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

Protein Organization

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....

Protein Organization

Protein Organization

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Protein Folding

Protein Folding

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 and Protein Structures

Protein and Protein Structures

You might also read

Related Articles

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

Sort by

Same author

Reconstruction of septin higher-order nano-size structures in ovarian cancer cells uncover susceptibility to the septin-targeting small molecule UR214-9.

bioRxiv : the preprint server for biology·2026

Same author

Mechanistic role of APOE lipidation in Alzheimer's disease pathogenesis.

Theranostics·2026

Same author

Modular Deep Learning for Direct RNA Sequence Design via Self-Contained RNA Units.

bioRxiv : the preprint server for biology·2026

Same author

A diffusion-based framework for designing molecules in flexible protein pockets.

Science advances·2026

Same author

ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.

bioRxiv : the preprint server for biology·2026

Same author

Unified protein-small molecule graph neural networks for binding site prediction.

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

Same journal

Transpulmonary proteomic gradient analysis in women with pulmonary arterial hypertension associated with systemic sclerosis.

Journal of proteomics·2026

Same journal

Multiomic insights into fungal polylactic acid degradation: Metabolic adaptation and hydrolytic mechanisms of Sporobolomyces pararoseus.

Journal of proteomics·2026

Same journal

Temporal proteomic analysis reveals a three-phase adaptation strategy in Phytophthora cinnamomi during salinity stress.

Journal of proteomics·2026

Same journal

Proteomic and phosphoproteomic profiles of time-dependent dynamic changes in LPS-induced macrophage polarization.

Journal of proteomics·2026

Same journal

From prediction to mechanism: Explainable AI uncovers plasma and CSF proteomic signatures of Alzheimer's disease.

Journal of proteomics·2026

Same journal

Twenty years of the Mexican Proteomics Society.

Journal of proteomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 24, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Experimentally-driven protein structure modeling.

Nikolay V Dokholyan¹

¹Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.

Journal of Proteomics

|April 9, 2020

Summary

This summary is machine-generated.

Experimentally-driven computational modeling reveals protein structures and dynamics. This hybrid approach integrates diverse experimental data for a comprehensive molecular view, overcoming limitations of traditional methods.

Keywords:

Discrete molecular dynamics Mass spectrometry Molecular dynamics simulations Molecular modeling Statistical mechanics Structural proteomics

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

Related Experiment Videos

Last Updated: Dec 24, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

Area of Science:

Structural Biology
Computational Chemistry
Biophysics

Background:

Modern science utilizes theoretical, experimental, and computational methods to study molecular structures and dynamics.
Experimental techniques provide data at specific time and length scales, requiring tailored computational approaches.
Integrating multi-scale experimental data offers a comprehensive understanding of molecular structure and motion.

Purpose of the Study:

To describe computational approaches for utilizing experimental data to determine protein structure and dynamics.
To review the limitations and resolution of constraints-based modeling.
To highlight the significance of experimentally-driven computational modeling as an alternative to traditional methods.

Main Methods:

Utilizing experimental data within computational frameworks.
Tailoring computational methods to match experimental time and length scales.
Integrating data from various experiments for a holistic molecular picture.

Main Results:

Development of computational approaches to analyze experimental data for protein structure and dynamics.
Identification of limitations and resolution constraints in modeling.
Demonstration of the power of hybrid experimental-computational methods.

Conclusions:

Experimentally-driven computational modeling is a rapidly advancing field.
Hybrid approaches provide powerful insights into disordered proteins and molecular dynamics.
This review outlines various methods in experimentally-driven computational structure modeling.