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Integrating the Data

Prof:Rui Alvesralves@cmb.udl.es

973702406Dept Ciencies Mediques Basiques,

1st Floor, Room 1.08Website of the Course:http://web.udl.es/usuaris/pg193845/Courses/Bioinformatics_2007/

Course: http://10.100.14.36/Student_Server/

Outline

• Methods for reconstruction of functional protein networks– Why is it important?

• Methods for reconstruction of physical protein interactions

Proteins do not work alone!

Methods for network reconstruction

• Using text analysis

Publication databases are source of information

Meta text databases create network models from publication analysis

iHOP is a sofisticated context analysis motor

How does meta-text analysis create networks?

Literature database

Gene names

database

Language rules

database

scripts

Gene list Rule list

Server/

Program

Your genes

List of entries mentioning your gene

e.g Ste20e.g activate,

inhibit rescue

• Meta text analysis

• Evolutionary based protein interaction prediction

Proteins that have coevolved share a function

• If protein A has co-evolved with protein B, they are likely to be involved in the same process

• Looking for proteins that coevolved will help prediction social networks of proteins

• There are many methods to look for co-evolution of proteins– Phylogenetic profiling, gene neighbourhoods,

gene fusion events, phylogenetic trees…

Using phylogenetic profiles to predict protein interactions

Your Sequence (A) Server/

Program

Database of profiles for each protein in each organism

Database of proteins in fully sequenced genomes

Protein id A

Target Genome

Homologue in Genome 1?

Homologue in Genome 2?

00i/number of genomes<1C

1j/number of genomes

… …

B 0.11

… …

Proteins (A and C) that are present and absent in the same set of genomes are likely to be involved in the same process and therefore interact

Similarly, if protein A is absent in all genomes in which protein B is present there is a likelihood that they perform the same function! 2

Calculate coincidence index

Syntheny/Conservation of gene neighborhoods

Genome 1

Genome 2

Genome 3

Genome …

Protein A Protein B Protein C Protein D

Protein A Protein BProtein C Protein D

Protein AProtein B Protein CProtein D

Which of these proteins interact?

Proteins A and B are in a conserved relative position in most genomes which is an

indication that they are likely to interact

Gene fusion events

Genome 1

Genome 2

Genome 3

Genome …

Protein A Protein DProtein C Protein B

Which of these proteins interact?Proteins A and B have suffered gene fusion

events in at least some genomes, which is an indication that they are likely to interact

Building phylogenetic trees of proteins

Genome 1

Genome 2

Genome 3

Genome …

Protein A Protein BProtein C Protein D

…Get sequence of all homogues, align and

build a phylogenetic tree

Phylogenetic trees represent the evolutionary history of homologue

genes/proteins based on their sequence

Similarity of phylogenetic trees indicates interaction between proteins

… …

D2Proteins A and B have similar evolutionary trees and thus are likely to interact

• Using meta text analysis

• Using phylogenetic profiling

• Using omics data

Predicting gene functional interactions using micro array

datacells

Stimulum

Purify cDNA

Purify cDNA Compare cDNA levels of

corresponding genes in the different

populations

Genes overexpressed

as a result of stimulus

Genes underexpressed

Genes with expression

independent of stimulus

Group of genes/proteins

involved in response to the stimulus

Group of proteins involved in response

to the stimulus

Predicting protein functional interactions using mass spec data

Stimulum

Purify proteins

Purify proteins Identify Proteins and compare Protein

profiles/levels in the different populations

Proteins present

Proteins absent

Proteins Present

in both conditions

Predicting regulatory modules with CHIP-ChIp experiments

Crosslink

Protein/DNA Break DNA

Break DNA

Reverse cross link & Purify DNA Pieces

Afinity Purification of Transcription factor

Reverse cross link & Purify DNA Pieces bound to TF

Compare in Microarray

Predicting protein activity modulation with NMR/IR/MS

Metabolomics

Stimulus

Measuring Metabolitescells

Measuring Metabolites

Compare changes in metabolic levels to infer changes in protein activity

• Using meta text analysis

• Using phylogenetic profiling

• Using protein docking

• Using omics data

• Using protein interaction data

Predicting protein networks using protein interaction data

Database of protein

interactions

Server/

Program

Your Sequence (A)

FContinue until you are satisfied

or completed the network

Outline

• Methods for reconstruction of functional protein networks

• Methods for reconstruction of protein interactions

How do proteins work within the network?

