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

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

Force and Potential Energy in One Dimension

Force and Potential Energy in One Dimension

Force can be calculated from the expression for potential energy, which is a function of position. The component of a conservative force, in a particular direction, equals the negative of the derivative of the corresponding potential energy with respect to the displacement in that direction. For regions where potential energy changes rapidly with displacement, the work done and force is maximum. Also, when force is applied along the positive coordinate axis, the potential energy decreases with...

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

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 form...

You might also read

Related Articles

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

Sort by

Same author

Modeling bond correlations in denatured proteins and polypeptides.

Biopolymers·2016

Same author

Optimization of Monte Carlo trial moves for protein simulations.

The Journal of chemical physics·2011

Same author

Comparison between molecular dynamic based and knowledge based potentials for protein side chains.

Journal of computational biology : a journal of computational molecular cell biology·2010

Same author

Empirical model of residue contact probabilities for polypeptides.

The Journal of chemical physics·2010

Same author

Coarse-grained protein model with residue orientation energies derived from atomic force fields.

The journal of physical chemistry. B·2009

Same author

Another look at the conditions for the extraction of protein knowledge-based potentials.

Proteins·2008

Search research articles

Related Experiment Video

Updated: Jun 22, 2026

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.

Marcos R Betancourt¹, Sheyore J Omovie

¹Department of Physics, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD156-J Indianapolis, Indiana 46202, USA. mbetancourt@mailaps.org

The Journal of Chemical Physics

|May 27, 2009

Summary

This summary is machine-generated.

This study developed a simplified protein coarse-grained model using molecular dynamics. The model effectively identifies native protein structures, showing promise for computational biology despite some discrepancies in residue interactions.

More Related Videos

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

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: Jun 22, 2026

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

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:

Computational Biology
Biophysics
Protein Structure Prediction

Background:

Protein structure prediction is crucial for understanding biological function.
Coarse-grained models offer a computationally efficient alternative to all-atom simulations.
Accurate energy parametrization is key to the success of coarse-grained models.

Purpose of the Study:

To develop and validate a statistically derived coarse-grained model for polypeptides.
To assess the model's ability to identify native protein structures.
To compare the model's performance against knowledge-based potentials and hydrophobicity scales.

Main Methods:

Atomic-level simulations in explicit water for all amino acid pairs.
Calculation of radial density functions and extraction of statistical energies via Boltzmann inversion.
Comparison of the derived model with existing knowledge-based potentials and hydrophobicity scales.

Main Results:

The coarse-grained model shows significant similarities to existing potentials and scales.
Certain residues (glutamine, asparagine, lysine, arginine) exhibit unexpected attractive interactions.
Equally charged residues display greater repulsion than anticipated.
The model successfully identifies native structures in decoy databases, comparable to more complex methods.

Conclusions:

The developed coarse-grained model provides a simplified yet effective approach for protein structure identification.
Discrepancies in specific residue interactions may stem from limitations in knowledge-based potentials and hydrophobicity scales.
The model's performance in identifying native states highlights its utility in computational protein studies.