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Protein Structure
Nimrod Rubinstein
Bioinformatics Seminar
Protein Synthesis
1.
2.
3.
4.
Attachment of correct
amino acids (AAs) to their
corresponding tRNAs.
Initiation: forming the
initiation complex.
Elongation: sequentially
forming peptide bonds.
Termination: synthesis is
terminated and the
polypeptide is released.
From Sequence to Structure
Structure Hierarchies:
Primary structure: the sequence of AAs covalently
bound along the backbone of the polypeptide chain.
Gly
Ala
Cys
O
ψ
N
ф
Cα
C
Cα
N
ф
ψ
N
C
O
-1800 ≤ ф ≤ 1800
-1800 ≤ ψ ≤
C
ф
Cα
ψ
O
From Sequence to Structure
Structure Hierarchies:
Secondary structure: local conformation of some
part of the polypeptide.
β Sheet
α Helix
Anti Parallel
Parallel
From Sequence to Structure
Structure Hierarchies:
Tertiary structure: the overall
3-dimensional arrangement of all the
atoms in the protein.
From Sequence to Structure
Structure Hierarchies:
Quaternary structure: some proteins contain two or
more separate polypeptide chains, which may be
identical or different.
Globular
Fibrous
From Sequence to Structure
Additional Parameters:
Surface accessibility:
The surface area of the molecule that is
exposed to the solvent, derived from
the complete structure.
•VDW surface: the surface area of an
atom.
•Connolly surface: the interface between
the molecule and the solvent sphere
(conventionally with r = 1.4Å) .
•Solvent accessible surface: the path of
the center of the solvent sphere rolled ov
the VDW surface.
•Relative accessibility = (SAS)/(maxSAS)
•maxSAS = SAS(Gly-X-Gly)
From Sequence to Structure
Additional Parameters:
Coordination number:
•The number of structure stabilizing
contacts each residue in the structure
makes.
•Computation: encapsulating an AA with
a sphere, centered at the residue’s
center of mass, and counting the
number of residues falling inside this
sphere.
•Usually done with different cutoff radii.
From Sequence to Structure
Protein Folding:
The Levinthal paradox: [Levinthal C.; J. Chym. Phys. (1968)]
Assume a protein is comprised of 100 AAs. Assume each
AA’s backbone can take up 10 different conformations,
defined by ф and ψ values. Altogether we get:
10100 conformations.
If each conformation were sampled in the shortest
possible time (time of a molecular vibration ~ 10-13 s) it
would take an astronomical amount of time
(~1077 years) to sample all possible conformations, in
order to find the Native State.
NPC even in the 2D case
Luckily, nature works out with these sorts of numbers and the
correct conformation of a protein is reached within seconds.
From Sequence to Structure
Folding Models:
The Backbone-Centric view:
•Sequence order dependent
interactions (фψ - propensities and Hbonds), produce local secondary
structure elements (SSEs).
•Local SSEs later overgo longerrange interactions to form
supersecondary structures.
•Supersecondary structures of
ever-increasing complexity thus
grow, ultimately into the native
conformation.
From Sequence to Structure
Folding Models:
The Sidechain-Centric view:
•Hydrophobic sidechain interactions are
the strongest for AAs in a water solution.
•A few key hydrophobic residues are
responsible for a “hydrophobic collapse”
to the “molten globule” state.
Molten globule
states
•The “molten globule” might not include
SSEs, yet about this structure the
remainder of the polypeptide chain
condenses.
•The conformation space is viewed as
“funnel shaped”.
From Sequence to Structure
Folding Models:
The Sidechain-Centric view - Larger proteins:
•Intermediate states exist, which are highly
populated.
•These states may assist in finding the
Native Structure or may serve as traps that
inhibit the folding process.
•Structurally aligning intermediate states
against the SCOP found the corresponding
Native Structures to have the highest
scores.
•But, many features were missing:
• Well defined SSEs.
• A well formed hydrophobic core.
• High RMSDs (7-10Å).
[Dobson C. M.; TRENDS in Biochemical Sciences; Jan 2005]
From Sequence to Structure
Folding Models:
Post-translational
Vs.
Co-translational
Anfinsen’s experiments:
•Exposure of a purified
RNase-A enzyme to a
concentrated urea solution
in the presence of a
reducing agent denaturizes
the folded conformation
resulting in a complete loss
of catalytic activity.
