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Related Concept Videos

Protein Folding01:25

Protein Folding

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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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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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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Updated: Sep 16, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Mapping the Conformational Heterogeneity Intrinsic to the Protein Native Ensemble.

Adithi Kannan1, Athi N Naganathan1

  • 1Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.

Biochemistry
|July 4, 2025
PubMed
Summary
This summary is machine-generated.

Protein structure prediction is advancing, but a single structure is insufficient for understanding function. A dynamic ensemble of protein states is crucial for a complete functional picture.

Keywords:
MD simulationsWSME modelensemblemass spectrometrynuclear magnetic resonancesingle-molecule FRETspectroscopystructure

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Deep learning models like AlphaFold accelerate protein structure prediction.
  • A single static protein structure often fails to capture the full functional complexity.
  • Understanding protein dynamics is essential for elucidating biological function.

Purpose of the Study:

  • To review experimental and computational methods for characterizing protein conformational landscapes.
  • To emphasize the importance of protein dynamics and conformational heterogeneity.
  • To advocate for an integrative 'sequence-ensemble-function' paradigm.

Main Methods:

  • Overview of experimental techniques for probing protein dynamics.
  • Discussion of computational approaches for modeling conformational ensembles.
  • Highlighting integrative strategies combining different resolution data.

Main Results:

  • Native protein ensembles exhibit significant conformational heterogeneity.
  • High-resolution methods reveal greater complexity in protein dynamics.
  • Partially structured states and transient conformations are common.

Conclusions:

  • A single protein structure is a limited view; the ensemble of states is key.
  • The 'sequence-ensemble-function' paradigm is vital for understanding protein behavior.
  • Integrative approaches with multiprobe experiments and physical models are necessary.