• Assume we now have the network our protein is involved in.

• How do we further analyze the role of the protein?

Proteins work by binding

EffectDNA

Proteins work by binding!

So what?

So, if we can predict how proteins DOCK to their ligands, then we will be able to understand how the binding allows them to work systemically

Design drugs to overcome mutations in binding sites

Design proteins to prevent/enhance other interactions

What is in silico protein docking?

• Given two molecules find their correct association using a computer:

tor Ligand

Complex

What types of in silico docking exist?

• Sequence Based Docking:

In silico two hybrid docking

E. coli

S. typhi

Y. pestis

AGGMEYW….

AA – CDWY…

AGG –DYW

Protein AE. coli

S. typhi

Y. pestis

VCHPRIIE….

VCH -KIIE…

VCH –KIIE…

Protein B

V C H P K I I E…

D/K or E/R may be involved in a salt bridge

Pearson Correlation

What types of in silico docking exist?

• Sequence Based Docking

• In silico structural protein docking

Structure based docking

• Protein-Protein docking

– Rigid (usually)

• Protein-Ligand docking

– Rigid protein, flexible ligand

Very demanding on computational resources

Structural docking in a nutshell

• Scan molecular surfaces of protein for best surface fit– First steric, then energetics – Can (and should) include biologically relevant

information (e.g. residue X is known from mutation experiments to be involved in the docking → discard any docking not involving this residue)

Atom based docking

• First, a surface representation is needed

Van der Waals Surface

Accessible (Connolly)Surface

Solvent accessibleSurface

Calculating the best docking

• Scan molecular surfaces of protein for best surface fit– Calculate the position where a largest number of

atoms fits together, factor in energy + biology and rank solutions according to that

Grid-based techniques

•Grid-based Techniques

–Alternative to calculating protein atom / ligand atom interactions. more efficient (number of grid points < number of atoms)

Grid based docking

Score 1

Score 2Score 3

Score 4

Place grid over protein

Calculate inter-molecular forces for each grid point

The docking function

• There are many and none is the best for all cases

•Scores will depend on the exact docking function you use

A docking function for surface matching

•Molecules a, b placed on l × m × n grid

•Match surfaces

•Fourier transform makes calculation faster

moleculetheofsurfacetheon

moleculetheinside

moleculetheoutside

ba nml

', ', ' 1, 2, 3 ', ', ' 1, 2, 3' 1 ' 1 ' 1

,N N N

l m n l step m step n step l m n l step m step n stepl m n

Ca b a b

•Tabulate and rank all possible conformations

A docking function for electrostatics

• There are many

•they use different force field approximations to calculate energy of electrostatic interactions.

•The basics:

dVrrrrE bbaabbaaticelectrosta

Charge distributions for proteins

Potential for proteins

The full docking function

• Calculates a relative binding energy that integrates electrostatic and shape matching factors. For example:

tot Electrostatic Electrostatic shape matching shapematchingE c E c E

Overall process of docking

1, 2,,,

( , )i jp p

Energy Form Matching Electrostatics

Mol 1 Mol 2

Rigid Body energy calculation

List of Complexes

Re-rank using statistics of residue contact, H/bond, biological information, etc

Re-rank using rotamers, flexibility in protein backbone angles, Molecular dynamics, etc.

Final list of solutions

Summary

• Methods for reconstruction of functional protein networks– Bibliomics

– Genomics

– Phenomics, etc

• Methods for reconstruction of protein interactions– Sequence based

– Structure based

Grid-based techniques

• Grid-based Techniques

– Notes:

• Grids spaced <1 Å

– Results show very little change in error for grids spacing between .25 and 1 Å

Problem Importance

• Computer aided drug design – a new drug should fit the active site of a specific receptor.

• Many reactions in the cell occur through interactions between the molecules.

• No efficient techniques for crystallizing large complexes and finding their structure.

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