Tema 3.

Estructura tridimensional de les proteínes

• Nivells d'estructuració de les proteïnes.

• Descripció de l'hèlix alfa i fulla plegada beta.

• Proteïnes fibroses i globulars.

• Plegament de proteïnes.

• Estructura quaternària.

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 ❖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 an entropy cost to folding the protein into one specific native
fold.

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 ❖ Four Levels of Protein Structure

I. Primary Structure: The Peptide Bond

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II. Secondary Structures

➢ The 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 quite rigid and nearly planar
✓ To exhibit a large dipole moment in the favored trans configuration

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 The Rigid Peptide Plane and the Partially Free Rotations

➢ Rotation around the peptide bond is not permitted due to resonance

structure.
➢ Rotation around bonds connected to the  carbon is permitted.
✓ φ (phi): angle around the  carbon—amide nitrogen bond
✓ ψ (psi): angle around the  carbon—carbonyl carbon bond

➢ The organization around the peptide bond, paired with the identity of the
R groups, determines the secondary structure of the protein.

➢ Secondary structures are regular structures elements.

➢ The main chain is relatively polar having a hydrogen donor (NH) and a
hydrogen acceptor (C=O) for peptide unit
➢ Polar groups of the main chain are neutralized forming hydrogen bonds.

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➢ Secondary structure refers to a local spatial arrangement of the polypeptide
backbone.
➢ Two regular arrangements are common:
✓ The  helix
▪ stabilized by hydrogen bonds between nearby residues
✓ The  sheet
▪ Stabilized by hydrogen bonds between adjacent segments that may not be nearby
An additional structure called  -Turn.

➢ Irregular arrangement of the polypeptide chain is called the random coil.

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 II. Secondary Structures C-terminal

II. 1. The  Helix

5 It is a right-handed helix with

3.6 residues (5.4 Å) per turn.
Helical backbone is held together by 4
hydrogen bonds between backbone 3
oxygen of an n residue and
backbone amide of n + 4 residue 2
1 Hydrogen bonds are aligned
What Is a Right-Handed Helix? roughly parallel with the
helical axis.

N-terminal

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 Sequence Affects Helix Stability
Propensity of Amino Acid
TABL
Residues to Take Up an α-
E 4-2
Helical Conformation
➢ Not all polypeptide sequences adopt -helical structures.
ΔΔG°
➢ Small hydrophobic residues such as Ala and Leu are strong Amino
acid
ΔΔG°
(kJ/mol)a
Amino
acid
(kJ/mol
helix formers. )a
Ala 0 Leu 0.79
➢ Pro acts as a helix breaker because the rotation around the
Arg 0.3 Lys 0.63
N-Cα (φ-angle) bond is impossible.
Asn 3 Met 0.88
➢ Gly acts as a helix breaker because the tiny R group Cys 3 Pro >4
supports other conformations.
Gln 1.3 Ser 2.2
➢ Attractive or repulsive interactions between side chains 3 Glu 1.4 Thr 2.4
to 4 amino acids apart will affect formation. Gly 4.6 Tyr 2.0
His 2.6 Trp 2.0
Ile 1.4 Val 2.1
Sources: Data (except proline) from J. W. Bryson
et al., Science 270:935, 1995. Proline data from
J. K. Myers et al., Biochemistry 36:10,923, 1997.
aDDG° is the difference in free-energy change,

relative to that for alanine, required for the

amino acid residue to take up the α-helical
conformation. Larger numbers reflect greater
difficulty taking up the α-helical structure. Data
are a composite derived from multiple
experiments and experimental systems.
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 II. Secondary Structures

II.2.  -Sheets
➢The planarity of the peptide bond and tetrahedral
geometry of the  carbon create a pleated sheet-like
structure.

➢Sheet-like arrangement of the backbone is held

together by hydrogen bonds between the backbone
amides in different strands.

➢Side chains protrude from the sheet, alternating in an

up-and-down direction.

Peptide bond 9
 Parallel and Antiparallel  Sheets
➢ Multi -strand interactions are called sheets.
➢ Sheets are held together by the hydrogen bonding of amide and carbonyl
groups of the peptide bond from opposite strands.
➢ Two major orientations of  sheets are determined by the directionality of the
strands within:
✓Parallel sheets have strands that are oriented in the same direction.
✓Antiparallel sheets have strands that are oriented in opposite directions.

