structure and stability of globular proteins n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Structure and stability of globular proteins. PowerPoint Presentation
Download Presentation
Structure and stability of globular proteins.

Loading in 2 Seconds...

play fullscreen
1 / 40

Structure and stability of globular proteins. - PowerPoint PPT Presentation


  • 182 Views
  • Uploaded on

Structure and stability of globular proteins. Aliphatic amino acids and Gly. Cyclic Imino Acid: Proline. Hydroxyl amino acids. Acidic amino acids. Amide amino acids. Basic amino acids. Histidine. Sulfur-containing amino acids. Aromatic amino acids.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Structure and stability of globular proteins.' - alec


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
protein folding anfinsen s experiments

Protein folding.Anfinsen’s experiments.

Assumption: amino acid sequence completely and uniquely determines the protein tertiary structure.

Protein folding problem: find native conformation among the large number of alternative conformations.

Ex: polypeptide chain of 100 residues can have ~ 9^100 different conformations.

native proteins are marginally stable
Native proteins are marginally stable.

Scale of interactions in proteins:

- Interactions less than kT~0.6 kcal/mol

are neglected.

- ΔG ~ 5 - 20 kcal/mol

Potential energy = Van der Waals + Electrostatic + …

G

U

F

ΔG

Reaction coordinate

electrostatic force
Electrostatic force.

Coulomb’s law for two point charges in a vacuum:

q – point charge,

ε – dielectric constant

ε = 2-3 inside the protein,

ε = 80 in water

Na+

Cl-

d = 2.76 Å,

E = 120 kcal/mol

dipolar interactions
Dipolar interactions.

- 0.42

Dipole moment:

O

+0.42

C

Interaction energy of two dipoles separated by the vector r:

-0.20

N

Peptide bond:

μ = 3.5D,

Water molecule:

μ = 1.85D.

+0.20

H

van der waals interactions
Van der Waals interactions.

E (kcal/mol)

Lennard-Jones potential:

0.2

repulsion

0

attraction

- 0.2

2

4

6

8

10

12

Distance between centers of atoms

van der waals interactions1
Van der Waals interactions.

Three major types of interactions:

  • between two permanent dipoles
  • between a permanent and an induced dipole
  • between mutually induced dipoles
hydrogen bonding patterns in globular proteins
Hydrogen bonding patterns in globular proteins.

1. Most HB are local, close in sequence.

2. Most HB are between backbone atoms.

3. Most HB are within single elements of secondary structure.

4. Proteins are almost equally saturated by HB: 0.75 bond per amino acid.

disulfide bonds
Disulfide bonds.

PROTEIN + GS-SG PROTEIN + GSHPROTEIN + 2GSH

SH

HS

SH

S-SG

- Breakdown and formation of S-S bonds are catalyzed by disulfide isomerase.

- In the cell S-S bonds are reversible, the energetic equilibrium is close to zero.

- Secreted proteins have a lot of S-S bonds since outside the cell the equilibrium is shifted towards their formation.

properties of water
Properties of water.

O

HB determines properties of water:

- tetrahedral structure of ice, 4 HB neighbors,

very open lattice.

- liquid water forms HBonded “icebergs”.

Unusual physical properties:

- water expands when it freezes at 0 C. When ice is melted and then warmed, the liquid continues to contract upto 4C.

- water has high melting and boiling points, large heat capacity.

0.957 Å

104.5°

H

H

hydrophobic effect
Hydrophobic effect.

H

Hydrophobic interaction – tendency of

nonpolar compounds to transfer from an

aqueous solution to an organic phase.

  • The entropy of water molecules decreases when they make a contact with a nonpolar surface (TΔS = -9.6 kcal/mol for cyclohexane) .
  • The effect is entropic because the energy of HB is very high.
  • The hydrophobic effect is proportional to buried surface area, the energy is ~ 20-25 cal/mol/A^2

O

H

O

H

H

protein folding step by step
Protein folding: step by step.

