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The correct 3-D structure of a protein is often dependent on an intricate network of H-bonds. These can occur between a variety of atoms, involving: atoms on two different amino acid sidechains atoms on amino acid sidechains and protein backbone atoms atoms on amino acid sidechains and water molecules at the protein surface backbone atoms and water molecules at the protein surface backbone atoms on two different amino acids Examples of several of these types of H-bonds may be illustrated using amino acids of the model peptide.
Seen here, an H-bond donor O on the sidechain of serine and its corresponding H-bond acceptor N on the sidechain of histidine 57 "share" a partially charged hydrogen. Glycine provides an H-bond acceptor its backbone carbonyl O and histidine 40's sidechain provides an - N H donor, forming a hydrogen bond. Most of the model peptide residues is a beta strand that is extensively H-bonded to an adjacent, antiparallel beta strand residues Here, two H-bonds between backbone atoms in leucine and glycine are shown.
Water Shells and Polar Surface Residues Polar amino acids, mostly found on protein surfaces, promote appropriate folding by interacting with the water solvent. Polar water molecules can form shells around charged or partially charged surface residue atoms, helping to stabilize and solubilize the protein. Another example is an H-bond between an H 2 O hydrogen and the sidechin O of glutamine Only a fraction of the water molecules that surround a protein in vivo are visualized in the chymotrypsin crystal structure of this exhibit PDB ID 1AB9.
These can be seen interacting with the protein surface. Hydrophobic Interactions. Hydrophobic interactions "bonds" are a major force driving proper protein folding. They juxtapose hydrophobic sidechains by reducing the energy generated by the intrusion of amino acids into the H 2 O solvent, which disrupts lattices of water molecules.
Hydrophobic bonding forms an interior, hydrophobic, protein core, where most hydrophobic sidechains can closely associate and are shielded from interactions with solvent H 2 O's. For more information on these interactions, see the hydrophobic bonds page. Proline and valine are two of six, interior, hydrophobic amino acids in the model peptide. The close association of the hydrocarbon sidechains of these aa's and those of leucine , valine , and tryptophan are shown here.
Not all hydrophobic amino acids are in the interior of proteins, however. When found at the surface, exposed to polar H 2 O molecules, hydrophobic sidechains are usually involved in extensive hydrophobic bonding. Here, packing of the hydrophobic sidechains of proline 24 and phenylalanine 71 is observed. Van der Waals Forces. The Van der Waals force is a transient, weak electrical attraction of one atom for another. Van der Waals attractions exist because every atom has an electron cloud that can fluctuate, yielding a temporary electric dipole.
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