➢ In parallel  sheets, the H-bonded strands run in the same direction.

✓Hydrogen bonds between strands are bent (weaker).
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 ➢ In antiparallel  sheets, the H-bonded strands run in opposite directions.
▪ Hydrogen bonds between strands are linear (stronger).

II.3.  Turns
➢  turns occur frequently whenever strands in  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
 turns.
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 III. Protein Tertiary Structures

➢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)
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 ❖ Fibrous Proteins: From Structure to Function
➢ Just an element of secondary structure
✓ Insoluble (high number of hydrophobic residues)
✓ Function: Structural

TABLE 4-3 Secondary Structures and Properties of Some Fibrous Proteins

Structure Characteristics Examples of occurrence

α Helix, cross-linked by Tough, insoluble protective α-Keratin of hair, feathers, nails

disulfide bonds structures of varying hardness and
flexibility
β Conformation Soft, flexible filaments Silk fibroin
Collagen triple helix High tensile strength, without stretch Collagen of tendons, bone matrix

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 Fibrous Proteins: From Structure to Function
1. Structure of -Keratin in Hair

➢ Elongated α helix with somewhat thicker elements near the amino and carboxyl termini.
➢ Pairs of these helices are interwound in a left-handed sense to form two-chain coiled
coils.
➢ These then combine in higher-order structures called protofilaments and protofibrils.
➢ about four protofibrils—32 strands of α-keratin in all—combine to form an intermediate
filament.
➢ Disulfur bridges stabilize structure

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 Fibrous Proteins: From Structure to Function
2. Structure of Collagen

➢ Pro acts as an α helix breaker because the rotation around

the N-Cα (φ-angle) bond is impossible.
➢ But polyPro can form a left-handed helix with 3 residues for
turn.
➢ Modified to hydroxiPro can form hydrogen bonds stabilizing
the helix

➢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 left-handed
helix. Repetitions of Gly-X-Pro(4-Hyp).
➢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
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 2. Structure of Collagen
a) Hydroxyproline in Collagen

Proline HydroxyProline
➢ Forces the proline ring into a favorable pucker
➢ Offers more hydrogen bonds between the three strands of collagen

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 Fibrous Proteins: From Structure to Function
3. Silk Fibroin

➢ Extremely strong material

✓ stronger than steel
✓ rigid structure and tensile strength
➢ Fibroin is the main protein in silk from moths and spiders.
➢ Antiparallel  sheet structure side chains (Ala and Gly) allow the close packing of
sheets.
➢ Structure is stabilized by:
✓ hydrogen bonding within sheets
✓ London dispersion interactions between sheets

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 ❖ Water-Soluble Globular Proteins
➢ Globular protein structures are compact and varied

❖ Motifs (folds) (supersecondary structure)

➢ They are specific arrangement of several secondary structure
elements
✓ all  helix
✓ all  sheet
✓ both
➢ Motifs can be found as recurring structures in numerous
proteins.
➢ Globular proteins are composed of different motifs folded
together.
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 ❖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.

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 4. Quaternary Structure

➢ A quaternary structure is formed by the assembly of individual polypeptides

into a larger functional cluster.

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 ❖ Protein 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 (interfere weak interactions)

Example: Ribonuclease Refolding Experiment

➢ Ribonuclease is a small protein that contains eight Cys 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.
➢ The experiment is quite “simple” but so important it earned Chris Anfinsen
the 1972 Chemistry Nobel Prize.
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 Chaperones Prevent Misfolding and Aggregation of Unfolded Peptides

➢ The chaperones do not actively promote the folding of the

substrate protein, but instead prevent aggregation of
unfolded peptides.

➢ For a population of polypeptide molecules, some fraction

of the molecules released at the end of the cycle are in the
native conformation.

Protein Misfolding Is the Basis of Numerous Human Diseases

➢ Native (correctly folded)  amyloid is a soluble globular protein,

➢ Misfolded  amyloid promotes aggregation at newly exposed protein-
protein interface.
➢ Correctly folded helices are lost and peptides form  strands,  helices,
and  sheets.

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