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Related Concept Videos

Protein Folding01:25

Protein Folding

8.2K
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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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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Amyloid Fibrils03:03

Amyloid Fibrils

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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining,...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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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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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Rethinking the protein folding problem from a new perspective.

Jorge A Vila1

  • 1IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina. jorgevila84@gmail.com.

European Biophysics Journal : EBJ
|May 10, 2023
PubMed
Summary
This summary is machine-generated.

Understanding protein folding remains a challenge. This study re-examines protein folding as an analytic whole, proposing new approaches to accurately predict protein structures and understand folding mechanisms.

Keywords:
AlphaFoldAnalytic wholeAnfinsenForce fieldLeibniz and KantProtein folding

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational chemistry

Background:

  • Anfinsen's work highlighted the link between amino acid sequence and protein conformation.
  • Key questions in structural biology: why proteins fold and how sequences encode folding.
  • The thermodynamic hypothesis addresses 'why' proteins fold, but 'how' remains challenging.

Purpose of the Study:

  • To re-examine the protein folding problem from a new perspective: an 'analytic whole'.
  • To analyze the limitations of current force-field-based methods in predicting protein 3D structures.
  • To propose improvements for these methods and explore the success of current numerical prediction techniques.

Main Methods:

  • Conceptual redefinition of protein folding as an 'analytic whole'.
  • Critical analysis of force-field-based approaches in structural biology.
  • Exploration of numerical methods for protein structure prediction.

Main Results:

  • Identified reasons for the failure of force-field-based methods in accurate 3D structure prediction.
  • Proposed modifications to force-field methods to overcome current limitations.
  • Conjectured on the underlying principles enabling the success of advanced numerical methods.

Conclusions:

  • A holistic 'analytic whole' perspective offers new insights into protein folding.
  • Redefining force-field approaches is crucial for accurate protein structure prediction.
  • Understanding the success of numerical methods can advance the field of structural biology.