Modeling Protein Function

MED260
Philip E. Bourne
Department of Pharmacology, UCSD
pbourne@ucsd.edu
http://www.sdsc.edu/pb
Slides on-line at:
http://www.sdsc.edu/pb/edu/med260/med260.ppt

MED260 Modeling Protein Function 1

- October 11, 2006
 Agenda
• Why model protein function?
• Where does it fit as a technique in modern medical
research?
• The data deluge as a motivator
• The extent of what can be modeled
• Ontologies – establishing order from chaos
• Examples of what can be learnt
• Accuracy – a word of caution

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 Why Model Protein Function
• The rate of discovery of new proteins far
outweighs our ability to functionally characterize
them
• Functional discovery of new proteins has
implications in:
– Drug discovery
– Biomarker identification
– Understanding of biological processes
– Identification of disease states and treatment regimes

MED260 Modeling Protein Function 3

Why model protein function? - October 11, 2006
REPRESENTATIVE EXAMPLE
UNITS SCIENTIFIC RESEARCH REPRESENTATIVE
DISCIPLINE
& DISCOVERY TECHNOLOGY

Anatomy MRI Organisms Migratory

Sensors

Physiology Heart Ventricular

Organs
Modeling

Cell Biology Neuron Cells Electron

Microscopy

Proteomics Structure Macromolecules X-ray

Genomics Sequence Biopolymers Crystallography

Medicinal Atoms & Molecules Protein

Protease
Chemistry Docking
Inhibitor

Where does it fit as a technique

in modern medical research?
REPRESENTATIVE EXAMPLE
UNITS SCIENTIFIC RESEARCH REPRESENTATIVE
DISCIPLINE
& DISCOVERY TECHNOLOGY

Anatomy MRI Organisms Migratory

Sensors

Physiology Heart Ventricular

Organs
Modeling

Translational
Cell Biology Neuron
Medicine Cells Electron
Microscopy

Proteomics Structure Macromolecules X-ray

Genomics Sequence Biopolymers Crystallography

Medicinal Atoms & Molecules Protein

Protease
Chemistry Docking
Inhibitor

Where does it fit as a technique

in modern medical research?
 The Ability to Model Protein Function
Influences and can be Influenced by Any
Level of Biological Complexity - Examples
• Genome - rapid increase in sequenced genomes provides
new raw material
• Proteome – large increase in the number of 3D structures
highlights new functions
• Interactome – identification of a binding partner points to
a new function
• Metabolome – isolation of a protein within a metabolic
pathway
• Cell - localization points to function
• Organ – gene expression in heart tissue points to function
• Organism – different physiology observed in species can
be related to protein functions
MED260 Modeling Protein Function 6
Where does it fit as a technique - October 11, 2006
in modern medical research?
REPRESENTATIVE EXAMPLE
UNITS SCIENTIFIC RESEARCH REPRESENTATIVE
DISCIPLINE
& DISCOVERY TECHNOLOGY

Anatomy MRI Organisms Migratory

Sensors

Physiology Heart Ventricular

Organs
Modeling

Cell Biology Neuron Cells Electron

Microscopy
We will focus here
Proteomics Structure Macromolecules X-ray
Genomics Sequence Biopolymers Crystallography

Medicinal Atoms & Molecules Protein

Protease
Chemistry Docking
Inhibitor

MED260 Modeling Protein Function 7

- October 11, 2006
 At All Levels We Are Being Driven By Data

Biological Experiment Data Information Knowledge Discovery

Collect Characterize Compare Model Infer

Complexity Technology
Data
Higher-life 1 10 100 1000 100000 Computing
Power
Organ Brain Cardiac
Mapping Modeling
Virtual
Cellular Communities
Model Metaboloic
Pathway of E.coli
Sub-cellular 106 102 Neuronal 1
Modeling # People/Web Site

