,5H x8 means 8 any amino acids X2,4 means 2 to 4 X (any amino acids) (L,I,V) means L, I, or V at this location x,4 means 04 any amino acid
6、s x2, means 2350,000 any amino acids,Demo 2,How to Get The Documentation of A Pattern? (Zinc_Finger_C3hc4),If You Find A New Motif, and You Want to Check Its Exist in Other Sequences,Define Your Own Patterns in prosite.patterns “Motifs” Search,Format of Prosite.patterns,Name Offset Pattern PDoc_Name
7、 11s_Seed_Storage 1 NGx(D,E)2x(L,I,V,M,F)C(S,T)x11,12(P,A,G)D 0284.pdoc 1433_1 1 RNL(L,I,V)S(V,G)(G,A)YKN(I,V) 0633.pdoc 1433_2 1 YK(D,E)STLI(I,M)QLL(R,H)DN(L,F)TLW(T,A)(S,A) 0633.pdoc 25a_Synth_1 1 GGSx(A,G)(K,R)xTxL(K,R)(G,S,T)xSD(A,G) 0653.pdoc 25a_Synth_2 1 RPVILDPx(D,E)PT 0653.pdoc (Add your ow
8、n patterns here. Name, offset, pattern, and pdoc_name, are required.) AIDS 1 AIDS aids.pdoc,Standard Analysis of A Cloned Gene,Database Search,Pattern Recognition,Protein Analysis,Find Similar Sequence?,Publication,Gene Searching,Consistent?,Fragment Assembly,Multiple Sequence Alignment,Profile Anal
9、ysis,Find Consensus?,Phylogenetic Analysis,Yes,Yes,Yes,No,No,No,Protein Analysis,PepPlot PeptideStructure/PlotStructure Moment HelicalWheel SPScan HtHScan CoilScan,New Programs in Ver 9.1,Some Important Properties of Proteins,Secondary structure or higher Antigenicity, flexibility, hydrophilicity, a
10、nd surface probability,Secondary Structure Information May Connote Interactions between Molecules,e.g. Leucines are placed along one side of the alpha helix of leucine zipper,PepPlot vs PeptideStructure,PeptideStructure predicts the properties PepPlot reveals the tendencies of properties,PepPlot Rev
11、eals Tendencies of Properties,Demo 3,Use PeptideStructure to predict the secondary structure and other properties of TFIIIA,Output of PeptideStructure Predicts the Properties at Every Location,Pos AA GlycoS HyPhil SurfPr FlexPr CF-Pred GORPred AI-Ind 1 M . 1.475 1.270 1.000 H H 0.900 2 G . 0.820 1.0
12、04 1.000 H H 0.900 3 E . 0.050 0.648 1.000 H H 0.450 4 K . 0.271 1.012 1.000 H H 0.600 5 A . -0.057 0.759 0.996 H H -0.300 6 L . -0.714 0.325 0.969 H H -0.600 7 P . -1.029 0.255 0.945 . H -0.600 8 V . -1.029 0.505 0.941 B H -0.600 9 V . -0.129 1.198 0.952 B B -0.150 10 Y . 0.600 1.214 0.967 B B 0.75
13、0 ,Correlation of Zn-Finger and the Predicted -Helix in TFIIIA,Zn-Finger Range GOR Chou & Fasman* 1 13-17 28-34 28-37 (h) 2 38-67 46-59 46-51 (H) 3 68-98 82-96 81-94 (h) 4 99-129 109-124 114-119 (H) 5 130-159 151-158 151-159 (h) 6 160-188 184-188 182-188 (h) 7 189-214 189-200, 207-212 200-214 (h) 8
14、215-246 none 215-217, 240-246 (h) 9 247-276 260-276 247-257, 263-276 (h) *H: stronger helix former, h: weak helix former,Exercise 1,Print the squiggles output of the predicted secondary structure with hydrophilicity on it.,Protein Analysis,PepPlot PeptideStructure/PlotStructure Moment HelicalWheel S
15、PScan HtHScan CoilScan,New Programs in Ver 9.1,Exercise 2,Use HelicalWheel to examine the distribution of hydrophobic residues in 115-129 aa,Demo 4,Use Moment to examine the hydrophobic property of TFIIIA protein,Standard Analysis of A Cloned Gene,Database Search,Pattern Recognition,Protein Analysis,Find Similar Sequence?,Publication,Gene Searching,Consistent?,Fragment Assembly,Multiple Sequence Alignment,Profile Analysis,Find Consensus?,Phy
