Related Experiment Video
Updated: Jul 19, 2026
06:35
Construction and Systematical Symmetric Studies of a Series of Supramolecular Clusters with Binary or Ternary Ammonium Triphenylacetates
Published on: February 15, 2016
Structural transitions in the polyalanine alpha-helix under uniaxial strain
Joel Ireta1, Jörg Neugebauer, Matthias Scheffler
1Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin-Dahlem, Germany. ireta@fhi-berlin.mpg.de
Journal of the American Chemical Society
|December 8, 2005
Summary
Stretching or compressing a polyalanine alpha-helix causes structural changes. Compressing induces a pi-helix, while stretching results in a 3(10)-helix, with length adjusting before helix twist.
Area of Science:
- Computational chemistry
- Biophysics
- Materials science
Background:
- The alpha-helix is a fundamental protein secondary structure.
- Understanding its mechanical properties is crucial for protein folding and function.
- Deformation of helical structures can alter biological activity.
Purpose of the Study:
- To investigate the mechanical response of an infinite polyalanine alpha-helix under strain.
- To identify structural transitions induced by compressive and tensile strain.
- To elucidate the step-by-step mechanism of these strain-induced transitions.
Main Methods:
- Density functional theory (DFT) calculations were employed.
- Simulations analyzed the behavior of a polyalanine chain in alpha-helical conformation.
- The response to varying degrees of compressive and tensile strain was modeled.
Main Results:
- Compressive strain (>10% length reduction) induced a transition to a pi-helix.
- Tensile strain (>10% length increase) resulted in a transition to a 3(10)-helix.
- Structural transitions occurred in two distinct steps: initial length change followed by helix twist adjustment.
Conclusions:
- Polyalanine alpha-helices exhibit distinct structural transitions under mechanical strain.
- The sequence of length change preceding helix twist adjustment is a key feature of these transitions.
- These findings provide insights into the mechanical stability and deformation mechanisms of helical peptides.
More Related Videos
Related Concept Videos
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
02:06Newman 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 conformers.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
02:11Conformations of Cyclohexane
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
02:02Chair Conformation of Cyclohexane
The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
01:28Structures of Carboxylic Acid Derivatives
Structure of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
01:19Structure of Amines
The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...