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....

Fischer Projections

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.

Stereoisomerism of Cyclic Compounds

Stereoisomerism of Cyclic Compounds

In this lesson, we delve into the role of ring conformation and its stability, which determines the spatial arrangement and, consequently, the molecular symmetry and stereoisomerism of cyclic compounds. 1,2-Dimethylcyclohexane is used as a case study to evaluate the possible number of stereoisomers. Here, given the multiple (n = 2) chiral centers, there are 2n = 4 possible configurations that lack a plane of symmetry, as the ring skeleton exists in a non-planar chair conformation. In addition,...

Prochirality

Prochirality

The concept of prochirality leads to the nomenclature of the individual faces of a molecule and plays a crucial role in the enantioselective reaction. It is a concept where two or more achiral molecules react to produce chiral products. A typical process is the reaction of an achiral ketone to generate a chiral alcohol. Here, the achiral reactant reacts with an achiral reducing agent, sodium borohydride, to generate an equimolar mixture of the chiral enantiomers of the product. For example, an...

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration

Regioselectivity and Stereochemistry of Acid-Catalyzed Hydration

The rate of acid-catalyzed hydration of alkenes depends on the alkene's structure, as the presence of alkyl substituents at the double bond can significantly influence the rate.

You might also read

Related Articles

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

Sort by

Same author

pH Sensitivity of the SERF1a Conformational Ensemble.

ACS omega·2026

Same author

Protein-membrane interactions with a twist.

Soft matter·2025

Same author

Conformational Space of the Translocation Domain of Botulinum Toxin: Atomistic Modeling and Mesoscopic Description of the Coiled-Coil Helix Bundle.

International journal of molecular sciences·2024

Same author

New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand.

Molecules (Basel, Switzerland)·2023

Same author

Secondary structure assignment of proteins in the absence of sequence information.

Bioinformatics advances·2023

Same author

Low-resolution description of the conformational space for intrinsically disordered proteins.

Scientific reports·2022

Search research articles

Related Experiment Video

Updated: Jun 7, 2025

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

Influence of Stereochemistry in a Local Approach for Calculating Protein Conformations.

Wagner da Rocha¹, Leo Liberti¹, Antonio Mucherino²

¹LIX CNRS, École Polytechnique, Institut Polytechnique de Paris, Palaiseau 91128, France.

Journal of Chemical Information and Modeling

|November 19, 2024

Summary

This study introduces a novel method for protein structure prediction using only local conformational data and stereochemistry, improving accuracy for proteins with beta secondary structures. The approach connects torsion angle variations to rare DNA codons, enhancing computational efficiency.

More Related Videos

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

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 7, 2025

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

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

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
Structural Biology

Background:

Protein structure prediction often relies on template structures or sequence alignments.
Sequence alignment methods face accuracy limitations with few aligned sequences.
Local conformational information and long-range restraints are key components.

Purpose of the Study:

To develop a protein conformation derivation method using solely local conformational knowledge.
To enhance computational efficiency in protein structure prediction.
To explore the relationship between stereochemistry, torsion angles, and DNA codons.

Main Methods:

Utilized the interval Branch-and-Prune algorithm.
Incorporated stereochemical knowledge, including bond angles and omega (ω) torsion angles.
Systematically enumerated possible conformations.
Analyzed DNA codons to link torsion angle variations.

Main Results:

Successfully derived protein conformations using only local information.
Demonstrated improved computational efficiency linked to stereochemistry, especially omega (ω) angle variations.
Showcased a strong impact of stereochemistry on protein topologies with extensive long-range restraints, like beta secondary structures.
Established a connection between omega (ω) torsion angle variations and the positions of rare DNA codons.

Conclusions:

The interval Branch-and-Prune algorithm offers an effective approach for protein structure prediction using local data.
Stereochemistry, particularly omega (ω) torsion angle dynamics, significantly influences prediction accuracy and efficiency.
The findings provide insights into the interplay between protein structure, stereochemistry, and genetic code.