Lecture 19 (Dobbek) Flashcards
Building Blocks - Protein Structure (32 cards)
Overview of Molecule Interactions
Typical ranges for bond energies of side chain interactions
Overview of Molecule Interactions
- Logarithmic scale applied
- Covalent bonds have the highest stability among chemical bonds.
- Weak bonds, despite their lower stability, play a important role in protein dynamics and interactions.
- Ionic interactions extend over longer distances
Hydrogen bonds
Interaction
Hydrogen bonds
- The hydrogen atom has a partial positive charge.
- The acceptor atom (e.g., oxygen or nitrogen) has lone pairs of electrons (negative charge).
- The hydrogen gets “pulled” towards the lone electrons of the acceptor.
- Most significant interactions in molecular biology.
- Involves two electronegative atoms (e.g., O, N) and one proton.
- Polar bonds create partial charges that facilitate interaction.
Structural Characteristics
- Reasonably stable under optimal conditions.
- Strength depends on the angle between donor and acceptor atoms and the distance between them.
- The hydrogen atom points towards the non-bonding electrons of the acceptor.
Specific Roles of Atoms
- Oxygen (O) or Nitrogen (N) act as hydrogen acceptors.
- Carbon (C) cannot act as an acceptor due to its lack of polarity (not partially negative).
Low Barrier Hydrogen Bond (LBHB):
- Standard H-bond: Proton stays mostly with the donor; energy barrier to the acceptor is high.
- Equal sharing: The proton has an equal chance of being with the donor or the acceptor, but it still “chooses” one at a time—it jumps back and forth.
- LBHB : The proton is truly shared simultaneously between the donor and acceptor because the energy barrier is effectively gone, creating a more stable bond.
Hydrogen bonds and the Hydrophobic effect
Hydrogen bonds with non-polar parts
- Water is polar and can’t interact well with non-polar (hydrophobic) surfaces.
- To keep their hydrogen bonds, water molecules form a “cage” around the non-polar surface, but this cage limits water’s ability to move freely, which is unfavorable.
Hydrophobic Effect
- To avoid the costly cage structure, non-polar surfaces (or molecules) group together.
- By clustering, they expose less surface to water, which reduces the amount of water stuck in the cage structure.
Entropy (∆S)
- Water molecules like to move freely (disorder = high entropy).
- When proteins interact and push out water molecules, those water molecules become free to move, increasing disorder (higher entropy), which makes the interaction favorable.
Ionic interactions (salt bridges)
Interactions
Ionic interactions (salt bridges)
- occur between positive and negative charged groups in a molecule (often between aminoacids)
- The strength of the interaction depends on the distance r. As distance increases, the energy of the interaction decreases.
- Ionic interactions can work over longer distances compared to other forces, making them effective when other interactions are no longer significant.
- The dielectric constant D measures how much weaker the interaction becomes when moved from a vacuum to a medium (e.g., water). In non-vacuum environments, the medium dampens the charges, weakening the interaction.
- Salt bridges are important stabilizers in protein structures because they maintain strong ionic interactions even in dampening environments like within cells.
- Coulomb’s law: Opposite charges attract, and the force is stronger when they are closer. The surrounding medium (like water) weakens this attraction based on the dielectric constant (D)
Van-der-Waals Forces
Interactions
Van-der-Waals Forces
- weak, non-covalent interactions that occur between atoms or molecules due to temporary or permanent dipoles.
- They are individually weak but become significant when summed up over many atoms or molecules.
- Include all dipole-dipole interactions, both permanent and temporary.
- London dispersion forces occur when temporary dipoles are induced between non-polar groups.
- The optimal distance between interacting atoms is 2-3 Å:
- If they are too far, the interaction weakens.
- If they are too close, they repel.
- Example: Aromatic groups interact through van der Waals forces. Aromatic groups are polar because the ring current creates:
- A negative partial charge above and below the ring.
- A positive charge along the edges of the ring.
Disulfide Bridges
Interactions
Disulfide Bridges
- Disulfide bridges are strong covalent interactions that form between the side chains of two cysteine residues
- They occur when two cysteines are oxidized, forming a disulfide bond (S-S)
- The bond forms at a specific geometry, requiring a 90° angle between the sulfur-carbon bonds.
- These bridges stabilize the structure of extracellular proteins, as the external environment is more oxidizing.
- Cytoplasmic proteins are not stabilized by disulfide bridges because the cytoplasm is a reducing environment, which prevents the formation of disulfide bonds by keeping cysteines in their reduced (S-H) form.
L-Amino Acids
Primary structure
L-Amino Acids
- The alpha carbon is attached to four different groups: carboxyl group (CO), amino group (N), hydrogen (H), and side chain (R).
- This makes the carbon chiral, meaning it has two mirror image forms (L-form and D-form) that cannot be aligned.
- Proteins in nature use only the L-form.
To determine chirality
- Arrange the molecule with the hydrogen pointing away.
- Follow the order CO → R → N:
- Clockwise: L-form.
