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Related Concept Videos

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 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 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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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.
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-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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Recent Advances in Protein Folding Pathway Prediction through Computational Methods.

Kailong Zhao1, Fang Liang1, Yuhao Xia1

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

Current Medicinal Chemistry
|October 13, 2023
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Summary
This summary is machine-generated.

Computational methods are advancing the study of protein folding mechanisms, crucial for understanding life processes and diseases. This review explores AI-driven simulations and predictions for protein structure and folding pathways.

Keywords:
AI technologyProtein folding pathwaycomputational methodsconformational samplingmachine learningremote templates.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology and Bioinformatics
  • Structural Biology

Background:

  • Protein folding mechanisms are fundamental to biological processes and disease pathogenesis.
  • Understanding protein structure is key to developing treatments and preventative strategies for various diseases.
  • Advancements in Artificial Intelligence (AI) are revolutionizing protein structure prediction and folding studies.

Purpose of the Study:

  • To review the current progress in understanding protein folding mechanisms using computational methods.
  • To highlight the application of AI and simulation techniques in predicting protein folding pathways and intermediates.
  • To discuss future challenges and perspectives in computational protein folding research.

Main Methods:

  • Simulation of inverse folding pathways (native to unfolded states).
  • Machine learning for predicting early folding residues.
  • Conformational sampling for exploring protein folding pathways.
  • Template-based prediction of protein folding intermediates.

Main Results:

  • Computational methods, particularly AI, are increasingly effective in studying protein folding.
  • Diverse computational approaches offer insights into different aspects of the folding process.
  • Progress has been made in simulating folding pathways and predicting key folding events.

Conclusions:

  • Computational methods are essential tools for unraveling complex protein folding mechanisms.
  • AI and advanced simulations hold significant promise for future discoveries in protein folding.
  • Addressing current challenges will further enhance our ability to predict and understand protein folding.