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Related Concept Videos

Enzymes02:34

Enzymes

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 Kinetics01:19

Enzyme Kinetics

Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
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...
Induced-fit Model01:13

Induced-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...
Introduction to Enzyme Kinetics01:19

Introduction to Enzyme Kinetics

Enzyme kinetics studies the rates of biochemical reactions. Scientists monitor the reaction rates for a particular enzymatic reaction at various substrate concentrations. Additional trials with inhibitors or other molecules that affect the reaction rate may also be performed.
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

3D-Fun: predicting enzyme function from structure.

Marcin von Grotthuss1, Dariusz Plewczynski, Gert Vriend

  • 1CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

Nucleic Acids Research
|June 3, 2008
PubMed
Summary
This summary is machine-generated.

3D-Fun is a new software tool that annotates protein function using 3D structure comparison when sequence analysis fails. This structural genomics approach aids in understanding protein function from structural data.

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09:51

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • The 'omics' revolution generates vast amounts of data requiring functional annotation.
  • Protein function is often inferred through sequence similarity (e.g., BLAST), but this fails for novel proteins.
  • Structural genomics provides 3D structures for proteins, offering an alternative avenue for functional prediction.

Purpose of the Study:

  • To present 3D-Fun, a novel software tool for annotating protein function using 3D structural comparisons.
  • To provide a freely accessible web server for researchers to determine protein function when sequence-based methods are insufficient.

Main Methods:

  • 3D-Fun accepts protein coordinates in Protein Data Bank (PDB) format.
  • It performs 3D structural superposition against a database of known protein structures using the 3D-Hit software.
  • Results include functional annotations and comparison statistics for structurally similar proteins.

Main Results:

  • 3D-Fun successfully identifies proteins with known functions based on structural similarity.
  • The system provides interactive graphical displays of superposition results.
  • Currently, it predicts enzyme function, with future expansion to Gene Ontology predictions.

Conclusions:

  • 3D-Fun offers a valuable complementary approach to sequence-based methods for protein function annotation.
  • The software addresses a critical need in structural genomics for interpreting the function of proteins with known structures but unknown roles.
  • The accessibility of the 3D-Fun server facilitates broader research applications in understanding protein function.