ArticleScientific reports2016
Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- GDEE: A Structure-Based Platform for Gene Discovery and Enzyme Engineering.Journal of chemical information and modeling · 2026Article
- An MD View of Ligand Binding.Molecules (Basel, Switzerland) · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Enhancing the activity and succinyl-CoA specificity of 3-ketoacyl-CoA thiolase Tfu_0875 through rational binding pocket engineering.Synthetic and systems biotechnology · 2024Article
- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design.International journal of molecular sciences · 2022Article
- Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.Journal of biological physics · 2022Review
- Examining a Thermodynamic Order Parameter of Protein Folding.Scientific reports · 2018Article
- Quantum mechanics implementation in drug-design workflows: does it really help?Drug design, development and therapy · 2017Review
- Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases.International journal of molecular sciences · 2016Review
- Protein dynamics: Conformational footprints.Nature chemical biology · 2016Article
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Authors and funding
2 authors.
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Abstract
Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the "hot-spot" within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.
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