4.3 Structure-function relationships in proteins

Proteins are nature's molecular machines, performing countless tasks in our bodies. Their structure dictates their function, from enzymes catalyzing reactions to antibodies fighting infections. Understanding these structure-function relationships is key to unlocking proteins' potential in medicine and biotechnology.

Active sites, motifs, and domains are crucial elements of protein structure. These features determine how proteins interact with other molecules, catalyze reactions, and carry out their specific functions. By studying and manipulating these elements, scientists can design drugs and engineer proteins for various applications.

Active Sites and Substrate Binding

Enzyme-Substrate Interactions

• Active site: region of an enzyme where the substrate binds and the catalytic reaction occurs
• Binding pocket: three-dimensional space within the active site that accommodates the substrate
  • Formed by specific amino acid residues that interact with the substrate
  • Shape and chemical properties of the binding pocket determine substrate specificity
• Substrate specificity: ability of an enzyme to recognize and bind to a specific substrate or group of substrates
  • Enzymes have high specificity due to complementary shape and chemical interactions between the active site and substrate (lock and key model)
  • Some enzymes exhibit broad specificity and can catalyze reactions with multiple substrates (induced fit model)
• Enzyme catalysis: process by which enzymes accelerate chemical reactions without being permanently altered
  • Enzymes lower the activation energy required for a reaction by stabilizing the transition state
  • Catalysis involves formation of an enzyme-substrate complex, chemical transformation of the substrate, and release of the product

Factors Influencing Enzyme Activity

• Enzyme concentration: increasing enzyme concentration generally increases reaction rate until substrate becomes limiting
• Substrate concentration: reaction rate increases with substrate concentration until enzyme active sites are saturated (Michaelis-Menten kinetics)
• pH: enzymes have optimal pH ranges where they function most effectively due to changes in amino acid protonation states
  • Extreme pH can denature enzymes by disrupting their structure
• Temperature: increasing temperature increases reaction rate up to the enzyme's optimal temperature
  • Excessive heat denatures enzymes by disrupting non-covalent interactions and unfolding the protein

Protein Structural Elements

Motifs and Domains

• Protein motifs: short, conserved sequences of amino acids that form specific secondary structures
  • Examples include alpha helices, beta sheets, and turns
  • Motifs often contribute to protein function by forming binding sites or catalytic centers
• Domains: independently folding units within a protein that have distinct functions
  • Proteins can consist of single or multiple domains
  • Domains can be classified based on their structure (e.g., globular, fibrous) or function (e.g., catalytic, binding)
  • Multidomain proteins can have increased functional versatility and regulation through domain-domain interactions

Structure-Function Relationships

• Primary structure: linear sequence of amino acids determines the protein's higher-order structures and ultimate function
• Secondary structure: regular, repeating patterns stabilized by hydrogen bonds (alpha helices and beta sheets)
  • Secondary structures contribute to protein stability and can form functional motifs
• Tertiary structure: three-dimensional arrangement of a protein's secondary structures and side chains
  • Tertiary structure is stabilized by non-covalent interactions (hydrogen bonds, van der Waals forces, hydrophobic interactions) and disulfide bonds
  • Proper folding into the native tertiary structure is essential for protein function
• Quaternary structure: arrangement of multiple polypeptide subunits in a multi-subunit protein complex
  • Subunit interactions can be stabilized by the same non-covalent forces as in tertiary structure
  • Quaternary structure allows for cooperative effects, allosteric regulation, and increased functional complexity

Protein Design and Applications

Structure-Based Drug Design

• Structure-based drug design: rational design of drugs based on the three-dimensional structure of a target protein
  • Involves determining the structure of the target protein, often through X-ray crystallography or NMR spectroscopy
  • Computational methods (e.g., molecular docking) are used to identify or design compounds that interact with the target protein
• Drug-target interactions: designed drugs typically interact with specific sites on the target protein
  • Drugs can be designed to inhibit enzymes by binding to the active site or allosteric sites
  • Drugs can also be designed to modulate protein-protein interactions or disrupt protein aggregation
• Advantages of structure-based drug design include increased specificity, reduced side effects, and faster drug development timelines compared to traditional screening methods

Protein Engineering

• Protein engineering: deliberate modification of a protein's sequence or structure to alter its function
  • Can involve rational design (based on structure-function knowledge) or directed evolution (using random mutagenesis and selection)
• Applications of protein engineering include:
  • Improving enzyme stability, specificity, or catalytic efficiency for industrial processes
  • Designing novel proteins with desired functions (e.g., biosensors, molecular machines)
  • Creating antibodies with enhanced affinity or specificity for therapeutic or diagnostic use
• Protein engineering techniques: site-directed mutagenesis, domain swapping, fusion proteins, and incorporation of unnatural amino acids
  • Advances in computational protein design and high-throughput screening have accelerated the field of protein engineering