- Counterclockwise: D-form.
Hydrophobic (non polar) amino acids
Primary structure: L-amino acids
Hydrophobic (non polar) amino acids
- Hydrophobic amino acids have side chains made primarily of carbon and hydrogen (C-H), making them non-polar.
Glycine is unique because
- It’s not chiral (does not have an L-form).
- It has the smallest side chain (just a single hydrogen atom), taking up very little space.
- This allows it to fit into tight spaces and adopt conformations that other amino acids cannot.
In proteins
- A mix of different amino acids is needed to form a tight, stable package.
- Flexibility in side chains is important for efficient folding and interactions.
Charged (acidic & basic) amino acids
Primary structure: L-amino acids
Charged (acidic & basic) amino acids
Positively charged (basic)
- Lysine (K), Arginine (R), and Histidine (H)
- Their side chains have positive charges at physiological pH, often interacting with negatively charged groups.
Negatively charged (acidic)
- Aspartate (D) and Glutamate (E).
- Their side chains carry a negative charge at physiological pH, often forming salt bridges with positively charged residues.
These amino acids are key for
- Stabilizing protein structure through ionic interactions.
- Participating in enzymatic reactions or binding negatively/ positively charged molecules.
(uncharged) Polar Amino Acids
Primary structure: L-amino acids
(uncharged) Polar Amino Acids
- These amino acids have polar side chains without a net charge at physiological pH.
Examples
- Serine (S) and Threonine (T): Contain hydroxyl groups (-OH), allowing hydrogen bonding.
- Asparagine (N) and Glutamine (Q): Have amide groups (-CONH₂) for hydrogen bonding.
- Tyrosine (Y): Contains a hydroxyl group attached to an aromatic ring, making it polar and capable of hydrogen bonding.
Function
- Participate in hydrogen bonding within proteins or with water molecules.
- Tyrosine’s aromatic ring also allows interactions like π-π stacking.
Degree of ionization as a function of pH.
Primary structure: L-amino acids
Degree of ionization as a function of pH
- At low pH, both the amino group (NH₃⁺) and carboxyl group (COOH) are protonated.
- At neutral pH, the zwitterionic form exists, with NH₃⁺ and COO⁻.
- At high pH, both groups are deprotonated, forming NH₂ and COO
- Henderson-Hasselbalch equation: Used to calculate the pH based on the ratio of protonated (HA) to deprotonated (A⁻) forms:
pH = pKa + log(A⁻/HA)
- pKa: Gives you pH where both states are in same amounts
Primary structure: Peptide bond
Primary Structure: Peptide bond
- The α-carboxyl group of one amino acid is linked to the α-amino group of a second amino acid via a peptide bond
- The equilibrium of this reaction lies on the side of hydrolysis; therefore, the biosynthesis of peptide bonds requires energy.
- A polypeptide chain is polar because its two ends are different – one carries an α-amino group, and the other carries an α-carboxyl group.
- Structure is planar
Double Bond Character
- The peptide bond oscillates between a single bond and a double bond.
- The bond between the carbon (C) and nitrogen (N) is stronger than a typical single bond but not as strong as a real double bond.
- This happens because the electrons in the bond can spread out a bit, making it stable
- No free rotation around the peptid bond
Peptide bond conformation
Peptide bond conformation
- In the trans configuration, the two α-carbon atoms are on opposite sides of the peptide bond
- in the cis configuration, these groups are on the same side.
- Almost all peptide bonds are in the trans configuration.
- The preference for trans over cis can be explained by steric clashes between the side chain groups at the α-carbon in the cis configuration
Ramachandran plot
Ramachandran plot
- The rotation angle around the bond between the nitrogen atom and the α-carbon atom is called phi (φ)
- The angle around the bond between the α-carbon atom and the carbonyl carbon atom is called psi (ψ).
- Ramachandran recognized that many combinations are prohibited due to steric clashes between the individual atoms
- The allowed combinations can be represented in a two-dimensional graph, the Ramachandran plot
- Three-quarters of all possible (φ-ψ) combinations are excluded solely by local steric hindrance.
Geometry of a Helix
Geometry of a Helix
- a-Helices are the most stable and common type found in proteins
- 3 10 (n+3) and π (n+5) helices also excist only for short stretches
α-helices
Secondary Structure
α-Helices
- The α-helix has a tightly wound backbone with side chains extending outward.
- Hydrogen bonds between NH and CO groups stabilize the helix, with each CO bonding to the NH of an amino acid four residues away.
- In each hydrogen bond, the NH group is slightly positive and the CO group is slightly negative, creating individual dipoles. These dipoles combine to form an overall dipole moment along the helix axis.
- Each residue shifts 0.15 nm along the helix axis and rotates by 100°.
- One full turn of the helix contains 3.6 amino acids, with amino acids 3-4 residues apart being close in 3D space.
- The pitch (length of one turn) is 0.54 nm, calculated by multiplying the shift of each amino acid along the axis of the helix (0.15 nm) by 3.6 residues.
