Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, the...
Conformations of Butane02:20

Conformations of Butane

Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are degenerate and have...
¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of...
Energy to Drive Translocation01:37

Energy to Drive Translocation

Mitochondrial protein import is powered by two distinct energy sources: ATP hydrolysis and electrochemical potential across the inner membrane. Newly synthesized precursors are bound by cytosolic chaperones of the Hsp70 family, which guide them to the import receptors on the mitochondrial surface. Utilizing the energy of ATP hydrolysis, Hsp70 chaperones transfer these precursors to the TOM receptors on the mitochondrial outer membrane.
Generally, polypeptides are unfolded by two distinct...
π Electron Effects on Chemical Shift: Overview01:27

π Electron Effects on Chemical Shift: Overview

An applied magnetic field causes loosely bound π-electrons in organic molecules to circulate, producing a local or induced diamagnetic field over a large spatial volume. As the molecules tumble in solution, the field generated by π-electrons in spherical substituents results in a zero net field. However, the net field generated by π-electrons in non-spherical substituents is not zero. The effect of this induced field depends on the orientation of the molecule with respect to B0, resulting in...
Protein Folding01:25

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...

You might also read

Related Articles

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

Sort by
Same author

Conformations of polyglutamate chains near single walled carbon nanotubes.

Biophysical chemistry·2026
Same author

Conformations of semiflexible ring polymers.

Physical chemistry chemical physics : PCCP·2026
Same author

Local Structure and Dynamics of Hydration Water in Amyloid-β Aggregation and Caffeine-Mediated Inhibition.

The journal of physical chemistry. B·2025
Same author

Radical Formation by Direct Single Electron Transfer between Nitrobenzene and Anionic Organo Bases.

ACS omega·2025
Same author

Evaluating multi-state free energy profiles from splitting probability.

The Journal of chemical physics·2025
Same author

Rheology of Ring Copolymers in Dilute Solutions.

The journal of physical chemistry. B·2024

Related Experiment Video

Updated: May 26, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Are ambivalent α-helices entropically driven?

Nicholus Bhattacharjee1, Parbati Biswas

  • 1Department of Chemistry, University of Delhi, Delhi 110007, India.

Protein Engineering, Design & Selection : PEDS
|December 21, 2011
PubMed
Summary

Structurally ambivalent helices form due to favorable native contacts, despite lower backbone conformational entropy. This study reveals the driving forces behind these protein structures.

Area of Science:

  • Protein structure and dynamics
  • Biophysics
  • Computational biology

Background:

  • Structurally ambivalent sequences adopt multiple secondary structures within different protein contexts.
  • Understanding the factors governing these conformational preferences is crucial for protein design and function.

Purpose of the Study:

  • To characterize the conformational preference of ambivalent helices using backbone conformational entropy.
  • To identify the key stabilizing factors for helical conformations in ambivalent sequences.

Main Methods:

  • Calculation of backbone conformational entropy using the phi-psi dihedral angle range of entire peptide segments and individual amino acids.
  • Analysis of native contacts in protein structures.
  • Validation using conserved helices from the non-redundant database and the Structural Classification of Proteins database.

More Related Videos

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Related Experiment Videos

Last Updated: May 26, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Main Results:

  • Variable ambivalent helices exhibit lower conformational entropy in helical states when considering the entire segment's dihedral angles.
  • Favorable native contacts are a primary stabilizer for helical conformations.
  • An opposite trend in conformational entropy is observed when analyzing individual amino acid dihedral angles.
  • Peptide segments show reluctance to form helices but are driven by native contacts and optimal phi-psi angles.

Conclusions:

  • Ambivalent helices are formed due to a balance between intrinsic conformational preferences and stabilizing interactions like native contacts.
  • Context plays a significant role in determining the final conformation of ambivalent sequences.
  • Findings can aid in understanding ambivalent helix formation and designing novel proteins.