IBGP/BMI 705 Lab 4:Protein structure and alignment

TA: L. Cooper

Why Align Structures

1. For homologous proteins (similar ancestry), this provides the “gold standard” for sequence alignment – elucidates the common ancestry of the proteins.

2. For nonhomologous proteins, allows us to identify common substructures of interest.

3. Allows us to classify proteins into clusters, based on structural similarity.

Example of Structural Homologs4DFR: Dihydrofolate reductase1YAC: Octameric Hydrolase of Unknown Specificity5.9% sequence identity (best alignment)1YAC structure solved without knowing function.Alignment to 4DFR and others implies it is a hydrolase of some sort.

DHFR: yellow & orangeYAC: green & purple

Sheets only

Helices only

Example of Structural Homologs

Sequence alignmentSLSAAEADLAGKSWAPVFANKNANGLDFLVALFEKFPDSANFFADFK-GKSVADIKA-SVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG

PKLRDVSSRIFTRLNEFVNNAANAGKMSAMLSQFAKEHVGFGVGSAQFENVRSMFPGFVAKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP

Structural alignmentXSLSAAEADLAGKSW-APVFANKN-ANGLDFLVALFEKFPDSANFF-ADFKGKSVA—-DIK V-LSPADKTNVKAAWGK-VGAHA-GEYGAEALERMFLSFPTTKTYFPHF-------DLS-H

ASPKLRDVSSRIFTRLNEFVNNAANAGKMSA-MLSQ-FAKEHV-GFGVGSAQFENVRSM-FGSAQVKGHGKKVADALTNAVAHV-D—-DMPNAL—-SALSDLHAHKLRVDPVNFKLLS-HCL

PGFVALVTLAAHLPAEFTP

How to Align Structures1. Visual inspection (by eye)

2. Computational approach• Point-based methods using point distances and other properties to

establish correspondences• Secondary structure-based methods use vectors representing

secondary structures to establish correspondences.

motif

Global

local

Structural Alignment AlgorithmsAlignment algorithms create a one-to-one mapping of subset(s) of one sequence to subset(s) of another sequence. Structure-based alignment algorithms do this by minimizing the structure difference score or root-mean-square difference (rmsd) in alpha-carbon positions.

• Find correspondence set• Find alignment transform

(protein superposition problem)• Chicken-and-egg

Parameter Space

Torsion angles () are:- local by nature (error propagation)- invariant upon rotation and translation of the molecule- compact (O(n) angles for a protein of n residues)

Add 1 degreeTo all

Problem: find the rotation matrix, R and a vector, v, that minimize the following quantity:

Structural Alignments Methods• STRUCTAL [Levitt, Subbiah, Gerstein]

• Using dynamic programming with a distance metric

• DALI [Holm, Sander]• Analysis of distance maps

• LOCK [Singh, Brutlag]• Analysis of secondary structure vectors,

followed by refinement with distances• SSAP [Orengo and Taylor, 1989]• VAST [Gibrat et al., 1996]• CE [Shindyalov and Bourne, 1998]• SSM [Krissinel and Henrik, 2004]• …

VAST (Vector Alignment Search Tool)

• It places great emphasis on the definition of the threshold of significant structural similarity. By focusing on similarities that are surprising in the statistical sense, one does not waste time examining many similarities of small substructures that occur by chance in protein structure comparison. Very many of the remaining similarities are examples of remote homology, often undetectable by sequence comparison. As such they may provide a broader view of the structure, function and evolution of a protein family.

• At the heart of VAST's significance calculation is definition of the "unit" of tertiary structure similarity as pairs of secondary structure elements (SSE's) that have similar type, relative orientation, and connectivity. In comparing two protein domains the most surprising substructure similarity is that where the sum of superposition scores across these "units" is greatest. The likelihood that this similarity would be seen by chance is then given as a simple product: the probability that one would obtain this score in drawing so many "units" at random, times the number of alternative SSE-pair combinations possible in the domain comparison, from which one has chosen the best.

• http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/iucrabs.html#Ref_6

Today’s lab

• Answer questions bolded on handout (There are five)

PDB: Protein structure viewing

PDB- Protein structure viewing

PDB- Protein structure viewing

PDB- Protein structure viewing

SCOP: Protein Classification

SCOP: Protein Classification

SCOP: Protein Classification

VAST: Alignment

VAST: Alignment

VAST: Alignment