Lab Meeting 10/08/20041 SuperPose: A Web Server for Automated Protein Structure Superposition Gary Van Domselaar October 08, 2004

Lab Meeting 10/08/20042 Introduction Who Cares? Review of Superposition Identifying Corresponding Points Between Structures Multiple Structure Superposition RMSD Calculation The SuperPose Web Site

Lab Meeting 10/08/20043 Who Cares? NMR Spectroscopists 1YUA-26 Chains 1YUA, 26 Chains

Lab Meeting 10/08/20044 Who Cares? Structural Biologists 1YUA-26 Chains 1LUC:A, 1CNV

Lab Meeting 10/08/20045 Who Cares? Evolutionary Biologists 1MYK & 1MYN - 1BK8

Lab Meeting 10/08/20046 Principles of Superposition 1MYK & ● How do we superimpose these two cubes?

Lab Meeting 10/08/20047 Principles of Superposition 1MYK & 1.Identify corresponding points.

Lab Meeting 10/08/20048 Principles of Superposition 1MYK & 2.Identify the common center and the principle axes for each structure.

Lab Meeting 10/08/20049 Principles of Superposition 3.Translate the two structures so their centers overlap.

Lab Meeting 10/08/ Principles of Superposition 4.Rotate the two structures so the average distance between corresponding points is minimized,and their principal axes overlap.

Lab Meeting 10/08/ Principles of Superposition Rotations can be accomplished by multiplying each atom coordinate with an appropriate rotation matrix, but this is slow: cos  sin  0 -sin  cos  cos  sin  0 -sin  cos  Clockwise about xClockwise about z cos  -sin  0 sin  cos  cos  -sin  0 sin  cos  Counterclockwise about xCounterclockwise about z

Lab Meeting 10/08/ Principles of Superposition A faster way is to use quaternion-based superposition to both rotate and minimize the sum of residuals S.K.Kearsley, On the orthogonal transformation used for structural comparisons, Acta Cryst. A45, 208 (1989) structure.llnl.gov/xray/comp/suptext.htmhttp://www- structure.llnl.gov/xray/comp/suptext.htm

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures PDB_Entry_A 1 SDKIIHLTDDSFDTDVLKA--DGAILVDFWAEWCGPCKMIAPILDEIADE 48.:..:...:...:.|.| |..::|||.|.||||||||.|....:::: PDB_Entry_B 1 MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEK 48 PDB_Entry_A 49 YQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQ 98 |...:.: ::::|.....|.:..::..||...||.|: |||..| |. PDB_Entry_B 49 YSNVIFL-EVDVDDCQDVASECEVKCTPTFQFFKKGQ----KVGEFS-GA 92 PDB_Entry_A 99 LKEFLDANLA 108.||.|:|.:. PDB_Entry_B 93 NKEKLEATINELV 105 Sequence Alignment 2TRX:A - 3TRX:A

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Problem: Low Homology # Length: 163 # Identity: 11/163 ( 6.7%) # Similarity: 14/163 ( 8.6%) # Gaps: 139/163 (85.3%) # Score: 16.0 # #======================================= 3TRX_model_de 1 MVKQIESK 8 |:|:.... 3GRX_model_1_ 1 ANVEIYTKETCPYSHRAKALLSSKGVSFQELPIDGNAAKREEMIKRSGRT 50 3TRX_model_de 9 TAFQ EALDAAG--DKLVVVDFSATWCGPCKMIKPFF 42 |..|.||||.| |.|:. 3GRX_model_1_ 51 TVPQIFIDAQHIGGYDDLYALDARGGLDPLLK 82 3TRX_model_de 43 HSLSEKYSNVIFLEVDVDDCQDVASECEVKCTPTFQFFKKGQKVGEFSGA 92 3GRX_model_1_ TRX_model_de 93 NKEKLEATINELV 105 3GRX_model_1_ TRX - 3GRX:1

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Solution: Secondary Structural Alignment Sequence1: 3TRX_model_default_chain_default Sequence2: 3GRX_model_1_chain_default Score....: 600 Test Stat: 5.31 Matches..: 64 Sequence1: CEEEECCHHHHHHHHHHHCCEEEEEEEEECCCHHHHHCCCCCCHHHHHCC Matching.: ||||||||||||||| ||||||| Sequence2: CEEEEEEECCCHHHHHHHH HHHHHCC Structure: CBBBBBBBCCCHHHHHHHH HHHHHCC Sequence1: CEEEEEEEECCCHHHHHHHCCCCEEEEEEEECCCCCEEECCCCHHHHHHH Matching.: ||||||| || ||||||| ||| |||||||||| | ||||||| Sequence2: CEEEEEECCCCHHHHHHHHHCCCCCCEEEEECCCCC CHHHHHHHH Structure: CBBBBBBCCCCHHHHHHHHHCCCCCCBBBBBCCCCC CHHHHHHHH Sequence1: HHHCC Matching.: ||||| Sequence2: HHHCCCCCCCC Structure: HHHCCCCCCCC 3TRX - 3GRX:1

