unit 2, lesson 2, lecture 2

• Proteins are large molecules composed of several hundred amino acids
• Artificial intelligence has largely solved one of biology's biggest mysteries in protein structures
• Predicting how a protein folds into a unique three-dimensional shape has puzzled scientists for half a century
• A better understanding of protein shapes could play a pivotal role in the development of novel drugs to treat disease

Primary Structure

• The linear sequence of amino acids in a peptide is called the primary (1°) structure of the protein

Native Conformation

• A polypeptide chain is not linear and folds into a biologically active shape
• The biologically active form of a polypeptide chain is known as its native conformation

Enzyme Active Sites

• Biological functions of many proteins can be explained by their conformations or shapes
• An enzyme folds to form an active site that can recognize substrate molecules.

The Peptide Bond

• Properties of the peptide bond have considerable impact on the shape and function of proteins
• The peptide bond is planar and electron resonance gives it 40% double bond character
• It can be regarded as the average of two extreme resonance forms
• Some properties are a result of its double bond character, making it rigid and planar
• Rotation around the peptide bond is not possible

Peptide Bond Conformation

• Peptide bonds have a trans conformation
• Steric hindrance between side chain groups favors the trans conformation
• Since the peptide bond is rigid, only two free movements exist in a polypeptide chain
• Rotation about the αC-N bond is called the phi (Φ) torsion angle
• Rotation about the αC-C bond is called the psi (Ψ) torsion angle

Bonds and Conformation Restrictions

• Protein conformation depends on phi (Φ) and psi (Ψ) rotations
• Flexibility of these bonds allows the primary sequence to fold into its native conformation
• Rotation is limited by steric hindrance, where bulky groups cannot approach each other
• The rigidity of the peptide bond ultimately restricts movement
• Favorable interactions, like hydrogen bonds, with other regions of the polypeptide chain also limit rotation

Secondary Structure: Alpha-Helix

• Secondary (2°) protein structure is defined as 'the three dimensional arrangement of the primary amino acid sequence.'
• The α-helix results when consecutive amino acid residues have similar phi (Φ) and psi (Ψ) torsion angle values
• phi (Φ) = —57°, psi (Ψ) = —47°
• Alpha-helix is a SINGLE helix, not to be confused with DNA
• 3.6 amino acid residues are required for one complete turn of the helix
• Each backbone carbonyl oxygen is hydrogen bonded to the peptide nitrogen of the fourth residue along (towards C terminus), stabilizing the helix
• Hydrogen bonds are weak but hold the helix structure together
• Side chains are arranged on the outside of the helix.

Alpha-Helix Rich Proteins

• Receptors are proteins rich in alpha-helices with a trans-membrane domain composed entirely of alpha-helices
• An example of one is the crystal structure of the Adenosine Receptor in cardiac tissue
• Adenosine, a treatment for supraventricular tachycardia, binds to the trans-membrane domain

Secondary Structure: Beta-Sheet

• A beta-sheet is a secondary protein structure where strands of the peptide backbone are hydrogen bonded to themselves
• The beta-sheet is an elongated, reasonably flat 'sheet-like' structure
• Inter-strand hydrogen bonds between backbone carbonyl oxygen and amide nitrogens stabilize the beta-sheet
• Side chain interactions (hydrophobic) can provide additional stabilization

Types of Beta-Sheets

• Antiparallel beta-sheets are optimally hydrogen bonded, with linear hydrogen bonds
• These have better overlap and are stronger, with 2–15 strands possible (average 6)
• Parallel beta-sheets have distorted hydrogen bonds and are less stable
• Parallel beta-sheets have no more than 5 strands encountered

Fibrous Proteins

• Fibrous proteins contain only alpha-helix secondary protein structure with a simple, elongated structure
• Provide mechanical support in skin, tendons, and bones and are physically durable, chemically inert, and water-insoluble
• Structure is maintained by hydrogen bonding within the alpha-helix
• Hair is composed mostly of alpha-keratin, a double coil of alpha-helices
• Many double coils are packed together to form a strand of hair
• Collagen from chicken cartilage is a triple coil of alpha-helices

Tertiary Structure

• Tertiary (3°) protein structure is the three-dimensional (spatial) arrangement of secondary structure
• Tertiary proteins, like enzymes, often contain an assortment of secondary features
• Receptors also have tertiary structure and trans-membrane domain attached to a cytoplasmic domain.
• The precise structure of membrane-bound receptors is difficult to determine

Globular Proteins

• Globular proteins are tertiary proteins with greater structural diversity
• All enzymes are globular proteins with a unique and complex structure
• Are water-soluble, compact, roughly spherical, with tightly folded peptide chains
• Exhibit a hydrophobic interior and hydrophilic surface, maintained by covalent and hydrogen bonding, non-covalent crosslinks, and hydrophobic interactions
• They possess indents or clefts, forming an active site
• Enzymes function by binding to a protease enzyme (e.g., trypsin)
• It is not as obvious how the tertiary structure of an enzyme is responsible for its properties

Stabilization of Tertiary Structure

• Proteins are more stable in water due to hydrophobic side chains tucked into the protein interior
• Non-polar substances minimize contact with water, causing non-polar chains to aggregate and fold the protein
• Non-polar side chains aggregate to the inside and polar sidechains at the outside
• Efficient packing maximizes van der Waals interactions between non-polar residues and excludes water from the interior
• Enzymes must be water-soluble and the amino acids Val, Leu, Ile, Met, Phe and Ala are rarely encountered on protein exteriors
• Proteins are arranged to form all possible hydrogen bonds
• Polar side chains forced into the protein interior neutralize their polarity by forming hydrogen or electrostatic bonds
• Folding maximizes hydrogen, hydrophobic non-covalent and covalent interactions, stabilizing protein

Covalent Bonds

• Disulfide bonds are cross links between adjacent cysteine residues and stabilize conformations of some proteins
• A covalent bond is stronger than a hydrogen bond or van der Waals forces
• Disulfide links are especially common in proteins secreted from cell

Temperature and pH Effects

• Heating a chemical reaction increases its rate, but enzymes function poorly at extremes of temperature or pH
• The tertiary structure of an enzyme is responsible for biological activity and maintained by weak interactions (hydrogen bonds and van der Waals forces)
• Changes to pH or temperature disrupt the stabilising interactions, causing changes to the tertiary structure.
• This causes the protein to be denatured
• Enzymes have evolved to function (maximum stabilization of tertiary structure) at physiological conditions of pH 7.4 and 37 °C.

Quaternary Structure

• Quaternary (4°) structure refers to proteins composed of more than one polypeptide strand
• Haemoglobin is composed of 4 globular protein subunits: two identical 'a units' with 141 amino acids and two identical 'ẞ units' with 146 amino acids
• Each subunit contains an iron atom, vital for oxygen transport in the blood
• Insulin, a hormone that controls glucose metabolism, has two peptide chains, linked and maintained in the biological active conformation by three disulfide bridges.

Obtaining Protein Structures

• Through X-ray crystallography or Cryogenic electron microscopy

protien structures