ArticleEuropean biophysics journal : EBJ2012
Ionizable side chains at catalytic active sites of enzymes.
Article in European biophysics journal : EBJ, 2012. 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.
- Repurposing Anti-Dengue Compounds against Monkeypox Virus Targeting Core Cysteine Protease.Biomedicines · 2023Article
- Setting Boundaries for Statistical Mechanics.Molecules (Basel, Switzerland) · 2022Review
- An Overview of Antennal Esterases in Lepidoptera.Frontiers in physiology · 2021Review
- On the polarization of ligands by proteins.Physical chemistry chemical physics : PCCP · 2020Article
- Hydrophobic ligands influence the structure, stability, and processing of the major cockroach allergen Bla g 1.Scientific reports · 2019Article
- Continuum Gating Current Models Computed with Consistent Interactions.Biophysical journal · 2019Article
- CASTp 3.0: computed atlas of surface topography of proteins.Nucleic acids research · 2018Article
- Insights into the structure and function of HV1 from a meta-analysis of mutation studies.The Journal of general physiology · 2016Review
- The novel structure of the cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment.The Journal of allergy and clinical immunology · 2013Article
- Interacting ions in biophysics: real is not ideal.Biophysical journal · 2013Review
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Authors and funding
3 authors.
Funding
Abstract
Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.
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