Protein Structure Analysis

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Derrick Holt
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BINF 731 Structure of the Rotor of the V-Type Na + -ATPase Protein Structure Analysis

, 25 NA repair factory model Kinesin motor The cartoon depicts a stationary

Goodman, 22 Kinesin is a dimeric motor protein that travels processively towards the

adjacent alpha/beta tubulin binding sites. R. Vale and R.

surface with amino-terminal His1-tags of the A subunits.

1 BINF 731 Structure of the Rotor of the V-Type Na + -ATPase Protein Structure Analysis Iosif Vaisman 215 A model for ion translocation by the V-ATPase of E. hirae T.Murata et al., 25 NA repair factory model Kinesin motor The cartoon depicts a stationary replication-repair complex encountering damaged NA rolled along as on a conveyer belt M. Goodman, 22 Kinesin is a dimeric motor protein that travels processively towards the microtubule plus end by taking 8 nm steps, which corresponds to the distance between adjacent alpha/beta tubulin binding sites. R. Vale and R. Milligan, 2 Rotation scheme of V1-motor The V1 was fixed on the Ni-NTA coated glass surface with amino-terminal His1-tags of the A subunits. A duplex bead was attached to the subunit through biotin strptavidin linkage. H. Imamura, 25 Protein engineering methods in the change information space R. J. Kazlauskas & U. T. Bornscheuer, 29

hange codon composition Nature 485, 185-194 (212) omputational Mutagenesis Residue and mutant score Assumption: the structural differences between each mutant and the wild-type

2 Bornscheuer et al. Nature 485, (212) Increase catalytic activity hange substrate binding site to increase specificity hange the thermal stability Increase proteins resistance to proteases hange codon composition Bornscheuer et al. Nature 485, (212) omputational Mutagenesis Residue and mutant score Assumption: the structural differences between each mutant and the wild-type protein are usually minor and, therefore, their tessellations are similar Approach: a single tessellation of either the wild-type or mutant protein structure can be used to develop environmental descriptors for quantitative evaluation of changes in mutant properties q 3 q 4 q 2 q 1 q 6 q 5 q res = q i wt mut Q mut = (q res q res )

Log-likelyhood ratio ealunay simplices classification elaunay Tessellation of Protein Structure (Asp) α or center of mass Abstract each amino acid to a point Atomic coordinates Protein ata Bank (PB)

Each simplex objectively defines a quadruplet of nearest-neighbor amino acids at its vertices. 63 G62 ompositional propensities of elaunay simplices i l k AAAA: = 4! / 4! = 1 AAAV: = 4! / (3! x 1!

3 Log-likelyhood ratio ealunay simplices classification elaunay Tessellation of Protein Structure (Asp) α or center of mass Abstract each amino acid to a point Atomic coordinates Protein ata Bank (PB) 3 A22 L6 F7 K4 S64 R5 elaunay tessellation: 3 tiling of space into non-overlapping, irregular tetrahedral simplices. Each simplex objectively defines a quadruplet of nearest-neighbor amino acids at its vertices. 63 G62 ompositional propensities of elaunay simplices i l k AAAA: = 4! / 4! = 1 AAAV: = 4! / (3! x 1!) = 4 AAVV: = 4! / (2! x 2!) = 6 AAVR: = 4! / (2! x 1! x 1!) = 12 AVRS: = 4! / (1! x 1! x 1! x 1!) ) = 24 j q ijkl log f ijkl p ijkl f- observed quadruplet frequency, p ijkl = a i a j a k a l, a - residue frequency 4! n ( t i!) i ounting Quadruplets assuming order independence among residues comprising elaunay simplices, the maximum number of all possible combinations of quadruplets forming such simplices is 8855 E F E Log-likelihood of amino acid quadruplets with different compositions S1,E1 reference PB Reversibility Analysis S1,E2 alculated Mutant Y HH G H W S Q F Forward Mutation L IRRV AEYY KKRV KRS EKP HKKS GLR AKN elaunay simplices with distinct composition S2,E1 alculated reference Reverse Mutation S2,E2 Mutant PB

Mean Residual Score_ Structural Analysis omputational mutagenesis of T4 lysozyme Reversibility of mutations Protein Mutation Score change S1,E1 reference PB S1,E2 alculated Mutant 1l63 T26E -2.

4 Mean Residual Score_ Structural Analysis omputational mutagenesis of T4 lysozyme Reversibility of mutations Protein Mutation Score change S1,E1 reference PB S1,E2 alculated Mutant 1l63 T26E l E26T Reference ifference Mutant ifference 1l63 A82S l S82A l63 V87M cu3 M87V l63 A l 93A l63 T152S goj S152T R 2 =.9886 S2,E1 alculated reference S2,E2 Mutant PB NA binding residues in HMG1 Protein-protein and protein-na interfaces (HMG-) KPRGKMSSYAFFVQTREEHKKKHPASVNFSEFSKKSERWKTMSAKEKGKFEMAKAKARYEREMKTY A A` Score Score B` A-A` F37A A`-B` Residue number oordinate file 1ckt: Ohndorf U-M et al. Nature 399: Residue number oordinate file 1qrv: Murphy F V et al. EMBO Journal 18:661 Universal Model Approach: 98 Experimental Mutants from 2 Proteins Increased ecreased Mutant Protein Stability hange

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