Enzymes 2

Introduction to TIM and Its Functionality

Proton Movement in Isomerisation Reaction

  • Isomerisation Reaction: Internal RedOx reaction involving both oxidation and reduction processes.

    • Oxidation of C1: Process wherein C1 loses electrons.

    • Reduction of C2: Process wherein C2 gains electrons.

  • Ineffectively Move Protons: TIM has a role in transferring protons alongside electrons from C1 to C2, signifying its importance in biochemical reactions.

Acid-Base Catalysis and TIM

Overview of Acid-Base Catalysis in TIM

  • Acid-Base Catalysis: Essential mechanism where TIM catalyzes reactions through the transfer of protons mediated by amino acids.

  • Key Citations:

    • Williamson, 1st ed. "How Proteins Work", Ch. 5.4

    • Stryer, 7th ed. "Biochemistry", Ch. 16.1

    • Lehninger, 6th ed. "Principles of Biochemistry", Ch. 6

Mechanism of TIM in Acid-Base Catalysis

Role of Catalytic Amino Acids

  • Proton Abstraction and Donation: The chemical functions within TIM include:

    • Abstraction of proton by base B1- at C1.

    • Donation of proton by acid A1 at C2=O.

    • Further abstraction of proton by base B2- at C1OH.

    • Finally, the donation of proton by acid A2 at C2.

  • Outcome: Proton from C1 is ultimately transferred to C2, facilitating the reaction.

Dual Functions of Catalytic Amino Acids

  • Existence of dual functions (as both acids and bases) in the same catalytic amino acid side chain enhances catalytic efficiency.

  • Catalytic Amino Acids: Essential for the chemistry of enzymatic activity.

    • Example Amino Acids: Glu165 and His95 involved in TIM functions.

General Acid-Base Catalysis Concepts

General Features

  • Catalysis by Amino Acids: Many enzymatic processes are facilitated by amino acid side chains acting as either general acids or bases.

  • Specific Acid/Base Catalysis

    • In Solution: Catalyzed reactions that occur in either acidic or basic conditions, where proton transfer occurs prior to bond cleavage.

Detailed Mechanistic Insights on TIM

Catalytic Cycle Details

  • Example from literature: Mapping enzymatic reactions illustrates the interaction between specific amino acids and substrates.

  • Notable observations in TIM:

    • Glu165 functions as base B1- and acid A2H.

    • His95 behaves as acid A1H and base B2- throughout the catalytic cycle.

Challenges in Catalysis

Addressing Side Reactions

  • Importance: Understanding how TIM prevents side reactions is crucial to enhance efficiency.

  • Problem: Unwanted reactions produce physiologically irrelevant glyoxal. This reaction occurs significantly faster (100x) in solvent when compared to the formation of glyceraldehyde-3-phosphate (G3P).

Structural Insights: The (β/α)8 Barrel

Structural Characteristics

  • Most prevalent enzymatic fold in nature:

    • Present in nearly 10% of known structures, termed "Nature's blueprint" for functional evolution.

  • Noteworthy Features: Active sites positioned on the C-terminal side, with extensive functional units placed primarily in loops between β-strands.

Evolutionary Context of (β/α)8 Structures

Evolutionary Mechanisms

  • Distinct functionalities derived from a common ancestry through processes of convergent and divergent evolution:

    • Convergent Evolution: Different functions emerge from a common structure.

    • Divergent Evolution: Features indicate ancestral origins varying over time.

Detailed Exploration of Specific Biosynthetic Pathways

Histidine Biosynthesis

  • Branching Pathways: Histidine and purine pathways intersect at precursor molecules:

    • ImGP: Precursor in histidine biosynthesis.

    • AICAR: Essential in purine biosynthesis.

  • Key Enzymes:

    • HisA: Converts precursor to another form, facilitating production.

    • HisF: Branch-point enzyme enabling both histidine and purine outputs.

Conservation and Similarity in Enzymes

  • HisA and HisF demonstrate cross-reactivity and share substantial sequence identity.

  • Similar substrates support functional adaptability and diversification over time.

Gene Duplication and Functional Diversification

  • Suggests a model where gene duplication generates half-barrel structures leading to the development of full (β/α)8 barrels.

  • Enables different enzymes to evolve through adapted functionalities.

Conclusion

Summary of Catalytic Evolution

  • The (β/α)8-barrel structures exhibit a hallmark of evolutionary prowess where fold convergence leads to enhanced enzyme functionality. Genetic events pave the way for enzymatic diversity amidst shared biochemical pathways.

  • Provenance: Illustrative points in mutations demonstrate extensive collaborative evolution through the conservation of structural and functional traits, underscoring a rich enzymatic lineage.