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Related Concept Videos

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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Molecular Chaperones and Protein Folding03:00

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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.
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Conservation of Protein Domains Over Different Proteins02:26

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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.
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader.

Kailong Zhao1, Yuhao Xia1, Fujin Zhang1

  • 1College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China.

Communications Biology
|March 4, 2023
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PAthreader accurately identifies remote homologous structures, improving protein structure prediction and exploring folding pathways. This method enhances AlphaFold2 performance and reveals folding dynamics from distant protein relatives.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Remote homologous structure recognition is crucial for protein structure prediction tools like AlphaFold2.
  • Understanding protein folding pathways requires identifying subtle evolutionary relationships.

Purpose of the Study:

  • To develop PAthreader, a novel method for recognizing remote homologous structures and exploring protein folding pathways.
  • To enhance the accuracy of template identification for protein structure modeling.
  • To investigate the potential of remote homologs in revealing protein folding dynamics.

Main Methods:

  • Designed a three-track alignment comparing predicted distance profiles with structure profiles from PDB and AlphaFold DB.
  • Integrated PAthreader-identified templates to improve AlphaFold2 performance.
  • Explored protein folding pathways by analyzing information implicitly contained within remote homologous structures.

Main Results:

  • PAthreader demonstrated an 11.6% higher average accuracy in template recognition compared to HHsearch.
  • PAthreader-based structure modeling outperformed standard AlphaFold2, achieving top rankings on the CAMEO blind test.
  • Predicted folding pathways for 37 proteins, with 7 showing consistency with experimental data, suggesting folding information is derivable from remote homologs.

Conclusions:

  • PAthreader significantly improves remote template recognition and protein structure prediction accuracy.
  • The study validates the hypothesis that dynamic folding information can be extracted from remote homologous protein structures.
  • PAthreader offers a new avenue for exploring protein folding mechanisms and enhancing predictive modeling.