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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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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.
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Covalently Linked Protein Regulators02:04

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Protein Families02:47

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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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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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Related Experiment Video

Updated: Dec 1, 2025

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project
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FireProtDB: database of manually curated protein stability data.

Jan Stourac1,2, Juraj Dubrava1,3, Milos Musil1,2,3

  • 1Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.

Nucleic Acids Research
|November 9, 2020
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Summary

A new database, FireProtDB, offers experimental protein thermostability data for single-point mutants. This resource aids in developing more accurate computational tools for protein engineering, overcoming data limitations in machine learning approaches.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Protein Engineering

Background:

  • Proteins naturally function under mild conditions, limiting their use in harsh biotechnological applications due to insufficient thermostability.
  • Experimental screening for stabilizing protein mutations is costly and time-consuming.
  • In silico prediction tools are valuable but hindered by limited, low-quality training data.

Purpose of the Study:

  • To introduce FireProtDB, a novel database of experimental thermostability data for single-point protein mutants.
  • To provide a comprehensive resource for improving the accuracy of computational protein stability prediction tools.
  • To facilitate the development of machine learning models for protein engineering.

Main Methods:

  • Compilation of published datasets on protein thermostability.
  • Manual extraction of data from recent scientific literature.
  • Inclusion of experimentally determined data from the authors' laboratory.
  • Development of a user-friendly interface for data exploration and customized dataset generation.

Main Results:

  • Creation of FireProtDB, a centralized repository of experimental thermostability data for single-point mutants.
  • The database integrates diverse data sources, enhancing its comprehensiveness.
  • The interface supports interactive exploration and the creation of machine learning-ready datasets.

Conclusions:

  • FireProtDB addresses the critical bottleneck of data scarcity in computational protein stability prediction.
  • The database will accelerate the development and improve the accuracy of in silico tools for protein engineering.
  • Accessible data in FireProtDB will advance biotechnological applications requiring stable proteins.