Wide transition-state ensemble as key component for enzyme catalysis

Area of Science:

• Biochemistry
• Computational Chemistry
• Structural Biology

Background:

• Transition-state (TS) theory explains enzyme catalysis by accelerating reaction rates.
• Proteins exist as conformational ensembles, posing challenges for unique TS identification.
• Enzymatic phosphoryl-transfer reactions, like in adenylate kinase, are crucial biological processes.

Purpose of the Study:

• To investigate the nature of the enzymatic transition-state ensemble (TSE) for phosphoryl-transfer in adenylate kinase.
• To determine if enzymes utilize a broad TSE to overcome entropic bottlenecks.
• To link computational findings with experimental enzyme kinetics data.

Main Methods:

• Quantum-mechanics/molecular-mechanics (QM/MM) calculations were employed to model the enzymatic reaction.
• Analysis of the reaction coordinate to identify the range of transition-state configurations.
• Enzyme kinetics experiments were performed to measure the entropy of activation.

Main Results:

• A structurally diverse and energetically equivalent set of configurations defines the TSE.
• The enzyme's macroscopic nature leads to a conformationally delocalized and asymmetric TSE.
• Experimental kinetics confirm a reduced entropy of activation consistent with a broad TSE.

Conclusions:

• Enzymes employ broad transition-state ensembles, not unique structures, for efficient catalysis.
• Conformational flexibility and delocalization are fundamental to enzymatic rate enhancement.
• The concept of broad TSEs unifies understanding of protein folding, dynamics, and function.