Evolution of Protein Structure
Mario A. Fares
Evolutionary Genetics and Bioinformatics
Laboratory
Department of Genetics, Smurfit Institute of
Genetics, TCD
Phone: 8913521
Email: faresm@tcd.ie
http://bioinf.gen.tcd.ie/~faresm
Contents
1. In vivo, in vitro, in silico
•Proteins
•Protein structure and conformation: Basic concepts
•Proteins in diseases
2. Patterns and forms in protein structure
•Helices and sheets
•The hierarchical nature of protein architecture
•Structure based classification of proteins
•protein folding: Intra-cellular pathogens and the survival of the flattest
•Protein folding and disease: Amyloidoes, Parkinson, Huntington, Prion
disease
3. Conformational changes in protein
Structural changes arising from changes in state of ligation
Hinge motions in proteins
Mechanisms of conformation changes (Haemoglobin, Serpins,
muscle contraction)
Higher level structural changes (GroELS)
4: Protein Structure Prediction and Determination
Methods of protein structure determination
Critical assessment of structure prediction
Homology modelling
Threading
Prediction of novel folds
Protein design
5. Evolution of Protein Structure and Function
Protein structure classification
Structural relationships among homologous proteins
Changes in proteins during evolution uncovers
functionally/structurally important amino acid sites
Domain swapping
Classification of protein folding patterns
How do proteins evolve new functions?
Classification of protein functions
6. Molecular evolution
Evolution of Globins
Evolution of Serine proteinases
Evolution of visual pigments and related molecules
a) 7. Molecular Coevolution and mutation epistatic effects on protein structure
Defining molecular coevolution
Non-parametric methods to detect coevolution
Parametric methods to detect coevolution
acid sites
Intra-molecular coevolution and prediction of amino
three-dimensional proximity
Inter-protein coevolution and the identification of
protein-protein interfaces
8. Some examples of the immune system
Antibody structure
Protein of the Major histocompatibility Complex
T-cell receptors
Cancer and protein structures
REPRESENTATIVE
DISCIPLINE
EXAMPLE
UNITS
Anatomy
MRI
Physiology
Heart
Cell Biology
Proteomics
Genomics
Medicinal
Chemistry
SCIENTIFIC RESEARCH
& DISCOVERY
Organisms
Translational
Medicine
Neuron
Structure
Sequence
Protease
Inhibitor
REPRESENTATIVE
TECHNOLOGY
Migratory
Sensors
Organs
Ventricular
Modeling
Cells
Electron
Microscopy
Macromolecules
Biopolymers
Atoms & Molecules
X-ray
Crystallography
Protein
Docking
REPRESENTATIVE
DISCIPLINE
EXAMPLE
UNITS
Anatomy
MRI
Physiology
Heart
Cell Biology
Neuron
SCIENTIFIC RESEARCH
& DISCOVERY
Organisms
REPRESENTATIVE
TECHNOLOGY
Migratory
Sensors
Organs
Ventricular
Modeling
Cells
Electron
Microscopy
We will focus here
Proteomics
Genomics
Medicinal
Chemistry
Structure
Sequence
Protease
Inhibitor
Macromolecules
Biopolymers
Atoms & Molecules
X-ray
Crystallography
Protein
Docking
In vivo, in vitro, in silico
Proteins
Proteins roles
Structural
proteins
Catalytic
proteins
Viral capside proteins
Haemoglobin
Cytoskeleton
Myoglobin
Epidermal keratin
Ferritin
Regulatory
proteins
Hormones
Transcription factors
Estimated Functional Roles (by % of Proteins)
of the Proteome in a Complex Organism
(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
Step 3. What Can Be Got from Structure
When You Have it?
From Structural Bioinformatics
Ed Bourne and Weissig p394 Wiley 2002
Step 4. Proteins Do Not Function in Isolation
But are Part of Complex Interaction Networks
http://www.genome.jp/kegg/
•Proteins have the ability to organise themselves in three
dimensions
•Proteins have the ability to evolve due to the inheritable property
of protein structure variation
•Proteins are the direct responsibles for the cell viability in
normal physiological conditions as well as in stressful conditions
•Projects in development:
Strutural Genomics
Proteome project
Fascinating projects and questions under study:
1.
Interpretation of the mechanisms of function of individual
proteins
2.
