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Related Concept Videos

Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction 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...
Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Heterogeneous Catalysis01:22

Heterogeneous Catalysis

Heterogeneous catalysis involves a catalyst in a different phase from the reactants. It is a process where the catalyst and the reactants are in distinct phases, typically solid and gas or liquid.Most heterogeneous catalysts are metals, metal oxides, or acids. The list includes transition metals like iron (Fe), cobalt (Co), nickel (Ni), palladium (Pd), platinum (Pt), chromium (Cr), manganese (Mn), tungsten (W), silver (Ag), and copper (Cu). These metals possess partially vacant d orbitals that...
Allosteric Proteins-ATCase01:19

Allosteric 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,...

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Related Experiment Video

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Identification of Novel CK2 Kinase Substrates Using a Versatile Biochemical Approach
11:11

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Published on: February 21, 2019

Structure-based identification of catalytic residues.

Ran Yahalom1, Dan Reshef, Ayana Wiener

  • 1Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.

Proteins
|April 15, 2011
PubMed
Summary

We developed a novel structure-based method to identify enzyme catalytic residues, outperforming existing approaches. This method addresses challenges in structural genomics by effectively handling class imbalance for accurate enzyme functional characterization.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Identifying catalytic residues is crucial for understanding enzyme function.
  • Evolution-based methods struggle with enzymes lacking database homologs (structural genomics targets).
  • A purely structural approach is needed to overcome these limitations.

Purpose of the Study:

  • To present a novel, purely structure-based method for identifying catalytic residues in enzymes.
  • To address the challenge of class imbalance between catalytic and non-catalytic residues.
  • To provide a computational tool for functional characterization of enzymes, especially in structural genomics.

Main Methods:

  • Utilized a support vector machine (SVM) classifier with novel structural features, including spatial averaging and Z scoring.
  • Implemented strategies to handle class imbalance: optimizing performance criteria, under-sampling non-catalytic residues, and differential error penalization during SVM training.
  • Tested the method on four diverse enzyme datasets, including one mimicking the structural genomics scenario.

Main Results:

  • The structure-based classifier demonstrated performance comparable or superior to existing structure-based and hybrid (structure + evolution) methods.
  • The method effectively managed the class imbalance problem inherent in catalytic residue identification.
  • Case studies suggested that false positive predictions might indicate other functional sites, such as binding pockets.

Conclusions:

  • The developed structure-based method is a robust and effective tool for identifying enzyme catalytic residues.
  • This approach offers a valuable alternative for enzymes with limited evolutionary information.
  • The findings contribute to the functional characterization of enzymes and have implications for drug discovery and enzyme engineering.