Protein Function & Regulation

Shape and Function Are Linked

• Protein conformation (or shape)

  • the 3D arrangement of atoms within a folded-protein

• The amino acids exposed on the surface of a protein give proteins the ability to perform different unique processes that occur in the cell

  • binding to different molecules or proteins

Ligand

• The molecule that a protein can bind

• Can be either a small molecule, a macromolecule, or an ion

Binding Site

• The part of a protein that interacts with the ligand (allows it to “bind”)

• The site is specific in shape to the specific arrangement that makes up an amino acid

General Protein Interactions

• The activity of a protein is determined by its ability to bind specifically to other molecules

  • The # of molecules required to carry out an activity can vary from one to few to dozens

• The specificity of binding is due to the formation of weak, noncovalent interactions

  • Hydrogen bonds, van der Waals attractions, electrostatic interactions, hydrophobic forces

• Weak interactions occur b/c ligands need to have the ability to be released from a binding site once they have served their purpose

• B/c these interactions are so weak, it takes a lot of them in order for a ligand - binding site interaction to occur

  • As a result, only ligands that are strongly compatible with binding sites, both structurally and chemically, will result in successful interactions

    • ANALOGY: Multiple interactions will naturally occur between people who are alike and share many same interests

Specific Protein-Ligand Interactions

• Antibody Specificity

  • Each antibody contains a distinct antigen-binding site, allowing each antibody to recognize its antigen with great specificity

• Enzyme-Substrate

  • Enzymes are highly specific to their substrates, and as a result, catalyze only a single type of reaction

  • Enzymes bind one or more ligands (substrates) and convert them into chemically modified products

  • And since a biological system requires so many different functions, there exists an abundance of enzymes specific to each unique task

Protein Function - Small Molecules

• Some proteins require small molecules to perform their specific activity

  • These molecules may be covalently or non-covalently linked to the protein

• Example - Hemoglobin

  • Requires Heme and Fe

  • A Heme is primarily non-covalently bonded to each of the four polypeptide chains that make up the structure of hemoglobin

  • Having heme molecules attach allows hemoglobin to perform its main function, carrying oxygen molecules throughout the bloodstream

Importance of Protein and Enzyme Activity Regulation

• Most proteins and enzymes do not operate indefinitely

• Since many proteins have different functions/jobs, our biological systems do not need them at every moment

  • Using them only when needed helps conserve energy

• Protein regulation is important to helping cells maintain their optimal environment

  • Preventing unnecessary depletion of energy and resources

Protein Regulation

• Cells can control the amount of protein that is being made

• Cell can also control the rate at which proteins are being degraded

• Cell can regulate the location of the protein as it can influence the function of the protein. Also, regulating proteins’ locations help prevent them from interfering with other pathways

• The activity of a protein can be regulated at their own level as well

Feedback Inhibition

• Multiple enzymes are involved in a mechanistic pathway where the product from one enzyme becomes the substrate for another

• Feedback Inhibition

  • An enzyme earlier in the reaction pathway can be inhibited by a product produced by an enzyme later in the pathway

    • Allows recognition when there is enough “product” produced

    • Conserves cellular energy

    • Can be reversible when there becomes not enough products

Allostery (Allosteric Enzyme)

• Enzymes that have two or more binding sites

  • Active site where substrate binds too

  • One or more allosteric (regulatory) binding sites

• Allosteric Site

  • Binding of a product to the regulatory binding site causes change in the conformation'/shape of the enzyme

    • As a result, substrates can no longer bind or are less effectively able to bind to the active site → inactive site

    • When a product is no longer bound to the regulatory site, the enzyme can change its conformation back to its normal shape

Allosteric Negative Regulation

• A product binds to its regulatory binding site on an enzyme and turns OFF the active site

• The conformation/shape of the enzyme changes so that substrates specific to that enzyme can no longer bind to it

• Conserves cellular energy when the amount of products created by the enzyme is enough for a period of time

Allosteric Positive Regulation

• A product binds to its regulatory binding site on an enzyme and turns ON the inactive site

• The conformation/shape of the enzyme changes so that substrates specific to the enzyme can start binding again

• Uses cellular energy to drive the chemical reactions

Phosphorylation

• A phosphate group is added to an amino acid

  • Comes from ATP hydrolysis (ATP → ADP + Pi)

• Since a phosphate group is NEGATIVE, the addition of it can cause the protein to attract positively charged side chains

  • Change in protein conformation that either turns ON/OFF the enzyme

• Phosphorylation can also allow other molecules/proteins to become bound to the enzyme

  • Promoting different interactions

• Reversible

  • Phosphatases: Help remove phosphate groups

  • Kinases: Help add phosphate groups

• AMINO ACIDS CAPABALE OF BEING PHOSPHORYLATED

  • Serine, threonine, tyrosine (those with -OH)