Approaches to the protein folding problem
Dependence on environmental parameters
Protein structure prediction
3. Patterns of molecular evolution
Structural and functional selective constraints
relaxed amino acid sequence evolution
Structure evolution
4. Prediction of the structure of closely related proteins
Homology methods
Functional convergence leads to structure convergence
5. Protein engineering
Modifications to probe mechanisms of protein function
Molecular manipulation to enhance thermostability
Clinical aplications (therapeutic antibodies)
6. Drug design
Peptide inhibitors of HSPs
proteins inducers of the immune response
GENOME SEQUENCES
•
The genomes of 100 prokaryotes, many viruses, organelles and plasmids,
and over 12 eukaryotes, representing all major categories of living things
Completed eukaryotic nuclear genomes
Type of organism
Species
Primitive microsporidian
Fungi
Nematode worm
Insect: Fruit fly
mosquito
Malarial parasite
Plants: Thale cress
rice
Human
Mouse
Rat
Chicken
E. cuniculi
S. cerevisiae
Sc. pombe
N. crassa
C. elegans
D. melanogaster
A. gambiae
P. falciparum
A. thaliana
O. sativa
H. sapiens
M. musculus
R. norvegicus
G. gallus
Genome size (106 base pairs)
2.5
12.1
13.8
40
100
180
278
22.8
116.8
400
3400
3454
2556
1200
ENCODE (Encyclopedia of DNA Elements)
•
Determining the function of all significant regions of a selected region of
the human genome
•
For a selected 1% of the genome, the corresponding regions in 30
vertebrates genomes will be sequenced
•
A variety of experimental and computational techniques will be applied,
including comparative genomics
•
The results will feed up and engine new initiatives aimed at developing
models and computational tools to deal with the data in the human
genome
Amino acid sequences determine protein
structure: Protein structure and conformation
•
Proteins are polymers of amino acids containing a constant main chain
(backbone) of repeating units, with a variable side chain attached to each
Residue i -1 Residue i
Si-1
Si
Residue i +1
Si+1
Side chains variable
…N-C-C- N-C-C- N-C-C-…
Main chain constant
O
O
O
•
The amino acid sequence of a protein, together
with any post-translational modifications, specify
the primary structure of the protein, the fixed
chemical bonds.
•
Because the chain is flexible, the primary structure is compatible with a
very large number of spatial conformations of the main chain and side
chains
Sequence --> Structure
•
Given the right conditions, the same protein sequence will always* fold up into the
same structure, the native structure
•
The conformation of the native state is thus determined by the amino acid sequence
•
This routinely happens in the cell. However, for many proteins, it can also be made
to happen in a solution that only somewhat resembles cellular conditions
•
For a protein to take up a unique conformation means that evolution has produced
a set of interresidue interactions that stabilize the desired state, and that no
alternative conformation has comparable stability
How is that achieved?
The origins of bioinformatics
• Figuring out that “how” was one of the origins of
bioinformatics
• Structural biologists wanted larger and larger
collections of structure so they could extract rules
about sequence/structure relationships and apply them
to predict structure
• Extracting rules from protein sequence/structure data
precedes the exponential growth of the PDB and
GenBank by more than a decade
What’s interesting about proteins
• Sequence
• “Fold”
• 3D shape
– Surface crevices, interior holes, channels
• Surface properties
• Conformational changes
• Effects of variability/mutation
What can we do with structures?
• Establish relationships between sequence patterns and
structural features -- how have proteins evolved?
• Develop hypotheses about the function of a particular
protein
• Predict how a sequence will fold
• Build a model by comparison with a known structure of
similar sequence
What can we do with structures?
• Study the effects of mutation on structure and function
• Predict the effects of a novel mutation on structure or
function (protein engineering -- beginning)
• Design and build whole new proteins with novel
functionality (protein engineering -- advanced)
• Design drugs to interact with particular protein active sites
Protein structure basics
• Building blocks of protein structure
– Amino acids
– Organic cofactors
– Metal ions
•
•
•
•
Levels of structural description
Descriptors of protein geometry
Form and content of structure data
Visualization styles
Protein Secondary Structure
-helix
-sheet
These secondary structures are highly
present in proteins due to:
-They keep the main strain in an
unstrained conformation
- Satisfy the hydrogen-bonding potential
of the main-chain N-H and C=O groups
These secondary structures link in a specific way in different combinations to perform the
final protein structure
-helices are formed from a single consecutive set of residues in the amino acid sequence
The H-bond links the C=O group of residue i with the H-N group of residue i + 4
There are alternatives to the helix configuration giving more constrained or less
constrained structures:
-310 helices, in which hydrogen bonds form between residues i and i + 3
- -helices, in which hydrogen bonds form between residues i and i + 5
This configurations are much rarer due to the constraints and effects they have on the
protein stability.
-sheets are formed by lateral interactions of several
independent sets of residues.
They can bring together sections of the chain widely
separated in the amino acid sequence
In this figures, all the strands are anti-parallel
Protein in disease
Protein folding
Goal = lowest
energy
conformation
Problems of
protein folding
Energy trap
• Energy landscape is rough
– Red = slow track
• Peptide trapped in energy
minimum
(thermodynamically
favorable)
– Yellow = fast track
• Cell crowded
•  poor folding fidelity
Local energy
minimum =
intermediate
Protein misfolding
diseases = amyloidoses
Prions
• = “Protein-based infectious particles”
• Involved in multiple diseases
• Protein undergoes conformational
switch
– PrPc = cellular isoform
• Membrane-bound GPI anchored glycoprotein
– PrPSc = “scrapie” isoform
• Forms amyloid
Cellular isoform
“Scrapie” isoform