Module 2

**Module 3 – Lecture 3.2

Protein Structure and Function**

Overview of Protein Function

Proteins perform most essential tasks in cells. General protein functions include enzymes that catalyze chemical reactions, structural proteins that provide mechanical support, transport proteins that move molecules, motor proteins that generate movement, storage proteins, signal proteins, receptors, and regulatory proteins that control cellular processes.

How Proteins Work

Protein Binding

All proteins bind to other molecules called ligands. Protein–ligand binding is highly selective and depends on many weak, noncovalent interactions such as hydrogen bonds, electrostatic interactions, and van der Waals forces. Although each interaction is weak on its own, together they allow tight and specific binding. For binding to occur, the ligand must fit precisely into the protein’s binding site.

Binding Sites

Protein folding creates binding sites, which are crevices or cavities on the protein surface. Specific amino acid side chains within the binding site are positioned to form noncovalent bonds with specific ligands. Binding depends on shape complementarity, charge distribution, and chemical compatibility between the protein and ligand.

Enzymes

Enzyme Function

Enzymes are powerful and highly specific catalysts. Each enzyme has an active site where substrate molecules bind, forming an enzyme–substrate complex. The enzyme converts the substrate into product, forming an enzyme–product complex, after which the product is released. The enzyme itself remains unchanged and can catalyze the reaction repeatedly. Most enzymes catalyze the formation or breaking of a single covalent bond.

How Enzymes Speed Up Reactions

Enzymes accelerate chemical reactions by holding substrates together in a precise orientation, rearranging the distribution of charges in reaction intermediates, and straining bonds in substrates to favor the transition state. A single enzyme may use more than one of these mechanisms simultaneously.

Enzyme Inhibition

Competitive inhibitors reduce enzyme activity by competing with the substrate for the active site. The enzyme can bind either the substrate or the inhibitor, but not both at the same time. When the inhibitor is bound, the enzyme is inactive.

Classes of Enzymes

Common enzyme classes include hydrolases (hydrolysis reactions), ligases (joining molecules together), isomerases (rearranging bonds within a molecule), kinases (adding phosphate groups), phosphatases (removing phosphate groups), oxidoreductases (oxidation–reduction reactions), and ATPases (hydrolyzing ATP).

Regulation of Enzyme Activity

Feedback Inhibition

Feedback inhibition is a form of negative regulation in which the end product of a biosynthetic pathway inhibits an enzyme early in the pathway. The final product binds to the first enzyme specific to its own synthesis, preventing overproduction and helping maintain proper cellular concentrations.

Allosteric Regulation

Allosteric enzymes have two or more binding sites: an active site and one or more regulatory (allosteric) sites. Binding of a regulatory molecule at the allosteric site causes a conformational change that alters enzyme activity. This change can either inhibit or activate the enzyme. For example, cytosine triphosphate (CTP) binds to aspartate transcarbamoylase and turns the enzyme off when CTP levels are high.

Positive Regulation

Some regulatory ligands bind only to the active conformation of a protein. Binding stabilizes the active form and shifts the equilibrium toward activity. For example, rising levels of ADP signal low energy and promote enzyme activity involved in ATP production.

How Proteins Are Controlled

Protein Phosphorylation

Protein phosphorylation is a common mechanism for regulating protein activity. A protein kinase transfers a phosphate group from ATP to an amino acid side chain, usually serine, threonine, or tyrosine. Removal of the phosphate group is catalyzed by a protein phosphatase. Phosphorylation can either increase or decrease protein activity depending on the site of modification and the protein’s structure.

GTP-Binding Proteins

GTP-binding proteins act as molecular switches. They are active when bound to GTP and inactive when bound to GDP. The protein switches itself off by hydrolyzing GTP to GDP and inorganic phosphate. Reactivation requires GDP dissociation, which is slow, followed by rapid binding of GTP.

Motor Proteins and ATP

ATP-Driven Movement

Motor proteins move by cycling through different conformations. Directional movement requires energy from ATP hydrolysis. Without ATP input, proteins undergo random motion and do not achieve net movement.

Kinesin

Kinesin is a microtubule-based motor protein that uses ATP to “walk” along microtubules. The leading head binds ATP and undergoes a conformational change, causing the trailing head to move forward. ATP hydrolysis and release of ADP and inorganic phosphate coordinate movement and ensure unidirectional transport.

Protein Machines

Protein machines are large complexes made of multiple proteins that collaborate to perform specific cellular tasks. ATP hydrolysis coordinates conformational changes within these complexes, allowing controlled and directional activity.

Covalent Modifications of Proteins

Proteins can be modified at multiple sites to control their behavior. The transcription regulator p53 is regulated by phosphorylation, acetylation, and ubiquitination, which affect its activity, stability, and degradation. Many covalent modifications occur in relatively unstructured regions of proteins.

Scaffold Proteins

Scaffold proteins organize cellular processes by bringing interacting proteins together. Structured domains bind specific proteins, while unstructured regions act as flexible tethers that increase the rate of protein–protein interactions and formation of functional complexes.

Intracellular Condensates

Intracellular condensates are membrane-less biochemical subcompartments formed by phase separation driven by many weak interactions between macromolecules. These condensates concentrate specific proteins and RNAs, creating regions with specialized biochemical activity. Examples include the nucleolus, centrosome, and synaptic protein assemblies involved in memory formation.