Disordered globule: hydrophobic – inside, hydrophilic - outside

Extended chain

Native highly ordered conformation

hierarchy of protein structure
Hierarchy of protein structure.
  • Amino acid sequence
  • Secondary structure
  • Tertiary structure
  • Quaternary structure

Picture from Branden & Tooze “Introduction to protein structure”

right handed alpha helix
Right-handed alpha-helix.
  • Helix is stabilized by HB between backbone –NH and backbone carbonyl atom.
  • Geometrical characteristics:
  • 3.6 residues per turn
  • translation of 5.4 Å per turn
  • translation of 1.5 Å per residue
loop regions are at the surface of protein molecules
Loop regions are at the surface of protein molecules.

Adjacent antiparallel β-strands are joined by hairpin loops.

Loops are more flexible than helices and strands.

Loops can carry binding and active sites, functionally important sites.

Branden & Tooze “Introduction to protein structure”

fibrous proteins
Fibrous proteins.
  • Have extended structures, regular conformations, insoluble.
  • Basis for regularities in structure is in regularities in sequence.
  • Coiled coils (heptad repeats in sequence).
  • Collagen triple helix (every third residue is Gly).
classwork i cn3d viewer
Classwork I: CN3D viewer.
  • Go to http://ncbi.nlm.nih.gov
  • Select alpha-helical protein (hemoglobin)
  • Select beta-stranded protein (immunoglobulin)
  • Select multidomain protein 1I50, chain “A”
  • View them in CN3D
pdb databank
PDB databank.
  • Archive of protein crystal structures was established in 1971 with several structures.

in 2002 – 17000 structures including NMR structures

  • Data processing: data deposition, annotation and validation
  • PDB code – nXYZ, n – integer, X, Y, Z -characters
content of data in the pdb
Content of Data in the PDB.
  • Organism, species name
  • Full protein sequence
  • Chemical structure of cofactors and prosthetic groups
  • Names of all components of the structure
  • Qualitative description of the structural characteristics
  • Literature citations
  • Three-dimensional coordinates
protein secondary structure prediction
Protein secondary structure prediction.

Assumptions:

  • There should be a correlation between amino acid sequence and secondary structure. Short aa sequence is more likely to form one type of SS than another.
  • Local interactions determine SS. SS of a residues is determined by their neighbors (usually a sequence window of 13-17 residues is used).

Exceptions: short identical amino acid sequences can sometimes be found in different SS.

Accuracy: 65% - 75%, the highest accuracy – prediction of an α helix

methods of ss prediction
Methods of SS prediction.
  • Chou-Fasman method
  • GOR (Garnier,Osguthorpe and Robson)
  • Neural network method
chou fasman method
Chou-Fasman method.

Amino acid itself determines the type of secondary structure, which it is likely to adopt.

Analysis of frequences for all amino acids to be in different types of SS.

Ala, Glu, Leu and Met – strong predictors of alpha-helices,

Pro and Gly predict to break the helix.

Prediction of an alpha-helix - if four of six adjacent amino acids have high probability to be a helix.

Prediction of a beta-strand – if three of five adjacent amino acids have high probability to be a strand.

gor method
GOR method.

Assumption:formation of SS of an amino acid is determined by the neighboring residues (usually a window of 17 residues is used).

GOR uses principles of information theory for predictions.

Method maximizes the information difference between two competing hypotheses: that residue “a” is in structure “S”, and that “a” is not in conformation “S”.

neural network method
Neural network method.

Input layer

Input sequence window

Output layer

Predicted SS

Hidden layer

L

A

W

P

G

E

V

G

A

S

T

Y

P

α

Si

Hj

Oi

1

β

0

coil

0

WijSj

HjOi

phd neural network program with multiple sequence alignments
PHD – neural network program with multiple sequence alignments.
  • Blast search of the input sequence is performed, similar sequences are collected.
  • Multiple alignment of similar sequences is used as an input to a neural network.
  • Sequence pattern in multiple alignment is enhanced compared to if one sequence used as an input.
classwork
Classwork
  • Go to http://ncbi.nlm.nih.gov, search for protein “flavodoxin” in Entrez, retrieve its amino acid sequence.
  • Go to http://cubic.bioc.columbia.edu/predictprotein and run PHD on the sequence.