Download CHAPTER 4 Proteins: Structure, Function, Folding

Protein Structure: Nature’s Robots
Lectures 7 and 8
Chem 464 Spring 2017
Abrol Section
1
CHAPTER 4
Proteins: Structure, Function, Folding
Learning goals:
– Structure and properties of the peptide bond
– Structural hierarchy in proteins
• Primary, Secondary, Tertiary, Quaternary
• Primary and Secondary structure building blocks.
– Structure and function of fibrous proteins
– Structure analysis of globular proteins
– Protein folding and denaturation
Structure of Proteins
• Unlike most organic polymers, protein molecules
adopt a specific three-dimensional conformation.
• This structure is able to fulfill a specific biological
function
• This structure is called the native fold
• The native fold has a large number of favorable
interactions within the protein
• There is a cost in conformational entropy of folding
the protein into one specific native fold
Favorable Interactions in Proteins
• Hydrophobic effect
– Release of water molecules from the structured solvation layer around
the molecule as protein folds increases the net entropy
• Hydrogen bonds
– Interaction of N-H and C=O of the peptide bond leads to local regular
structures such as α-helices and β-sheets
• London dispersion
– Medium-range weak attraction between all atoms contributes
significantly to the stability in the interior of the protein
• Electrostatic interactions
– Long-range strong interactions between permanently charged groups
– Salt-bridges, esp. buried in the hydrophobic environment strongly
stabilize the protein
Levels of Protein Structure
Sequence
Structure
Globular
Proteins
Membrane
Proteins
Primary Structure of Proteins
Primary Structure of Proteins
Lone Amino Acid
Amino Acid
In Protein
Structure of the Peptide Bond
• Structure of the protein is partially dictated by
the properties of the peptide bond
• The peptide bond is a resonance hybrid of two
canonical structures
• The resonance causes the peptide bonds
– to be less reactive compared to esters, for
example
– to be quite rigid and nearly planar
– to exhibit a large dipole moment in the
favored trans configuration
Resonance in the Peptide Bond
Was amide C-N bond length a clue?
Bond
Bond Length
C-C
1.54 Å
C-C Benzene
1.40 Å
C=C
1.34 Å
C≡C
1.20 Å
C-N
1.49 Å
C-N Amide
1.32 Å
C=N
1.27 Å
C≡N
1.14 Å
Bond Type
Single
Resonant
Double
Triple
Single
Resonant
Double
Triple
The Rigid Peptide Plane and
the Partially Free Rotations
• Rotation around the peptide bond is not permitted
• Rotation around bonds connected to the alpha carbon
is permitted
• φ (phi): angle around the α-carbon—amide nitrogen
bond
• ψ (psi): angle around the α-carbon—carbonyl carbon
bond
• In a fully extended polypeptide, both ψ and φ are 180°
The polypeptide is made up of a series of
planes linked at α carbons
Secondary Structures
• Secondary structure refers to a local spatial
arrangement of the polypeptide backbone
• Two regular arrangements are common:
• The α helix
– stabilized by hydrogen bonds between nearby residues
• The β sheet
– stabilized by hydrogen bonds between adjacent
segments that may not be nearby
• Irregular arrangement of the polypeptide chain is
called the random coil
The α Helix
• Helical backbone is held together by hydrogen bonds
between the backbone amides of an n and n+4
amino acids
• Right-handed helix with 3.6 residues (5.4 Å) per turn
• Peptide bonds are aligned roughly parallel with the
helical axis
• Side chains point out and are roughly perpendicular
with the helical axis
What is a right-handed helix?
The α Helix: Top View
• The inner diameter of the helix (no side chains) is
about 4–5 Å
•
Too small for anything to fit “inside”
• The outer diameter of the helix (with side chains) is
10–12 Å
•
Happens to fit well into the major groove of dsDNA
• Residues 1 and 8 align nicely on top of each other
• What kind of sequence gives an α helix with one
hydrophobic face?
