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Structural View of Biology >> Protein Synthesis >> Protein Folding - Modification - Degradation

Structural View of Biology


The major molecules of protein synthesis, from DNA to RNA to ribosomes to folded proteins, are available in the PDB archive. Proteins are built in several steps in all living organisms. The blueprint for each protein is stored in the genome, encoded in strands of DNA. This information is transcribed into an RNA copy, which is then used to construct the protein chain. After the chain is synthesized, it may be modified with special chemical groups, chaperoned into its proper folded shape, and ultimately destroyed when it is not needed any longer.

Cells carefully manage their proteins from synthesis to disposal. Unfolded proteins, such as chains that are newly synthesized, can aggregate into dangerous clumps, so cells have a diverse set of molecules to chaperone new chains until they fold properly. Many proteins are then modified with special chemical groups or cofactors. The lifespan of a protein is also carefully controlled, and proteins are destroyed when they are damaged or no longer needed.

Scroll to a Molecule of the Month Feature in this subcategory:

  • AAA+ Proteases

    AAA+ Proteases

    How would you make a protein cutting machine that would be safe to use inside a cell? Digestive proteases like trypsin and pepsin are small and efficient–they diffuse up to proteins and start cutting. This would never work inside a cell. The cell needs to have more control, so that only obsolete or damaged proteins are destroyed. The AAA+ proteases are one solution to this problem. They use two tricks to ensure that only certain proteins are destroyed. First, they hide the protein destruction machinery inside a closed container, and second, they use a special protein pump to feed proteins into this destruction chamber.

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    Discussed Structures
    ATP-dependent protease HslUV
    ATP-dependent protease HslUV
    helicase from SV40 T-antigen
    helicase from SV40 T-antigen
    NSF ATPase
    NSF ATPase
  • Chaperones

    Chaperones

    This is not a trivial problem. Cells cannot merely wait for proteins to fold properly. Misfolded proteins often have carbon-rich amino acids on their surfaces, instead of tucked safely inside. These carbon-rich patches associate strongly with similar patches on other proteins, forming large aggregates. Random aggregates are death to cells: diseases such as sickle cell anemia, mad cow disease, and Alzheimer's disease are caused by unnatural aggregation of proteins into cell-clogging fibrils.

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    Discussed Structures
    GroEL-GroES
    GroEL-GroES
    Heat Shock Protein (HSP)-70 ATP-binding domain
    Heat Shock Protein (HSP)-70 ATP-binding domain
    Heat Shock Protein (HSP-70) peptide-binding domain
    Heat Shock Protein (HSP-70) peptide-binding domain
    prefoldin
    prefoldin
  • Hsp90

    Hsp90

    When cells are challenged with extreme heat, they build a collection of protective proteins called heat shock proteins (typically abbreviated as "Hsp" with the approximate molecular weight afterwards). Many of these proteins are chaperones that work to keep cellular proteins folded and active when conditions get bad. They also play important roles in the normal life of the cell, helping proteins fold and limiting the dangerous aggregation of immature proteins. Some of these proteins, such as Hsp70 and Hsp60 are general chaperones. Hsp90, on the other hand, plays a more specific role.

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    Discussed Structures
    HSP90 and Sba1
    HSP90 and Sba1
    HSP90
    HSP90
  • Inteins

    Inteins

    In most cases, each gene encodes a single protein, but cells have found ways around this limitation. Viruses, with their tiny genomes, often contain genes that encode long polyproteins, which are then chopped into a bunch of functional pieces by enzymes. Inteins are another way that cells make several proteins from one gene.

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    Discussed Structures
    intein from vacuolar ATPase
    intein from vacuolar ATPase
    intein and DNA
    intein and DNA
    mini-intein
    mini-intein
  • O-GlcNAc Transferase

    O-GlcNAc Transferase

    Cells use many methods to control their proteins, to make sure that they perform their jobs when and where they are needed. Some are brutally irreversible, such as the continuous breakdown of obsolete proteins by the ubiquitin/proteasome system. Others, such as the modulation of enzyme function by allosteric motions, are far more subtle and respond to the second-by-second needs of the cell. Often, chemical groups are added to amino acids in proteins to modulate their function. Phosphate groups are a familiar example: they are widely used to turn signaling proteins on and off, controlled by a diverse collection of kinases and phosphatases that add and remove these regulatory phosphate groups.

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    Discussed Structures
    GlcNAc Transferase
    GlcNAc Transferase
    GlcNAc Transferase
    GlcNAc Transferase
    GlcNAcase
    GlcNAcase
  • Proteasome

    Proteasome

    Proteasomes are the cell's protein recyclers. Proteins need to be destroyed for many reasons: they may be damaged, or they may be part of an invading virus, or they simply may not be needed any more. Proteasomes provide a controlled method for breaking down proteins safely within the environment of the cell. They chop obsolete or damaged proteins into small pieces, about 2 to 25 amino acids in length. Most of these are then completely broken down into amino acids by peptidases in the cell.

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    Discussed Structures
    Proteasome
    Proteasome
    Proteasome
    Proteasome
    Immunoproteasome core
    Immunoproteasome core
    proteasome
    proteasome
  • Rhomboid Protease GlpG

    Rhomboid Protease GlpG

    Proteases, enzymes that cut protein chains, come in many shapes and sizes. The most familiar proteases, like trypsin and pepsin, are machines of destruction used to digest proteins in our diet. However, most of the proteases in our cells are used in a more delicate task. They regulate the action of other proteins by making specific cuts in their protein targets.

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    Discussed Structures
    Rhomboid Protease GlpG
    Rhomboid Protease GlpG
    Rhomboid Protease GlpG
    Rhomboid Protease GlpG
    Site-2 Protease
    Site-2 Protease
  • Ubiquitin

    Ubiquitin

    Nothing lasts forever. Many proteins, in fact, don't last more than a few minutes. Our cells are continually building proteins, using them for a single task, and then discarding them. For instance, proteins that are used for signaling or control, such as transcription regulators and the cyclins that control division of cells, lead very brief lives, carrying their messages and then being thrown away. Specialized enzymes are also built just when they are needed, allowing cells to keep up with their minute-by-minute synthetic needs. This approach of planned obsolescence may seem wasteful, but it allows each cell to respond quickly to its constantly changing requirements.

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    Discussed Structures
    ubiquitin
    ubiquitin
    tetraubiquitin
    tetraubiquitin
    ubiquitin-activating enzyme E1
    ubiquitin-activating enzyme E1
    ubiquitin-conjugating enzyme E2
    ubiquitin-conjugating enzyme E2
    ubiquitin-ligase E3
    ubiquitin-ligase E3
    ubiquitin-ligase E3
    ubiquitin-ligase E3
    proteasome
    proteasome

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