Bonds in Protein

Chemical Bonds in Proteins
Chemical bonds in proteins can be classified as:

 Intramolecular Bonding: Bonds within a single protein molecule.
 Intermolecular Bonding: Bonds between different protein molecules.
Covalent Bonds
Covalent bonds are formed by the sharing of electrons between atoms.
There are two main types:
 Non-Polar Covalent Bonds: Electrons are shared equally between atoms.
 Polar Covalent Bonds: Electrons are attracted more to one atom than
the other.
Example:
 A• + B• → A..B
Types of Covalent Bonds:
1. Single Bond: Sharing of one pair of electrons.
o Example: Cl• + Cl• → Cl₂ (Cl-Cl)
2. Double Bond: Sharing of two pairs of electrons.
o Example: O •• + O •• → O₂ (O=O)
3. Triple Bond: Sharing of three pairs of electrons.
o Example: N••• + N••• → N₂ (N≡N)
Covalent Bonds in Proteins:
 Covalent bonds connect atoms within a single amino acid and between
amino acids in a protein chain.
 Disulfide bonds (a type of covalent bond) are formed between cysteine
side chains.
o These bonds are strong and not easily broken without denaturing
agents.
o Disulfide bonds contribute significantly to the three-dimensional
structure of proteins.
Protein Engineering Example:
 Disulfide bonds can be added to proteins through site-directed
mutagenesis to increase thermal stability.
 T4 Lysozyme: Incorporation of disulfide bonds can either increase or
decrease stability.
o Stabilization is due to reduced conformational entropy in the
unfolded state.
o Destabilization is often due to the introduction of dihedral angle
stress.
o Natural proteins may not tolerate disulfide bonds in most positions
without constraint on the α-carbon chain.
Ionic Bonds
Ionic bonds are formed through electrostatic attraction between oppositely
charged ions.
 Example: Na⁺ + Cl⁻ → NaCl
 In proteins, ionic bonds (or salt linkages) form between charged R groups
of amino acids within a polypeptide chain.
 Example: The carboxylate group (RCOO⁻) of aspartic or glutamic acid can
interact with the ammonium group (RNH₃⁺) of lysine, arginine, or
histidine.
o Effective distance: Less than 4Å
 Disruption of ionic bonds can significantly affect protein stability.
 In T4 lysozyme, disrupting the salt bridge between His 31 and Asp 70
through mutation results in destabilization (31-21 kJ/mol).
Hydrogen Bonds
Hydrogen bonds form between a hydrogen atom covalently attached to an
electronegative atom (e.g., oxygen or nitrogen) and another electronegative
atom.
Characteristics of Hydrogen bonds:
o Stronger than van der Waals forces.
o Hydrogen bonds are highly directional and form straight bonds
between donor hydrogen and acceptor atoms.
o Specificity arises from complementary hydrogen donor and
acceptor groups.
 The contribution of H is said to be minor in the stability of folded
protein because H-bonding interactions can also occur with water in the
unfolded protein.
 Studies on enzymes like barnase, ribonuclease T1, ribonuclease A,
lysozyme, cytochrome c, and myoglobin show that intramolecular H-
bonds can significantly stabilize proteins, rivaling the hydrophobic effect.
Van der Waals Attractive Forces
Van der Waals forces arise from induced electrical interactions between
closely approaching atoms or molecules.
 Types include dipole-dipole, dipole-induced dipole, and induced dipole-
induced dipole interactions.
 Individually weak but collectively significant within a molecule.
 Van der Waals forces play roles in protein-protein recognition, such as
antibody-antigen interactions, where complementary shapes yield
extensive van der Waals attractions.
Hydrophobic Interactions
Hydrophobic interactions result from water molecules' tendency to exclude
non-polar groups or molecules.
 Water prefers interacting with itself, raising its entropy when non-polar
molecules are excluded.
 Non-polar regions of biological molecules are often buried to avoid
aqueous environments.
 Hydrophobic interactions drive the clustering of non-polar molecules
and are crucial for the folding and stability of proteins.
Coordinate Bonds
Coordinate bonds (dative covalent bonds) involve electrons shared by atoms
coming from only one of the atoms.
 Examples: NH₄⁺, AlCl₄⁻, H₃O⁺
 Important in substances like hemoglobin and myoglobin.
Representation:
 An arrow indicates that both electrons in the bond originate from a
single atom.
These notes provide a comprehensive understanding of the different types of
bonds involved in protein structure and how they relate to protein
engineering. For detailed examples and diagrams, refer to the provided
document.

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Chemical Bonds in Proteins

Chemical bonds in proteins can be classified as:

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