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Mechanisms of Membrane-bending01:15

Mechanisms of Membrane-bending

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The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
Membrane bending can happen due to intrinsic changes in lipid composition or extrinsic association with different proteins. The proteins involved...
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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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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Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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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,...
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Adaptability of Cytoskeletal Filaments01:12

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The cytoskeleton is a complex dynamic structure performing varied functions based on cellular requirements. The adaptability of the individual filaments in the cytoskeleton determines their ability to perform various functions within the cell. It can undergo rapid reorganization during processes like cell division or remain stable for several hours as in the interphase. The adaptability of these filaments depends on stringent regulatory mechanisms. The microfilament and microtubules of the...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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Related Experiment Video

Updated: Mar 24, 2026

Flexural Rigidity Measurements of Biopolymers Using Gliding Assays
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Flexural Rigidity Measurements of Biopolymers Using Gliding Assays

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Large scale rigidity-based flexibility analysis of biomolecules.

Ileana Streinu1

  • 1Department of Computer Science, Smith College , Northampton, Massachusetts 01063, USA.

Structural Dynamics (Melville, N.Y.)
|March 10, 2016
PubMed
Summary
This summary is machine-generated.

The KINematics And RIgidity (KINARI) project introduces Kinari-2, an enhanced web server for protein flexibility analysis. This tool supports large-scale experiments on complex biomolecules and integrates seamlessly with the Protein Data Bank.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Protein flexibility analysis is crucial for understanding biomolecular function.
  • Existing tools may not adequately handle large-scale or complex biomolecular systems.

Purpose of the Study:

  • To introduce Kinari-2, an upgraded web server for in silico protein flexibility analysis.
  • To extend functionality for large biomolecules, bioassemblies, and collections of related molecules.
  • To improve reproducibility and user accessibility for computational experiments.

Main Methods:

  • Development of advanced web technologies for enhanced user experience.
  • Implementation of robust data processing and computational algorithms for large-scale analysis.
  • Integration with the Protein Data Bank for seamless access to biomolecular structures.

Main Results:

  • Kinari-2 offers extended functionality for analyzing large molecules like viruses and crystals.
  • The system efficiently handles large collections of biomolecules from simulations.
  • Improved tools and emphasis on reproducibility are provided to users.

Conclusions:

  • Kinari-2 represents a significant advancement in in silico protein flexibility analysis.
  • The enhanced capabilities cater to large-scale, complex biomolecular research.
  • The project addresses key computational and validation challenges in the field.