Protein Structure

1
Protein Structure

• Nimrod Rubinstein
• Bioinformatics Seminar

2
Protein Synthesis

• 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.

3
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
Ca
?
C
?
N
O
C
N
?
N
?
Ca
C
?
Ca
?
O
-1800 ? 1800
-1800 ? 1800
4
From Sequence to Structure

• Structure Hierarchies
• Secondary structure local conformation of some
  part of the polypeptide.
• ß Sheet

a Helix
Parallel
Anti Parallel
5
From Sequence to Structure

• Structure Hierarchies
• Tertiary structure the overall
  3-dimensional arrangement of all the atoms in the
  protein.

6
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
7
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 over the VDW
  surface.
• Relative accessibility (SAS)/(maxSAS)
• maxSAS SAS(Gly-X-Gly)

8
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 residues center of mass, and
  counting the number of residues falling inside
  this sphere.
• Usually done with different cutoff radii.

9
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 AAs backbone can take up 10
different conformations, defined by ? and ?
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.
10
From Sequence to Structure

• Folding Models
• The Backbone-Centric view

• Sequence order dependent interactions (?? -
  propensities and H-bonds), produce local
  secondary structure elements (SSEs).
• Local SSEs later overgo longer-range interactions
  to form supersecondary structures.
• Supersecondary structures of ever-increasing
  complexity thus grow, ultimately into the native
  conformation.

11
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.
• 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.

Molten globule states
12
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

13
From Sequence to Structure

• Folding Models
• Post-translational Vs. Co-translational

14
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.

15
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.

16
Structure Similarity

• Protein Families
• Structures seem to be preserved much more than
  sequences, which is easily explainable due to
  neutral mutations.

Rigid Ca Alignment RMSD 1.26Å
17
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.

18
Structure Prediction

• Homology (Comparative) Modeling
• Guideline At least 30 sequence identity is
  needed between probe and template.
• Template Assignment creating a robust
  probe-template alignment (PWA/MSA).
• Model Construction
• Generation of coordinates for conserved segments
  superimposing/averaging/restrain
  based.
• Generation of coordinates for variable segments
  
  DB scanning/Ab Initio/restrain
  based.
• Generation of coordinates for sidechain atoms
  
  superimposing/rotamer libraries/restrain based.
• Model Evaluation
• 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.

Peitsch et al. (1999)
19
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/physico-chemical
  environment SS type, solvent accessibility,
  coordination number, etc
• Profile construction encoding the templates 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.

But No adjustments to the template profile can
be made thus substantial rearrangements are
ignored
20
Structure Prediction

• Ab Initio Techniques
• Simulating the folding process
• Simplifying the energy landscape
• Reducing the number of degrees of freedom
• Representing a group of atoms by a single atom.
• Reducing the number of atom interactions.
• Sampling the conformation space
• Monte Carlo sampling.
• Genetic Algorithm.
• Simulated Annealing.
• Hierarchical folding simulation.

21
Blind Prediction

• Critical Assessment of Protein Structure
  Prediction CASP
• 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).