- The helix can be right- or left-handed, but right-handed is more stable.
- The helix’s rise per residue (d) is 1.5 Å.
Amino Acid distribution
Secondary structure: α-helices
Amino Acid distribution
- three different α-helix structures (Citrate synthase, Alcohol dehydrogenase, and Troponin C)
- The 100° angle shown between residues corresponds to the typical rotation per amino acid in the helix, with 3.6 residues per turn
- Green: Nonpolar amino acids (hydrophobic), usually found in the inner part of the helix.
- Blue: Polar, noncharged amino acids, often found on the surface of the protein.
- Red: Charged amino acids, usually located on the surface for interaction with the environment.
- 1st helix: inside protein
- 2nd: on surface of protein
- 3rd: Single helix (no interaction)
helix-helix interaction
α-Keratin
Secondary structure
helix-helix interaction
α-Keratin (Superspiral α-Helix)
- α-Keratin, the main component of wool and hair, consists of two right-handed α-helices.
- These helices twist around each other to form a left-handed superhelix (superspiraled α-helix).
- Every seventh residue in each helix is leucine
- The helices are held together by van der Waals interactions, especially between the leucine residues.
- They also form Ionic interactions around the hydrophobic core between both helices (stabilizes)
- Disulfide bridges contribute to the hardness of keratin.
- They are more abundant in nails, making them harder, and fewer in hair, making it less hard
helix-helix interaction
Collagen
Secondary structure
Collagen
- The extracellular matrix is composed to a great extend by collagen
(circa 30% of total human protein).
- Present in connective tissue (bones, teeth, cartilage, cords and
ligaments) and in skin.
- Collagen contains three helical polypeptide chains, each with around 1,000 residues.
- Every third residue is glycine, and the sequence glycine-proline-hydroxyproline frequently repeats.
- There are no hydrogen bonds within a single strand. Instead, the helix is stabilized by steric repulsion between the pyrrolidine rings of proline and hydroxyproline residues.
- The helix contains about three residues per turn. Three such strands twist together to form a superhelix.
- The superhelix is stabilized by hydrogen bonds between the NH groups of the glycine residues and the CO groups of other chains, as well as by the hydroxyl groups of hydroxyproline.
- The lack of hydroxyl groups leads to scurvy, a disease related to collagen instability.
β-strand & β-sheets
Secondary structure:
β-strand & β-sheets
- β-strands are almost fully extended, unlike the tightly coiled α-helix.
- The side chains of adjacent amino acids point in opposite directions.
- A β-sheet is formed by connecting two or more β-strands through hydrogen bonds
- Parallel β-sheet: Strands run in the same direction, but the hydrogen bonds are shifted
- Antiparallel β-sheet: Strands run in opposite directions, and hydrogen bonds form directly between NH and CO groups of adjacent strands.
- Typically, a β-sheet consists of 4-5 strands, but can have 10 or more.
- β-sheets can be arranged as purely parallel, purely antiparallel, or a mixture of both.
- Twisted/mixed β-sheet: (right-handed twist) most commonly occurring motif
β-turns / Hairpin loops
Secondary structure
β-turns / Hairpin loops
- Polypeptide chains can change direction by forming turns and loops.
- In many turns, the CO group of one residue forms a hydrogen bond with the NH group of the residue i+3, stabilizing sharp direction changes in the chain.
- In other cases, more complex structures, called loops (or Ω-loops), help in the change of direction.
a-helix or β-strand?
a-helix or β-strand?
- The formation of α-helices, β-strands, or turns in proteins is influenced by the amino acid sequence.
- Certain residues are more likely to form specific secondary structures:
- Glutamate, Alanine, and Leucine are commonly found in α-helices.
- Valine and Isoleucine tend to form β-strands.
- Glycine, Asparagine, and Proline are often found in turns.
- Branching at the β-carbon (as seen in Valine, Threonine, and Isoleucine) can cause steric hindrance, making it difficult for these residues to fit into α-helices.
- These branched residues are more suited for incorporation into β-sheets, where their side chains extend out of the plane of the sheet.
Schematic Diagrams
Secondary structure
Schematic Diagrams
Spheres model: Atoms shown with van der Waals radius
Sphere/stick model: Bonds are shown
Main-chain model
Ribbon model: Helps to see higher secondary structures
Secondary structure elements connected to form motifs (fold)
Simplest motif with specific function: helix-loop-helix
Secondary structure elements connected to form motifs (fold)
- Certain combinations of secondary structures occur frequently in proteins and often have similar functions.
- These combinations are called structural motifs or supersecondary structures.
- For example, in many DNA-binding proteins, a helix-turn-helix motif is common. This motif consists of one α-helix connected by a turn (β-turn) to another α-helix.
- other example hairpin β motif: consists of two β-strands connected by a short loop or turn, forming a sharp “hairpin” shape, typically in an antiparallel orientation
- β-α-β motif: consists of two β-strands connected by an α-helix, forming a stable and functional structure in proteins.
