Related Experiment Video
Updated: Jul 12, 2026
09:42
Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
The mutability of enzyme active-site shape determinants.
1Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306-4390, USA. miller@chem.fsu.edu
Protein Science : a Publication of the Protein Society
|September 4, 2007
Summary
Enzyme active sites rely on more than just hydrogen bonds. Non-hydrogen bonding interactions, like van der Waals contacts, significantly influence enzyme activity and can be altered to redesign enzyme properties.
Area of Science:
- Biochemistry and Molecular Biology
- Enzyme Kinetics and Engineering
Background:
- Enzyme catalysis traditionally emphasizes hydrogen bonding interactions between active site residues and substrates.
- The role of non-hydrogen bonding contacts in enzymatic rate acceleration remains less understood.
Purpose of the Study:
- To investigate the significance of non-hydrogen bonding van der Waals contacts in enzymatic activity.
- To explore the potential for redesigning enzyme catalytic properties by modifying these interactions.
Main Methods:
- Site-directed mutagenesis was used to randomize six residues involved in van der Waals contacts within Escherichia coli glucokinase.
- In vivo selection in a glucokinase-deficient bacterial strain identified functional amino acid substitutions.
- Analysis of enzyme variants to assess retained activity compared to wild-type.
Main Results:
- Small residues (e.g., alanine, glycine) showed limited tolerance for substitution.
- Larger amino acids were more amenable to diverse substitution patterns.
- A variant with glycine replacing six non-hydrogen bonding contacts retained approximately 1% of wild-type glucokinase activity.
Conclusions:
- Non-hydrogen bonding shape determinants are crucial for enzyme function and stability.
- These interactions represent promising targets for enzyme redesign and engineering efforts.
- Modifying van der Waals contacts offers a viable strategy for altering enzyme catalytic properties.
Related Concept Videos
01:13Induced-fit Model
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
01:13Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild...
02:34Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
01:19Allosteric Proteins-ATCase
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...