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Enzyme Binding Dynamics: History
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Contributor: Yu Peng

Enzyme binding dynamics encompasses the time-dependent molecular processes through which an enzyme associates with, interacts with, conformationally responds to, and dissociates from a binding partner such as a substrate, inhibitor, cofactor, or regulatory ligand. Binding occurs within an ensemble of interconverting enzyme conformations, and transitions among these conformational substates can alter the accessibility, geometry, and physicochemical properties of binding sites [1][2]. The concept includes the kinetics of molecular association and dissociation, transient enzyme–ligand configurations, conformational exchange accompanying complex formation, and fluctuations within the bound complex. These processes span multiple temporal and spatial scales, from local atomic and side-chain fluctuations to larger loop or domain rearrangements [2][3]. Enzyme binding dynamics therefore describes binding as a molecular trajectory through conformational and interaction states whose populations and interconversion rates determine how ligand recognition and occupancy develop over time [1,3]. Within enzyme function and inhibition, its scope encompasses substrate, product, cofactor, activator, and inhibitor interactions insofar as their association, residence, conformational coupling, and release are properties of the enzyme–ligand binding process [2][4].

  • Enzyme–ligand binding
  • binding kinetics
  • conformational dynamics
  • molecular recognition

🔵 Enzyme function and inhibition • 🟣 Molecular Biology • 🟡 Biochemistry, Genetics and Molecular Biology • 🔴 Life Sciences

References

  1. Gordon G. Hammes; Yu-Chu Chang; Terrence G. Oas; Conformational Selection or Induced Fit: A Flux Description of Reaction Mechanism. Proc. Natl. Acad. Sci. 2009, 106, 13737-13741, 10.1073/pnas.0907195106.
  2. Chitra Narayanan; David N. Bernard; Nicolas Doucet; Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies. Catal. 2016, 6, 81, 10.3390/catal6060081.
  3. Rajni Verma; Katie Mitchell-Koch; In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catal. 2017, 7, 212, 10.3390/catal7070212.
  4. Sharon Hammes-Schiffer; Stephen J. Benkovic; Relating Protein Motion to Catalysis. Annu. Rev. Biochem. 2006, 75, 519-541, 10.1146/annurev.biochem.75.103004.142800.
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