•Removal of the urea and
reducing agent causes the
enzyme to accurately refold
to its native structure and
restore its catalytic activity.
[Anfinsen C. et al.; PNAS (1961)]
•Denaturation-Renaturation
experiments are biased.
•An AA is added to the
polypeptide chain in: 10-2 s.
•The rate at which an SSE is
formed is: 10-7 – 10-4 s.
Determining the Structure
Crystallization:
•
Assembling a solution of protein molecules
into a periodic lattice.
X-Ray Diffraction:
•
•
•
The crystal is bombarded with X-ray beams.
The collision of the beams with the electrons
creates a diffraction pattern.
The diffraction pattern is transformed into an
electron density map of the protein from which
the 3D locations of the atoms can be deduced.
F
F
Determining the Structure
Nucleotide Magnetic
Resonance:
•
•
•
•
•
•
A solution of the protein is placed in a
magnetic field.
spins align parallel or anti-parallel to the
field.
RF pulses of electromagnetic energy
shifts spins from their alignment.
Upon radiation termination spins
re-align while emitting the energy they
absorbed.
The emission spectrum contains
information about the identity of the
nuclei and their immediate
environment.
The result is an ensemble of models
rather than a single structure.
Structure Similarity
Protein Families:
•
Structures seem to be preserved much more than sequences,
which is easily explainable due to neutral mutations.
1BRU:
Pancreatic Elastase
(Sus scorfa).
Global Alignment:
39% identity
1CHG:
Chymotrysinogen
(Bos taurus).
Rigid Cα Alignment:
RMSD 1.26Å
1CHG
1BRU
1CHG
1BRU
Structure Similarity
Protein Families:
•
•
•
Structures seems to be preserved much more than sequences,
which is easily explainable due to neutral mutations.
Structural Biologists claim that there are a limited number of
ways in which protein domains fold. There may be as few as
~2000 different folds (differing by their backbone topology).
Nearly a 1000 different folds have already been resolved.
http://scop.mrc-lmb.cam.ac.uk/scop/
Structure Prediction
Homology (Comparative) Modeling:
Guideline: At least 30% sequence identity is needed between
probe and template.
1.
Template Assignment: creating a robust probe-
2.
Model Construction:
3.
template alignment (PWA/MSA).
a.
Generation of coordinates for conserved segments:
b.
Generation of coordinates for variable segments:
c.
Generation of coordinates for sidechain atoms:
superimposing/averaging/restrain based.
DB scanning/Ab Initio/restrain based.
superimposing/rotamer libraries/restrain based.
Model Evaluation:
a.
b.
Assessment of to the ability to functionally identify
the active site of the model.
Assessment of physico-chemical or structural
environment based on statistical analyses of DBs
for characteristics such as:



Intramolecular packing.
Bond geometry.
Solvent accessibility.
bFGF
[Peitsch et al. (1999)]
Structure Prediction
Threading (Sequence-Structure Alignment):
Identifying evolutionary unrelated proteins that have converged to similar
folds.
• Scoring Scheme: describes the propensity of each AA for its structural/physicochemical environment: SS type, solvent accessibility, coordination number, etc…
• Profile construction: encoding the template’s AAs structural features to a 1D profile
and predicting such a profile for the probe.
• Threading Algorithm: Aligning the 1D profiles of the template and the probe using
DP and the defined scoring scheme.
template
probe
[Bryant, Lawrence; Proteins (1993)]
But:
No adjustments to the template profile can be made thus substantial rearrangements are ignored
Structure Prediction
Ab Initio Techniques:
Simulating the folding process
Simplifying the energy landscape:
•
Reducing the number of degrees of freedom:
•
•
•
Sampling the conformation space:
•
•
•
•
Representing a group of atoms by a single atom.
Reducing the number of atom interactions.
Monte Carlo sampling.
Genetic Algorithm.
Simulated Annealing.
Hierarchical folding simulation.
Blind Prediction
Critical Assessment of Protein Structure Prediction – CASP
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Goal: “ to obtain an in-depth and objective assessment of our current abilities and
inabilities in the area of protein structure prediction”.
Groups use their tools to model proteins with pre-published structures.
The predictions are thus evaluated against the subsequently determined structures.
CASP6 (2004) shows limited improvements compared to CASP5 (2003).