Hydrogen bonds This figure shows hydrogen bonds H-bonds in helix (white dash lines)are important to hold a small in place at the active site of an enzyme. Fibrillarin Peptide bond Nop5p
Hydrogen bonds This figure shows hydrogen bonds (white dash lines) are important to hold a small in place at the active site of an enzyme. H-bonds in helix Peptide bond
Hydrophobic Interactions Hydrophobic interactions minimizes interactions of non-polar residues with solvent. Thus nonpolar regions of biological macromolcules are often buried in the molecules interior to exclude them from the aqueous milieu. However non-polar residues can also be found on the surface of a protein.They may participate protein-protein interactions. This type of interaction is entropy driven
Hydrophobic Interactions Hydrophobic interactions minimizes interactions of non-polar residues with solvent. Thus nonpolar regions of biological macromolcules are often buried in the molecules interior to exclude them from the aqueous milieu. However non-polar residues can also be found on the surface of a protein. They may participate protein-protein interactions. This type of interaction is entropy driven
Electrostatic Interactions Charged side chains in protein can interact favorably with an opposing charge of another side chain according to Coulomb's law: F=99 Dr2 Examples of favorable electrostatic interaction include that between positively charged Lys and negatively charged Glu. Salts have the ability to shield electrostatic interactions
Electrostatic Interactions Charged side chains in protein can interact favorably with an opposing charge of another side chain according to Coulomb’s law: Examples of favorable electrostatic interaction include that between positively charged Lys and negatively charged Glu. Salts have the ability to shield electrostatic interactions. 2 1 2 Dr q q F =
Examples of Electrostatic Interactions Intramolecular ionic bonds between charged amino acid residues in a protein: Magnesium ATP NH2 -NH3*O-C-CH2 Mg2+ 0.NHg-(CH2)4 OH
Examples of Electrostatic Interactions Intramolecular ionic bonds between charged amino acid residues in a protein: NH3 + O C O CH2 H2C C O O - NH3 + (CH2 )4 N N N N NH2 O OH OH P O P O P O O O O O O O O Mg2 + Magnesium ATP
van der Waals Interactions van der Waals interaction between two atoms is a result of electron charge distributions of the two atoms. For atoms that have permanent dipoles: Dipole-dipole interactions(potential energy ~r3) Dipole-induced dipole interactions(potential energy r5) For atoms that have no permanent dipoles: Transient charge distribution induces complementary charge distribution(also called dispersion or London dispersion force)(potential energy ~r 6) (心+transient dipole 6+ transient dipole Repulsion between two atoms when they approach each other due to overlapping of electron clouds(potential energy ~r12)
van der Waals Interactions van der Waals interaction between two atoms is a result of electron charge distributions of the two atoms. For atoms that have permanent dipoles: Dipole-dipole interactions (potential energy ~r-3) Dipole-induced dipole interactions (potential energy ~r-5) For atoms that have no permanent dipoles: Transient charge distribution induces complementary charge distribution (also called dispersion or London dispersion force) (potential energy ~r-6) Repulsion between two atoms when they approach each other due to overlapping of electron clouds (potential energy ~r-12) d+ d- d+ dd+ dtransient dipole transient dipole