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Favorable Interactions in Protein Molecules
The native structure of protein has low energy than the denatured state of the protein. The denaturation of protein is therefore the consequence of breaking labile
(non-covalent) bonds that maintain this lower energy of native state. Several noncovalent forces that are responsible for stabilizing the structure of protein are the
van der Waals interactions, hydrogen bonding and hydrophobic effect. However
these forces are opposed by major destabilizing force, which is associated with
conformational entropy loss upon protein folding. Other forces, such as electrostatic
interactions, can be either favorable or unfavorable, depending on the context.
Nevertheless, the backbone of protein structure is stabilized by covalent bonds
(disulfide bonds), however non covalent interactions are required to maintain secondary, tertiary and quaternary structure of proteins molecules.
Non-Covalent Bonds
Hydrophobic Interactions
Regarding hydrophobic interactions they are not attractive in nature but result from
the inability of water to form hydrogen bonds with certain side chains. These interactions are the main forces that drive protein folding and are hence important in
determining the native structure of protein. Thermodynamically they are unfavorable interactions of protein molecules with water, thus minimize their association
with water. Hydropathies are used to describe the hydrophobic and hydrophilic tendencies of each amino acid residue, greater the hydropathy of an amino acid residue, the more likely it will orient orbury itself to the interior of the protein molecule.
Electrostatic Interactions
Electrostatic interactions like van der Waals forces may be attractive or repulsive
in nature resulting from induced dipole which is due to the polarization of electron cloud between neutral atoms in protein molecules. However, these forces are
relatively weak, the strength of these forces decrease rapidly with increase in
distance.
Hydrogen bonds are formed by sharing of a proton between donor and acceptor
groups. The strength of hydrogen bond is 2–5 kcal/mol and the ideal distance is
2.8–3 Å. Usually these bonds involve the interaction of hydrogen atom, which is
covalently attached to an electronegative atom such as O, N and S, with a second
electronegative atom. The most common types of hydrogen bonding include bonding between N–H and C=H groups in α-helix and β-sheet structure of protein.
N. A. Mir et al.
Favorable Interactions in Protein Molecules
The native structure of protein has low energy than the denatured state of the protein. The denaturation of protein is therefore the consequence of breaking labile
(non-covalent) bonds that maintain this lower energy of native state. Several noncovalent forces that are responsible for stabilizing the structure of protein are the
van der Waals interactions, hydrogen bonding and hydrophobic effect. However
these forces are opposed by major destabilizing force, which is associated with
conformational entropy loss upon protein folding. Other forces, such as electrostatic
interactions, can be either favorable or unfavorable, depending on the context.
Nevertheless, the backbone of protein structure is stabilized by covalent bonds
(disulfide bonds), however non covalent interactions are required to maintain secondary, tertiary and quaternary structure of proteins molecules.
Non-Covalent Bonds
Hydrophobic Interactions
Regarding hydrophobic interactions they are not attractive in nature but result from
the inability of water to form hydrogen bonds with certain side chains. These interactions are the main forces that drive protein folding and are hence important in
determining the native structure of protein. Thermodynamically they are unfavorable interactions of protein molecules with water, thus minimize their association
with water. Hydropathies are used to describe the hydrophobic and hydrophilic tendencies of each amino acid residue, greater the hydropathy of an amino acid residue, the more likely it will orient orbury itself to the interior of the protein molecule.
Electrostatic Interactions
Electrostatic interactions like van der Waals forces may be attractive or repulsive
in nature resulting from induced dipole which is due to the polarization of electron cloud between neutral atoms in protein molecules. However, these forces are
relatively weak, the strength of these forces decrease rapidly with increase in
distance.
Hydrogen bonds are formed by sharing of a proton between donor and acceptor
groups. The strength of hydrogen bond is 2–5 kcal/mol and the ideal distance is
2.8–3 Å. Usually these bonds involve the interaction of hydrogen atom, which is
covalently attached to an electronegative atom such as O, N and S, with a second
electronegative atom. The most common types of hydrogen bonding include bonding between N–H and C=H groups in α-helix and β-sheet structure of protein.
N. A. Mir et al.