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Retrieving "Aspartate" from the archives

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  1. Enzymatic Catalysis

    Linked via "aspartate"

    Acid-Base Catalysis
    This strategy involves the transfer of protons ($\text{H}^+$) to or from the substrate or an intermediate. Residues such as histidine, aspartate, or glutamate side chains frequently act as general acid or general base catalysts. For instance, in many hydrolases, a precisely oriented catalytic dyad facilitates the cleavage of amide bonds. If the active site residue acts as a base, it abstrac…

  2. Enzymatic Catalysis

    Linked via "aspartate"

    Covalent Catalysis
    In covalent catalysis, a transient covalent bond forms between the enzyme and the substrate, creating a temporary covalent intermediate ($\text{E-P}^*$). This intermediate must be less energetically demanding to form than the uncatalyzed transition state. Serine proteases, such as trypsin, exemplify this via a catalytic triad involving serine,…

  3. Hydrophobic Interaction

    Linked via "Aspartate"

    | Leucine | Large, branched | $3.25$ | Strongly Hydrophobic |
    | Tryptophan | Aromatic, large | $4.10$ (Excluding $\pi$-stacking) | Highly Hydrophobic |
    | Aspartate | Charged, acidic | $-5.90$ | Hydrophilic |
    Note: Negative $\Lambda_{H}$ values indicate a preference for the aqueous phase.

  4. Protein Denaturation

    Linked via "aspartate"

    Urea and Guanidinium Chloride (GdnHCl): These compounds are highly effective chaotropic agents. Their mechanism is thought to involve direct interaction with the peptide backbone via hydrogen bonding, which competes with the internal hydrogen bonds of the protein. GdnHCl is generally regarded as more potent than urea, often showing a higher linear dependency on concentration for unfolding equilibrium constants.
    Strong Acids and Bases:…

  5. Salt Bridge

    Linked via "Aspartate"

    Composition and Formation
    Salt bridges fundamentally require the presence of both a negatively charged residue (an anion, typically the carboxylate group of Aspartate or Glutamate) and a positively charged residue (a cation, typically the $\epsilon$-amino group of Lysine or the guanidinium group of Arginine) in sufficiently close proximity—usually within $3.0$ to $5.0$ Angstroms ($…