Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Cooperative Allosteric Transitions

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...

Ligand Binding Sites

Ligand 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...

Conserved Binding Sites

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

From First Principles to Function: How AI Is Reshaping Enzyme Design.

Biochemistry·2026

Same author

An engineered closed-shell, two-component, 480-subunit nucleocapsid.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Identification of overoxidizing and non-overoxidizing NAD-dependent methanol dehydrogenases and implications for synthetic methylotrophy.

Nature communications·2025

Same author

Computational design of cysteine proteases.

bioRxiv : the preprint server for biology·2025

Same author

Computational design of metalloproteases.

bioRxiv : the preprint server for biology·2025

Same author

Computational design of metallohydrolases.

Nature·2025

Search research articles

Related Experiment Video

Updated: May 12, 2026

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

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

Published on: July 25, 2013

Affinity maturation of a computationally designed binding protein affords a functional but disordered polypeptide.

Maren Butz¹, Peter Kast¹, Donald Hilvert¹

¹Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland.

Journal of Structural Biology

|March 30, 2013

Summary

Engineered proteins can be improved using yeast display, enhancing binding affinity to targets like human p21-activated kinase 1 (PAK1). Optimized variants unexpectedly show characteristics of partially disordered proteins, suggesting flexibility is key for protein design.

Keywords:

Computational design Directed evolution Intrinsically disordered proteins Molten globule Protein–protein interactions Protein–receptor interface Yeast surface display

More Related Videos

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: May 12, 2026

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

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

Published on: July 25, 2013

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Protein engineering
Computational biology
Structural biology

Background:

Protein-protein interactions are crucial in cellular signaling.
Computational methods are emerging for designing novel protein interfaces.
Initial design of Spider Roll protein showed specific but low-affinity binding to PAK1 kinase domain.

Purpose of the Study:

To optimize the binding affinity of the engineered Spider Roll protein to human p21-activated kinase 1 (PAK1).
To investigate the structural and biophysical properties of optimized protein variants.
To assess the role of conformational disorder in protein function and design.

Main Methods:

Protein engineering using computational design.
Optimization via yeast surface display and fluorescence-activated cell sorting.
Biophysical characterization including thermal denaturation and Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Results:

Three rounds of mutagenesis and screening yielded variants with significantly improved affinity for PAK1.
The optimized variant MSR7 exhibited >100-fold higher affinity on yeast and 6-11 fold higher affinity in solution compared to the original Spider Roll.
MSR7 displayed characteristics of partially disordered proteins, including reduced alpha-helical content and non-cooperative denaturation.

Conclusions:

Yeast surface display is effective for optimizing computationally designed proteins.
Conformational disorder may be an important feature for proteins involved in signaling and regulation.
Current computational design methods may need to incorporate structural flexibility for improved protein engineering.