Multiple Mapping Method with Multiple Templates (M4T): optimizing sequence-to-structure alignments and combining

unique information from multiple templates

András Fiser

Department of Biochemistry andSeaver Center for BioinformaticsAlbert Einstein College of MedicineBronx, New York, USA

Target – TemplateAlignment

Model Building

START

Template Search

Model Evaluation

END

Multiple Mapping Method

Loop, side chain modeling

Statistical potential

Comparative protein structure modeling

Multiple Templates

Why do we need sequence alignments?

#Sequence vs. structure To generate input alignment for comparative modeling / threading

#Sequence vs. databases:

Querying sequence databases

#Sequence vs. sequence:

Establishing residue equivalencies between two proteins to locate conserved/variable regions

Ranking of models built on alternative alignments

Problem: None of the currently available methods produce consistently superior results in all cases

Template VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKTarget CLW DWTDAERAAIKALWGKIDVGEIGP—-QALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNMTarget A2D DWTDAERAAIKALWGKI—-DVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNM

Template GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH-PGDFGADAQGAMNKALELFRKDIAAKYKELGYTarget CLW DNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH----Target A2D DNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKF-G---PSAFTPEIHEAWQKFLAVVVSALGRQYH

Example:Template: 1a6m; Target: 1spg, chain B

~21% sequence identity

Instead of relying on just one alignment method, one should combine results of several alternative techniques

Alternative solutions vs. sequence similarity

Multiple Mapping Method

• Idea:– Improve the accuracy of sequence-to-structure

alignment by optimally splicing alternative inputs.

• Three components:

- Sampling

- Algorithm

- Scoring function

MMM scoring function: increasing the dimensionality of input information

Template VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILTarget CLW DWTDAERAAIKALWGKIDVGEIGP—-QALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAV

Template KKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH-PGDFGADAQGAMNKALELFRKDIAAKYKELGYTarget CLW QNMDNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH----

Template VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILTarget A2D DWTDAERAAIKALWGKI—-DVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAV

Template KKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH-PGDFGADAQGAMNKALELFRKDIAAKYKELGYTarget A2D QNMDNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKF-G---PSAFTPEIHEAWQKFLAVVVSALGRQYH

Different mapping identifies a different environment for each residue to align

Assess the “fitness” of each mapping

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1

2

2

Multiple Mapping Method: Algorithm

Step 1: Identify variable regions from the consensus alignment of the input set

Step 2: Select the best scoring variable segments, and combine them with with the core region of the alignment.

Template VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKTarget CLW DWTDAERAAIKALWGKIDVGEIGP—-QALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNMTarget A2D DWTDAERAAIKALWGKI—-DVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNM

Template GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH-PGDFGADAQGAMNKALELFRKDIAAKYKELGYTarget CLW DNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH----Target A2D DNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKF-G---PSAFTPEIHEAWQKFLAVVVSALGRQYH

Example: Template 1a6m; Target 1spg, chain B

21% sequence id

ExperimentalClustalW, RMSD 2.0 ÅAlign2D, RMSD 2.7 Å

Template VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKTarget MMM DWTDAERAAIKALWGKI—-DVGEIGPQALSRLLIVYPWTQRHFKGFGNISTNAAILGNAKVAEHGKTVMGGLDRAVQNM

Template GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH-PGDFGADAQGAMNKALELFRKDIAAKYKELGYTarget MMM DNIKNVYKQLSIKHSEKIHVDPDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH----

ExperimentalMMM, RMSD 1.8 Å

CLUSTALW 2.6 ÅALIGN2D 6.1 Å

MMM example using ideal scoring function

CLUSTALW 4.6 ÅALIGN2D 1.1 Å

Multiple Mapping Method: scoring function (1)

A composite scoring function to assess the compatibility/fit of alternative variable segments in the template structural environment.

• The composite scoring function consists of three mostly non-overlapping components.

1. Environment-specific substitution matrices (FUGUE1).

2. A scoring scheme based on a comparison (PHD vs. DSSP) of the secondary structure types (H3P22).

3. Statistically derived residue-residue contact energy (Rykunov and Fiser3).1Shi et al. J. Mol. Biol. (2001) 310, 243-2572Rice et al., J. Mol. Biol (1997) 267, 1026-10383Rykunov & Fiser., Proteins. (2007) 67, 559-68

MMM performance on 1400 pairs

MMM performance on 87 pairs, meta-servers

ESypred3D Consensus

Sampling vs. Scoring

• Multiple Mapping Method optimally combines alternative alignments obtained from different methods or scoring function:

On a benchmark dataset of 6635 protein pair structural alignments, comparative models built using MMM alignments are approximately 0.3 Ǻ and 0.5 Å more accurate on average in the whole spectrum and in the <30% target-template sequence identity regions, respectively, than the average accuracy of models built using the alternative input alignments ( ~3 and ~4 Å).

Summary

Optimally combining multiple templates

Selecting multiple templates

• Target sequence: by PSI-BLAST.

• Hits selected if sequence overlap with the target is > 60% of the actual SCOP domain length or more than 75% of the PDB chain length in case of a missing SCOP classification.

• Iterative clustering procedure identifies the most suitable templates to combine. Templates are selected or discarded according to a hierarchical selection procedure that accounts for – sequence identity between templates and target sequence,

– sequence identity among templates,

– crystal resolution of the templates,

– contribution of templates to the target sequence (i.e. if a region is covered by several templates or by a single template only).

Single versus multiple templatesUsing a dataset of 765 proteins with known structure two sets of models were built: (1) using one template (best E-value hit; light bars), (2) using multiple templates (grey bars)

And…increased coverageHistogram of models’ difference length. Each query sequence is modeled using single and multiple templates. The histogram shows the frequency of (Lm–Ls). Lm: length of model built using multiple templates, and Ls length of the model built using a single template.

The x-ray structure, the model with multiple templates and with a single template are shown in grey, red, and blue, respectively.

Multiple templates agree much better in two exposed regions: A and B, than the model built using single template.

Increased Coverage

The x-ray structure, the model with multiple templates, and model with single templates are shown in grey, red, and blue, respectively.

The addition of extra templates allowed obtaining a longer model that include a beta-turn-beta-turn extra region (20 amino acids), depicted in ribbon.

• Lab members:

– Dmitrij Rykunov

– Rotem Rubinstein

– J. Eduardo Fajardo

– Carlos J. Madrid-Aliste

– Veena Venkatagiriyappa

– Joseph Dybas

– Mario Pujato

– Brajesh Rai

– Narcis Fernandez-Fuentes

– Elliot Sternberger

Acknowledgement

Http://www.fiserlab.org/servers