Secondary Structure of Proteins: α-Helix
C=O (nth) --- H—N (n+4th) hydrogen bond
n+4 = α Helix
n+3 = 310 Helix
n+5 = π Helix
Sequence affects helix stability
• Not all polypeptide sequences adopt α-helical structures
• Small hydrophobic residues such as Ala and Leu are
strong helix formers
• Pro acts as a helix breaker because the rotation around
the N-Ca bond is impossible
• Gly acts as a helix breaker because the tiny R-group
supports other conformations
• Attractive or repulsive interactions between side chains
3–4 amino acids apart will affect formation
The Helix Dipole
• Recall that the peptide bond has a strong dipole
moment
– Carbonyl O negative
– Amide H positive
• All peptide bonds in the α helix have a similar
orientation
• The α helix has a large macroscopic dipole moment
• Negatively charged residues often occur near the
positive end of the helix dipole
α-Helix: Dipole Moment
i
i+4
α-Helix: Coiled-Coil Structure
Residues a and d : Nonpolar
Residues b, c, e, f, g : Polar
β Sheets
• The planarity of the peptide bond and tetrahedral
geometry of the α-carbon create a pleated sheet-like
structure
• Sheet-like arrangement of backbone is held together by
hydrogen bonds between the backbone amides in
different strands
• Side chains protrude from the sheet alternating in up
and down direction
Secondary Structure of Proteins: β-Sheet
Parallel and Antiparallel β Sheets
• Parallel or antiparallel orientation of two chains
within a sheet are possible
• In parallel β sheets the H-bonded strands run in
the same direction
– Resulting in bent H-bonds (weaker)
• In antiparallel β sheets the H-bonded strands run
in opposite directions
– Resulting in linear H-bonds (stronger)
Secondary Structure of Proteins: β-Sheet
Antiparallel β sheet
Parallel β sheet
β Turns
• β turns occur frequently whenever strands in β sheets
change the direction
• The 180° turn is accomplished over four amino acids
• The turn is stabilized by a hydrogen bond from a
carbonyl oxygen to amide proton three residues down
the sequence
• Proline in position 2 or glycine in position 3 are
common in β turns
Ramachandran Plot for Secondary Structures
ψ
φ
G.N. Ramachandran, C. Ramakrishnan & V. Sasisekharan (1963): Stereochemistry of polypeptide chain configurations. In: J. Mol. Biol. vol. 7, p. 95-99.
Distribution of φ and ψ Dihedral Angles
• Some φ and ψ combinations are very unfavorable because of
steric crowding of backbone atoms with other atoms in the
backbone or side chains
• Some φ and ψ combinations are more favorable because of
chance to form favorable H-bonding interactions along the
backbone
• A Ramachandran plot shows the distribution of φ and ψ
dihedral angles that are found in a protein
• shows the common secondary structure elements
• reveals regions with unusual backbone structure
Ramachandran Plot
Secondary Structure: Amino Acid Propensities
Helix Breakers
Proline Isomers
• Most peptide bonds not involving proline are in the trans
configuration (>99.95%)
• For peptide bonds involving proline, about 6% are in the
cis configuration. Most of this 6% involve β-turns
• Proline isomerization is catalyzed by proline isomerases
Circular Dichroism (CD) Analysis
• CD measures the molar absorption difference ∆ε of leftand right-circularly polarized light: ∆ε = εL – εR
• Chromophores in the chiral environment produce
characteristic signals
• CD signals from peptide bonds depend on the chain
conformation
Group Discussion
• There is a transmembrane α-helix with 28 amino
acids that spans the cell membrane exactly. What is
the width of the cell membrane?
• Why can the Proline residue be considered a helix
breaker? Draw to explain your answer.
• Why is large portion of Ramachandran space empty
for proteins?
Protein Tertiary Structure
• Tertiary structure refers to the overall spatial
arrangement of atoms in a protein
• Stabilized by numerous weak interactions between
amino acid side chains.
− Largely hydrophobic and polar interactions
− Can be stabilized by disulfide bonds
• Interacting amino acids are not necessarily next to
each other in the primary sequence.
