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

Conservation of Protein Domains Over Different Proteins

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...

Protein Complexes with Interchangeable Parts

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Mechanical Protein Function

Mechanical Protein Function

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

Conservation of Protein Domains

Conservation of Protein Domains

You might also read

Related Articles

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

Sort by

Same author

The Phenotypic Landscape of a Circadian Clock.

bioRxiv : the preprint server for biology·2026

Same author

Cytoplasmic abundant heat-soluble proteins from tardigrades protect synthetic cells under stress.

Nature communications·2026

Same author

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq.

bioRxiv : the preprint server for biology·2026

Same author

Characterizing Defect Dynamics in Silicon Carbide Using Symmetry-Adapted Collective Variables and Machine Learning Interatomic Potentials.

Journal of chemical theory and computation·2026

Same author

Simple biological controllers drive the evolution of soft modes.

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

Same author

Global genomic diversity of the selfing nematode <i>Caenorhabditis tropicalis</i> correlates with geography.

bioRxiv : the preprint server for biology·2026

Same journal

The TaMYB55-TaSnRK1α1-TabZIP9 module confers heat stress tolerance in wheat.

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

Same journal

Superstatistics approach to turbulent circulation fluctuations.

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

Same journal

A molecular timescale for evolution of cobamide biosynthesis.

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

Same journal

Pierre Chambon, a pioneer of molecular biology and gene regulation in eukaryotes.

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

Same journal

Granulosa cell glycogen fuels the avascular corpus luteum.

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

Same journal

Synthetic essentiality of TRAIL/TNFSF10 in VHL-deficient renal cell carcinoma.

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

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 15, 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

ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design.

Emre Sevgen¹, Joshua Moller¹, Adrian Lange¹

¹Evozyne, Inc., Chicago, IL 60614.

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

|October 6, 2025

Summary

This summary is machine-generated.

We developed the Protein Transformer Variational AutoEncoder (ProT-VAE) for data-driven protein design. This model accelerates the discovery of synthetic proteins with enhanced functions, including enzymes with improved catalytic activity and thermostability for industrial applications.

Keywords:

generative modeling protein design protein language models transformers variational autoencoders

More Related Videos

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

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: Jan 15, 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

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

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:

Biotechnology
Computational Biology
Protein Engineering

Background:

Deep generative models excel at predicting protein sequence-function relationships.
Designing synthetic proteins with novel functionalities requires advanced computational tools.

Purpose of the Study:

Introduce the Protein Transformer Variational AutoEncoder (ProT-VAE) for data-driven protein design.
Leverage variational autoencoders and transformer-based models for enhanced protein sequence design.
Validate ProT-VAE's performance in functional prediction and design.

Main Methods:

Implemented ProT-VAE using NVIDIA's BioNeMo framework.
Combined variational autoencoders for latent embeddings with transformer models for featurization.
Validated the model through retrospective functional prediction and prospective functional design.

Main Results:

Identified a phenylalanine hydroxylase with 2.5x wild-type catalytic activity.
Engineered a gamma-carbonic anhydrase with a +61°C melting temperature elevation.
Demonstrated enzyme activity under industrially relevant conditions for carbon capture.

Conclusions:

ProT-VAE is an accurate, fast, and transferable model for protein design.
The model enables the discovery of synthetic proteins with engineered functions.
ProT-VAE serves as a powerful platform for machine learning-guided directed evolution.