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Related Concept Videos

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in 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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: Jun 9, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Conformational diversity and computational enzyme design.

Jonathan K Lassila1

  • 1Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. jklassila@gmail.com

Current Opinion in Chemical Biology
|September 11, 2010
PubMed
Summary
This summary is machine-generated.

Computational protein design can create new enzymes, but rigid backbones are limiting. This review explores incorporating protein dynamics and flexibility for improved enzyme design.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Computational protein design aims to create novel enzymes with specific catalytic functions.
  • Traditional methods often simplify protein backbones as rigid structures for computational efficiency.
  • Natural enzymes exhibit dynamic conformational changes crucial for their function, challenging fixed-backbone models.

Purpose of the Study:

  • To review the impact of protein conformational variation and dynamics on computational enzyme design.
  • To highlight advanced computational approaches that account for protein flexibility in enzyme design.

Main Methods:

  • Review of current literature on computational protein design and enzyme dynamics.
  • Analysis of strategies for incorporating multi-state design principles.
  • Examination of methods addressing backbone flexibility and computational library design.

Main Results:

  • Fixed-backbone approximations in computational design present significant challenges.
  • Protein dynamics and conformational diversity are critical factors for effective enzyme function.
  • Emerging computational techniques offer solutions to model and leverage protein flexibility.

Conclusions:

  • Integrating protein dynamics and conformational flexibility is essential for advancing computational enzyme design.
  • New methods like multi-state design and backbone flexibility modeling are key to future catalyst development.
  • Addressing conformational diversity will enable the creation of more efficient and specific artificial enzymes.