Assembly Virus Ribosome

Structure
Genetic
Circuits
Structure Human
Genome Yeast E.Coli C.Elegans 1 Small
Project Genome Genome Genome Genome/Mo.
ESTs Gene Chips Human Sequencing
Sequence Genome Technology
90 95 00 05
The Data Deluge Year
 Metagenomics A First Look
• New type of genomics
• New data (and lots of it)
and new types of data
– 17M new (predicted
proteins!) 4-5 x growth
in just few months and
much more coming
– New challenges and
exacerbation of old
challenges

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The Data Deluge - October 11, 2006
 Metagenomics: First Results

• More then 99.5% of DNA • Everything we touch

in very environment turns out to be a gold
studied represent unknown mine
organisms • Environments studied:
– Culturable organisms are
– Water (ocean, lakes)
exceptions, not the rule
– Soil
• Most genes represent
– Human body (gut, oral
distant homologs of known cavity, human
genes, but there are microbiome)
thousands of new families
MED260 Modeling Protein Function 10
The Data Deluge - October 11, 2006
 Metagenomics New Discoveries
Environmental (red) vs. Currently Known PTPases (blue)
1

2
3

4
Hi
gh
er
eu
ka
ryo
te
s

MED260 Modeling Protein Function 11

The Data Deluge - October 11, 2006
 The Good News and the Bad News

• Good news
– Data pointing towards function are growing at
near exponential rates
– IT can handle it on a per dollar basis
• Bad news
– Data are growing at near exponential rates
– Quality is highly variable
– Accurate functional annotation is sparse

MED260 Modeling Protein Function 12

The Data Deluge - October 11, 2006
 Genomes - 2004
• We all know about the human – what is not
so well known is:
– 191 completed microbial genomes
– 44 archaea
– 727 bacteria
– 785 eukaryotes (complete or in progress)
– Viroids ….

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The Data Deluge - October 11, 2006
 Proteome
• We are reasonably good at finding proteins
in genomes with intergenic regions but not
perfect – eg alternative initiation codons
• Regulatory elements provide a different set
of challenges
• We are not so good at assigning functions
to those proteins
• Moreover the devil is in the details

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The Extent of What Can Be Modeled - October 11, 2006
 Estimated Functional Roles (by % of
Proteins) of the Proteome in a Complex
Organism

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The Extent of What Can Be Modeled - October 11, 2006
 Functional Nomenclature Needs to be Consistent
for Orderly Progress – Enter EC and GO

• EC classifies all enzymes -

http://www.chem.qmul.ac.uk/iubmb/enzym
e/
• Gene Ontology Consortium characterizes
by molecular function, biochemiscal
process and cellular location http://
www.geneontology.org/

Ontologies – MED260 Modeling Protein Function 16

establishing order from chaos - October 11, 2006
 Functional
Coverage of the
Human Genome

40% covered

http://function.rcsb.org:8080/pdb/function_distribution/index.html

The Extent of What Can Be Modeled

 Step 1. Learn What You Can from
the Protein Sequence
• Find it

• Pay attention to the quality of the functional

annotation – errors are transitive

• Understand its 1-D structure – domain

organization, {signatures, fingerprints}

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Examples of what can be learnt - October 11, 2006
 Step 2. Is there a 3D Structure? If so
What Can You Learn from That?
• Find it
• Understand it
• Characterize it
• Understand its function(s) – these follow a
power law at the fold level – some folds are
promiscuous (many functions) others are
solitary or of unknown function

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Examples of what can be learnt - October 11, 2006
(a) myoglobin (b) hemoglobin (c) lysozyme (d) transfer RNA
(e) antibodies (f) viruses (g) actin (h) the nucleosome
(i) myosin (j) ribosome
Courtesy of David Goodsell, TSRI
 First Why Bother with Structure?
An Example: Protein Kinase A
This “molecular scene”
for cAMP dependant
protein kinase depicts
years of collective
knowledge.

Beyond basics, only

the atomic coordinates
are captured by the
PDB.

