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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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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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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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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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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.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Predicting protein flexibility with AlphaFold.

Puyi Ma1, Da-Wei Li2, Rafael Brüschweiler1,2,3,4

  • 1Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, USA.

Proteins
|January 21, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces cdsAF2, a novel method using AlphaFold2 structures to predict protein dynamics. It accurately estimates residue-level dynamics, crucial for understanding protein function.

Keywords:
AlphaFoldAlphaFold2NMR dynamicsbackbone NMR NH S2 order parameterscontact modelprediction of protein flexibility and dynamicsprotein structure prediction

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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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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • AlphaFold2 significantly advanced protein structure prediction from amino acid sequences.
  • Understanding protein dynamics is vital for elucidating protein function, complementing static structure information.

Purpose of the Study:

  • To develop a method for predicting protein dynamics at the residue level using AlphaFold2 outputs.
  • To assess the capability of AlphaFold2-derived data in capturing protein dynamics information.

Main Methods:

  • The cdsAF2 approach utilizes 3D protein structures generated by AlphaFold2.
  • A local contact model predicts backbone Nuclear Magnetic Resonance (NMR) 2H S2 order parameters, considering peptide plane contacts.
  • Combines AlphaFold2's pLDDT confidence scores with predicted S2 values for dynamic region estimation.

Main Results:

  • The developed method, cdsAF2, semi-quantitatively predicts backbone NMR 2H S2 order parameter profiles.
  • The approach successfully captures dynamic features across nine diverse proteins with varying dynamics and disorder.
  • Integration of pLDDT scores enhances the accuracy of dynamics prediction.

Conclusions:

  • AlphaFold2's structural predictions contain valuable information for inferring residue-level protein dynamics.
  • cdsAF2 offers a computational approach to predict protein dynamics, aiding functional studies.
  • This method bridges the gap between static structure prediction and dynamic functional insights.