ArticleBMC bioinformatics2014
Anatomy of enzyme channels.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Capturing Fast Gas Migration in Proteins.Molecules (Basel, Switzerland) · 2026Review
- Protein Structuromics Reveals a Loop-Controlled Half-Open Active Pocket Conformation Throughout Fe(II)/α-ketoglutarate-Dependent Dioxygenase Catalytic Cycle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Correction to: Pathogenicity patterns in cytochrome P450 family.Bioinformatics advances · 2026Article
- MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update).Bioinformatics (Oxford, England) · 2025Article
- Hybrid protein-ligand binding residue prediction with protein language models: does the structure matter?Bioinformatics (Oxford, England) · 2025Article
- Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins.Nucleic acids research · 2025Article
- Studying Noncovalent Interactions in Molecular Systems with Machine Learning.Chemical reviews · 2025Review
- Surveying Enzyme Crystal Structures Reveals the Commonality of Active-Site Solvent Accessibility and Enzymatic Water Networks.ACS omega · 2025Article
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.Journal of chemical information and modeling · 2025Article
- Pathogenicity patterns in cytochrome P450 family.Bioinformatics advances · 2025Article
- Systematic pore lipophilization to enhance the efficiency of an amine-based MOF catalyst in the solvent-free Knoevenagel reaction.Beilstein journal of organic chemistry · 2025Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.Nucleic acids research · 2024Article
- Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein fromBiomolecules · 2023Article
- Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls.Journal of chemical information and modeling · 2022Article
- Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.International journal of molecular sciences · 2022Article
- Enhancing the Biological Activities of Food Protein-Derived Peptides Using Non-Thermal Technologies: A Review.Foods (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEnzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common.
resultsHere, we analyze the long channels (i.e. >15 Å) leading to the active sites of 4,306 enzyme structures. We find that over 64% of enzymes contain two or more long channels, their typical length being 28 Å. We show that amino acid compositions of the channel significantly differ both to the composition of the active site, surface and interior of the protein.
conclusionsThe majority of enzymes have buried active sites accessible via a network of access channels. This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.