Functional annotation
requires the literature
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Examples of what can be learnt
 What Did that Picture Tell Us?
• Two domains with
associated functions
• So is structure
• ATP binding & substrate the answer to
binding
• Through conserved
functional
residues and their spatial modeling?
location details of the
ATP and substrate binding
and mechanism of the
phospho transfer reaction

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Examples of what can be learnt - October 11, 2006
 Question: So is structure the answer to
functional modeling?

Answer: Partly - The number of unique

protein sequences still outnumbers the
number of unique structures by 100:1

Enter Structural Genomics

Enter Structure Prediction

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Examples of what can be learnt
 The Structural Genomics Pipeline
(X-ray Crystallography)
Basic Steps
Crystallomics
• Isolation,
Target • Expression, Data Structure Structure Functional
Selection • Purification, Collection Solution Refinement Annotation Publish
• Crystallization

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Examples of what can be learnt - October 11, 2006
 Structural Genomics Will Give Us..

• Good news
– More structures (definitely)
– New folds (some but not as anticipated)
– New understanding of specific diseases and pathways
(maybe)
– Representatives from each major protein family
(maybe)
• Bad news
– Many new structures that are functionally unclassified
(definitely)

MED260 Modeling Protein Function 25

Examples of what can be learnt - October 11, 2006
 What About Structure Prediction?

• Current rule

We will be able to predict a structure when

we know all the structures 

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Examples of what can be learnt - October 11, 2006
 Why is Structure Prediction so Hard?
Random 1000 structurally similar PDB polypeptide chains with z > 4.5
(% sequence identity vs alignment length)

Twilight Zone
Midnight Zone

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Examples of what can be learnt - October 11, 2006
 Approaches to Structure Prediction

• Homology modeling
• Threading (aka fold recognition)
• Ab initio
• How well do we do? – see CASP
• Consensus servers
– Eva - http://cubic.bioc.columbia.edu/eva/
– LiveBench - http://bioinfo.pl/meta/
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Examples of what can be learnt - October 11, 2006
 Step 3. What Can Be Got from Structure
When You Have it?

From Structural Bioinformatics

Ed Bourne and Weissig p394 Wiley 2002
MED260 Modeling Protein Function 29
Examples of what can be learnt - October 11, 2006
 Specific Example
• Mj0577 – putative ATP molecular switch

Mj0577 is an open reading frame (ORF) of previously unknown function

from Methanococcus jannaschii. Its structure was determined at 1.7Å
(Figure 7a) (Zarembinski et al, 1998). The structure contains a bound
ATP molecule, picked up from the E. coli host. The presence of
bound ATP led to the proposition that Mj0577 is either an ATPase, or
an ATP-binding molecular switch. Further experimental work showed
that Mj0577 cannot hydrolyse ATP by itself, and can only do so in the
presence of M. jannaschii crude cell extract. Therefore it is more
likely to act as a molecular switch, in a process analogous to ras-GTP
hydrolysis in the presence of GTPase activating protein.

From Structural Bioinformatics

Ed Bourne and Weissig p402 Wiley 2002
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Examples of what can be learnt - October 11, 2006
 Step 4. Proteins Do Not Function in Isolation
But are Part of Complex Interaction Networks

http://www.genome.jp/kegg/
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Examples of what can be learnt
 Accuracy - A Word of Caution
• Errors are transitive
– Proteins A and B are observed to have similar
functions through sequence homology
– Proteins B and C are observed to have similar
functions through sequence homology
– Is protein A related to protein C?
– Up to 30% of current annotation may be wrong

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Accuracy - A Word of Caution
 Questions?

MED260 Modeling Protein Function 33

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 Demo of Steps 1-4
• Step 1. Learn What You Can from the Protein
Sequence
• Step 2. Is there a 3D Structure? If So, What Can
You Learn from That?
• Step 3. What Can Be Got from Structure When
You Have it?
• Step 4. Proteins Do Not Function in Isolation But
are Part of Complex Interaction Networks

MED260 Modeling Protein Function 34

- October 11, 2006