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Problem: Multiple Structural Forms # Length: 145 # Identity: 143/145 (98.6%) # Similarity: 143/145 (98.6%) # Gaps: 2/145 ( 1.4%) # Score: # #======================================= 1A29_model_de 1 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMI 50 ||||||||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 1 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMI 49 1A29_model_de 51 NEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISA 100 |||||||||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 50 NEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISA 99 1A29_model_de 101 AELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 144 |||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 100 AELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 144 1A29 - 1CLL

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Solution: Subdomain Alignment 1A29 - 1CLL

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures The Difference Distance Matrix Make a Distance Matrix for each structure:

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures The Difference Distance Matrix Subtract the dif matrices to make a DD Matrix Plot the magnitude of the distance as a color shade

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Analyze the difference distance matrix for similar subdomains. The DD Matrix will have regions that are similar, and regions that are different.

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Superposition restricted to residues 5-74

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures Superposition restricted to residues 5-74

Lab Meeting 10/08/ Identifying Corresponding Points Between Protein Structures # Length: 145 # Identity: 143/145 (98.6%) # Similarity: 143/145 (98.6%) # Gaps: 2/145 ( 1.4%) # Score: # #======================================= 1A29_model_de 1 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMI 50 ||||||||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 1 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMI 49 1A29_model_de 51 NEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISA 100 |||||||||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 50 NEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISA 99 1A29_model_de 101 AELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 144 |||||||||||||||||||||||||||||||||||||||||||| 1CLL_model_de 100 AELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 144

Lab Meeting 10/08/ Multiple Structure Superposition How do you optimally superimpose more than 2 structures?

Lab Meeting 10/08/ Multiple Structure Superposition Superimpose to an average structure Initial 2-Structure Superposition Structure 3 Average Structure 3-Structure Superposition 1 2 3

Lab Meeting 10/08/ Multiple Structure Superposition Superposition ordering is important –Structures should be superposed in order of their pairwise structural similarity. –An 'all-against-all' DD Matrix analysis can be used to quickly determine overall relative similarity between every pair of structures Avg RMSD for 3TRX chains A & C = 1.75 A Avg RMSD for 3TRX chains A & B = 1.5 A

Lab Meeting 10/08/ Multiple Structure Superposition A structure 'pileup' is created from the DD Matrix analysis to determine the superposition order. 3TRX_A,D:.5A 3TRX_A,B:.6A 3TRX_B,D:.7A 3TRX_B,C:.8A 3TRX_A,C:.9A 3TRX_C,D: 1.0 3TRX_A,D:.5A 3TRX_A,B:.6A 3TRX_B,C:.8A

Lab Meeting 10/08/ Multiple Structure Superposition Average structures can be sensibly generated only from a collection of structures with identical sequences How do you superimpose a collection of sequences with non-identical sequences? Progressive pairwise buildup using the pileup as a guide. 3TRX_A,D:.5A 3TRX_A,B:.6A 3TRX_B,C:.8A Superpose Structures A and D 'Anchor' Structure A, translate/rotate B, add B to A,D 'Anchor' Structure B, translate/rotate C, Add C to A,B,D

Lab Meeting 10/08/ Multiple Structure Superposition CLUSTAL W (1.83) multiple sequence alignment 2TRX_model_default_chain_A SDKIIHLTDDSFDTDVLKA--DGAILVDFWAEWCGPCKMIAPILDEIADE 2TRX_model_default_chain_B SDKIIHLTDDSFDTDVLKA--DGAILVDFWAEWCGPCKMIAPILDEIADE 3TRX_model_default_chain_defau --MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEK : ::..: :.*.* * ::*** * ******** *::..:::: 2TRX_model_default_chain_A YQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQ 2TRX_model_default_chain_B YQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQ 3TRX_model_default_chain_defau YSNVIFL-EVDVDDCQDVASECEVKCTPTFQFFKKGQ----KVGEFS-GA *.. : : ::::*:..*.: :: **: :**:*: *** :* * 2TRX_model_default_chain_A LKEFLDANLA--- 2TRX_model_default_chain_B LKEFLDANLA--- 3TRX_model_default_chain_defau NKEKLEATINELV ** *:*.:

Lab Meeting 10/08/ RMSD Calculation The degree of similarity between two or more structures is described by its average root mean square deviation (RMSD): x1x1 x1x1 x5x5 x4x4 x3x3 x2x2 y1y1 y2y2 y3y3 y4y4 y5y5

Lab Meeting 10/08/ SuperPose Superposition for 2 chains and for multiple chains Subdomain superposition Superposition of structures with low sequence identity