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

Assembly of Cytoskeletal Filaments

Assembly of Cytoskeletal Filaments

Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...

Fibrous Proteins

Fibrous Proteins

Fibrous proteins are either long and narrow proteins or assemble to form long and thin structures. They contain repetitive units and usually consist of either alpha helices or beta sheets and, in rare cases, a mix of both. The amino acids in the primary structure often consist of repeating amino acid sequences. The role of fibrous proteins is primarily structural. Many are located in the extracellular matrix and are present in connective tissues to impart strength and joint mobility. They are...

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 can...

Formation of Intermediate Filaments

Formation of Intermediate Filaments

Intermediate filaments are cytoskeletal proteins with higher tensile strength and flexibility than microfilaments and microtubules. Unlike the other two cytoskeletal proteins, intermediate filament formation lacks the enzymatic activity to hydrolyze nucleotides like ATP and GTP to generate energy for polymerization. Therefore, the formation of intermediate filaments is multistep self-assembly. The involvement of any accessory proteins in intermediate filament formation has not yet been reported.

Formation of Higher-order Actin Filaments

Formation of Higher-order Actin Filaments

The polymerization of G-actin monomers into filamentous F-actin is a multi-step process. Once the F-actins are formed, they can bundle together in different arrangements to form higher-order networks and regulate cellular functions. Common examples include the formation of lamellipodia and filopodia at the cell's leading edge by actin reorganization in a migrating cell. The microvilli on the brush border epithelial cells are also formed through the F-actin network.
The high-order actin networks...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

You might also read

Related Articles

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

Sort by

Same author

MDNA : a software module for DNA structure generation and analysis.

Nucleic acids research·2026

Same author

Nucleation of NaCl crystals from solution: Rate prediction and influence of noisy order parameters on the committor.

The Journal of chemical physics·2026

Same author

Understanding Mechanisms of Molecular Rare Events from Start to Finish.

Physical review letters·2026

Same author

To include or not to include? A prescription from the pharmacy on how to use active learning-assisted screening in systematic reviews.

Systematic reviews·2026

Same author

Combining multiple interface set path ensembles with MBAR reweighting.

The Journal of chemical physics·2026

Same author

Learned free-energy functionals from pair-correlation matching for dynamical density functional theory.

Physical review. E·2025

Search research articles

Related Experiment Video

Updated: Jun 16, 2026

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

A simple coarse-grained model for self-assembling silk-like protein fibers.

Marieke Schor¹, Bernd Ensing, Peter G Bolhuis

¹Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

Faraday Discussions

|February 18, 2010

Summary

We developed a coarse-grained model for collagen-silk-collagen polypeptides, enabling large-scale simulations of fiber formation and properties. This approach allows detailed investigation into fiber assembly and dynamics.

More Related Videos

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Related Experiment Videos

Last Updated: Jun 16, 2026

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

Published on: August 13, 2014

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Area of Science:

Biomaterials Science
Computational Biology
Polymer Physics

Background:

Collagen-silk-collagen triblock polypeptides self-assemble into micron-length fibers.
Previous all-atom simulations predicted a beta-roll structure for the silk domain.

Purpose of the Study:

Develop a coarse-grained model for silk domains to study fiber properties and formation at larger scales.
Optimize model parameters using all-atom simulation data and experimental results.

Main Methods:

Adapted and optimized a coarse-grained model (Brown et al., 2003).
Used steered molecular dynamics (MD) and Jarzynski relation to determine inter-residue attraction strength.
Simulated spontaneous folding of peptides and stability of beta-roll structures and fibers.

Main Results:

Optimized coarse-grained model successfully reproduced all-atom simulation structural data.
Observed spontaneous folding of short peptides and stability of beta-roll structures and fibers.
Predicted fiber persistence length aligns with experimental data.

Conclusions:

The coarse-grained model enables large-scale simulations of polypeptide fiber formation and properties.
This approach facilitates investigation into fiber nucleation, growth, cross-linking, network dynamics, and rheology.
Validated coarse-grained model efficacy for simulating complex biological structures.