{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

Lecture12-ProBinding - BIOC*2580Lecture12 ProteinStability,...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
BIOC*2580 Lecture 12. Protein Stability, Binding and Recognition. 1 Page 1 of 7 Protein Stability, Binding and Recognition Synopsis: The purpose of many proteins is to bind and recognize specific target molecules . Such proteins may include enzymes , which catalyze a reaction on their bound target, or antibodies that simply bind and tag foreign molecules for intervention by the body's defenses. Effective binding occurs through interaction very similar to the interactions that cause proteins to fold up, namely hydrophobic effects, van der Waals interactions (dependent of exact matching of molecular shape) and by pairing up opposite charges or hydrogen bonding partners on protein and bound ligand. Many proteins are able to bind and recognize specific molecules. Specific binding results from cavities and regions on the protein surface which complement the target molecule: non‐polar patches on the protein surface match with nonpolar groups on the ligand the binding site matches shape of ligand to maximize atom to atom contact oppositely charged groups on protein and ligand attract complementary hydrogen bonding groups on protein and ligand. Reading: Lehninger p. 183‐194 (4 th ed p.193‐199). Proteins exist as long polypeptide chains folded into a specific 3‐dimensional shape. The normal folded state or tertiary structure of a protein is called its native state. The exact spatial relationship of the amino acids in the native state give the protein a specific function. When the polypeptide is unfolded from its normal tertiary structure, the protein is said to be denatured. The spatial relationship of amino acids is disorganized, so a denatured protein loses all of its functions. In some cases, the denatured state may exist as a long extended polypeptide chain (e.g. by the action of sodium dodecyl sulfate in SDS electrophoresis), but any shape other than the precise native state is denatured and effectively inactive. Covalent bonding determines the first level of protein structure. The polypeptide backbone consists of a chain of covalently bonded amino acids linked in a specific sequence ‐ the primary structure . Non‐covalent interactions give rise to secondary and tertiary structure and dictate the precise pattern of folding and stability of the folded form. These effects include hydrophobic interaction, van der Waals forces, hydrogen bonding and ionic interactions .
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
BIOC*2580 Lecture 12. Protein Stability, Binding and Recognition. 2 Page 2 of 7 Hydrophobic effect : This describes the tendency of non‐polar amino acids to cluster in the core of a protein, out of contact with the surrounding H 2 O environment. This effect provides the major contribution, about 50% of the total, to the energy that stabilizes the folded state of the protein.
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}