• Two major classes
– Fibrous and globular (water or lipid soluble)
Fibrous Proteins
Fibrous Proteins
Globular Proteins
Water-soluble (Soluble Proteins)
Lipid-soluble (Membrane Proteins)
Fibrous Proteins:
From Structure to Function
Structure of α-Keratin in Hair
Chemistry of Permanent Waving
Structure of Collagen
• Collagen is an important constituent of connective
tissue: tendons, cartilage, bones, cornea of the eye
• Each collagen chain is a long Gly- and Pro-rich lefthanded helix
• Three collagen chains intertwine into a right-handed
superhelical triple helix
• The triple helix has higher tensile strength than a steel
wire of equal cross section
• Many triple-helices assemble into a collagen fibril
Collagen Fibrils
Silk Fibroin
• Fibroin is the main protein in silk from moths and
spiders
• Antiparallel β sheet structure
• Small side chains (Ala and Gly) allow the close
packing of sheets
• Structure is stabilized by
– hydrogen bonding within sheets
– London dispersion interactions between sheets
Spider Silk
• Used for webs, egg sacks, and wrapping the
prey
• Extremely strong material
– stronger than steel
– can stretch a lot before breaking
• A composite material
– crystalline parts (fibroin-rich)
– rubber-like stretchy parts
Supersecondary Structures
(Motifs or Folds)
• Specific arrangement of several secondary
structure elements
– All alpha-helix
– All beta-sheet
– Both
• Motifs can be found as reoccurring structures in
numerous proteins
• Proteins are made of different motifs folded
together
Supersecondary Structures (Motifs)
β-hairpin
Greek Key
Helix-turn-Helix
Jelly Roll
β−β−α (Zinc Finger)
Conservation of Supersecondary Motifs
(Helix-loop-Helix)
Yeast (Green)
Drosophila (Red)
DNA Binding Domains (Homeodomains) of organisms separated by a BILLION years!
Black dots (•) mark conserved residues.
Secondary Structure Packing
(Tertiary Structure Classification)
1. Alpha proteins (α)
2. Beta proteins (β)
3. Alpha and beta proteins
(α/β)
Mainly parallel beta sheets (betaalpha-beta units)
(α+β)
Mainly antiparallel beta sheets
(segregated alpha and beta regions)
4. Multi-domain proteins
(alpha and beta)
Folds consisting of two or more
domains belonging to different classes
5. Membrane and cell surface proteins
and peptides
Driving Force for Tertiary Structures (Globular Proteins)
I. Compact structures that minimize the
exposure of hydrophobic residues to solvent.
(the hydrophobic effect)
Driving Force for Tertiary Structure (Globular Proteins)
II. Buried H-bonding and salt-bridge groups should be paired up.
Tertiary Structure Highlights
Serine proteases
Myoglobin
NAD Binding Domain and Immunoglobin
Quaternary Structure
• Quaternary
structure is formed by the assembly of
individual polypeptides into a larger functional cluster
Quaternary Structures
Same driving forces apply as
in tertiary structure formation.
Hydrophobic Effect
Polar Residue Pairing
More H-bonds found buried!
Nature uses symmetry so
optimal use of resources!
Quaternary Structure Highlights
• Two identical protein subunits
binding together to form a
symmetric protein dimer.
• The Cro repressor protein from
bacteriophage lambda binds to
DNA to turn off viral genes.
• Its two identical subunits bind
head-to-head, held together by a
combination of hydrophobic
forces (blue) and a set of
hydrogen bonds (yellow region).
• Hemoglobin made of
2 α-globin (red) and
2 β-globin (blue) units.
• Heme group that binds to
Oxygen shown in Green.
Quaternary Structure Highlights
The Src protein with four different domains
• Two of the domains form a protein kinase enzyme.
• The other two (SH2 and SH3) domains perform
regulatory functions.
• ATP substrate in RED.
• The site that binds ATP is positioned at the interface
of the two domains that form the kinase.
Quaternary Structure Highlights
The enzyme neuraminidase exists as a
ring of four identical polypeptide chains.
The small diagram shows how the
repeated use of the same binding
interaction forms the structure.
Four fibronectin type 3 modules
from the extracellular matrix
molecule fibronectin form a linear
quaternary structure.
Viruses (Quaternary and a lot more!)
