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Related Concept Videos

The DNA Helix01:16

The DNA Helix

Overview
Chair Conformation of Cyclohexane02:02

Chair 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...
Newman Projections02:06

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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.
DNA Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
Conformations of Cyclohexane02:11

Conformations 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,...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

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Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
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An automated method for consistent helix assignment using turn information.

Oliver Koch1, Jason Cole

  • 1The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom. oliver.koch@sp.intervet.com

Proteins
|March 3, 2011
PubMed
Summary
This summary is machine-generated.

A novel automated method improves protein helix boundary identification, particularly for C-termini. This enhances structural analysis and protein database consistency.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate identification of protein secondary structures, specifically alpha-helices, is crucial for understanding protein function and dynamics.
  • Existing methods for defining helix termini can exhibit inconsistencies, particularly at the C-terminus, impacting structural analysis.

Purpose of the Study:

  • To introduce a new automated method for assigning protein helix boundaries with improved consistency.
  • To refine the definition of helix termini, with a specific focus on enhancing C-terminal boundary assignment.

Main Methods:

  • The method identifies helices based on adjacent helical turn structures and specific capping motifs (e.g., Schellman motif).
  • Helix termini are assigned by analyzing the hydrogen bonding potential of N-terminal NH and C-terminal CO groups, requiring them to be free for external interactions.

Main Results:

  • The automated method provides a more consistent definition of helix termini compared to previous approaches.
  • This leads to more reliable helix assignments, especially for the C-terminal regions of alpha-helices.

Conclusions:

  • The new automated helix assignment method offers enhanced accuracy and consistency in defining protein secondary structure elements.
  • The method and its assignments are integrated into structural databases (Secbase, Relibase+ 3.0) and are available for broader use in protein structure analysis.