Capsids of some viruses:
(A) Tomato bushy stunt virus; (B) poliovirus
(C) simian virus 40 (SV40); (D) satellite tobacco necrosis virus.
Structure of a Spherical Virus
Identical protein subunits pack together
to create a spherical shell (a capsid)
that encloses the viral genome,
composed of either RNA or DNA.
For geometric reasons, no more than 60
identical subunits can pack together in a
precisely symmetric way.
The tomato bushy stunt virus (TBSV)
shown here, for example, is a spherical
virus about 33 nm in diameter formed
from 180 identical copies of a 386
amino acid capsid protein plus an RNA
genome of 4500 nucleotides.
To construct such a large capsid, the
protein must be able to fit into three
somewhat different environments, each
of which is differently colored in the
virus particle shown here.
Protein Structure Methods:
X-Ray Crystallography
Steps needed
• Purify the protein
• Crystallize the protein
• Collect diffraction data
• Calculate electron density
• Fit residues into density
Pros
• No size limits
• Well-established
Cons
• Difficult for membrane proteins
• Cannot see hydrogens
Structure Methods:
Biomolecular NMR
Steps needed
• Purify the protein
• Dissolve the protein
• Collect NMR data
• Assign NMR signals
• Calculate the structure
Pros
• No need to crystallize the protein
• Can see many hydrogens
Cons
• Difficult for insoluble proteins
• Works best with small proteins
Intrinsically Disordered Proteins
• Contain protein segments that lack definable
structure
• Composed of amino acids whose higher
concentration forces less-defined structure
– Lys, Arg, Glu, and Pro
• Disordered regions can conform to many
different proteins, facilitating interaction with
numerous different partner proteins
Intrinsically Disordered Proteins
Proteostasis
Maintenance of cellular protein activity is accomplished
by the coordination of many different pathways.
Protein Stability and Folding
• A protein’s function depends on its 3D-structure
• Loss of structural integrity with accompanying loss of
activity is called denaturation
• Proteins can be denatured by:
• heat or cold
• pH extremes
• organic solvents
• chaotropic agents: urea and guanidinium
hydrochloride
Ribonuclease Refolding Experiment
• Ribonuclease is a small protein that contains 8 cysteines linked
via four disulfide bonds
• Urea in the presence of 2-mercaptoethanol fully denatures
ribonuclease
• When urea and 2-mercaptoethanol are removed, the protein
spontaneously refolds, and the correct disulfide bonds are
reformed
• The sequence alone determines the native conformation
• Quite “simple” experiment, but so important it earned Chris
Anfinsen the 1972 Chemistry Nobel Prize
How can proteins fold so fast?
• Proteins fold to the lowest-energy fold in the
microsecond to second time scales. How can they
find the right fold so fast?
• It is mathematically impossible for protein folding to
occur by randomly trying every conformation until
the lowest-energy one is found (Levinthal’s paradox)
• Search for the minimum is not random because the
direction toward the native structure is
thermodynamically most favorable
Proteins folding follow distinct paths
Proteins folding follow distinct paths
Protein Folding Movie
Simulation of millisecond protein folding: NTL9
(from Folding@home)
Chaperones prevent misfolding
Chaperonins facilitate folding
Protein misfolding is the basis of numerous
human diseases
Group Discussion
• Curling or straightening of hair is permanent. Why?
• Second "For Thought" Video:
Simulation of millisecond protein folding: NTL9 (from
Folding@home)
If one of the amino acids in this protein was mutated
to a different amino acid (like in a disease), how may
this mutation affect the protein structure as well as
function or even cause disease?
Ser  Thr
Ser  Pro
Leu Ile
Ala  Ser
Asp  Glu
Asp  Arg
Gly  Ala
Trp  Phe
Group Discussion: Effect of mutation
Ser  Thr
Ser  Pro
Leu Ile
Ala  Ser
Asp  Glu
Asp  Arg
Gly  Ala
Trp  Phe
Chapter 4: Summary
• the two most important secondary structures
– α helices
– β sheets
• tertiary and quaternary structures
• how properties and function of fibrous proteins are
related
• how to determine three-dimensional structures of
proteins
• how proteins fold?