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Related Concept Videos

Preparation of Amines: Alkylation of Ammonia and Amines01:30

Preparation of Amines: Alkylation of Ammonia and Amines

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Alkylation is one of the methods used to prepare amines. Direct alkylation of ammonia or a primary amine with an alkyl halide gives polyalkylated amines along with a quaternary ammonium salt through successive SN2 reactions. This process of making the quaternary salt through the direct alkylation method is called exhaustive alkylation.
Each alkylation step makes the nitrogen center more nucleophilic, which triggers successive alkylations until a quaternary ammonium salt is formed. Considering...
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Preparation of 1° Amines: Gabriel Synthesis01:28

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Direct alkylation is not a suitable method for synthesizing amines because it produces polyalkylated products. Gabriel synthesis is the most preferred method to exclusively make primary amines. The method uses phthalimide, which contains a protected form of nitrogen that participates in alkylation only once to predominantly give primary amines.
Strong bases like NaOH or KOH deprotonate the phthalimide to form the corresponding anion, which acts as a nucleophile. Further, the anion attacks an...
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Acid Halides to Amides: Aminolysis01:07

Acid Halides to Amides: Aminolysis

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Aminolysis is a nucleophilic acyl substitution reaction, where ammonia or amines act as nucleophiles to give the substitution product. Acid halides react with ammonia, primary amines, and secondary amines to yield primary, secondary, and tertiary amides, respectively.
In the first step of the aminolysis mechanism, the amine attacks the carbonyl carbon of the acyl chloride to form a tetrahedral intermediate. In the second step, the carbonyl group is re-formed with the elimination of a chloride...
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Structure of Amines01:19

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The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are...
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Aldehydes and Ketones with Amines: Enamine Formation Mechanism01:14

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Enamine formation involves the addition of carbonyl compounds to a secondary amine through a series of reactions. The mechanism begins with the generation of carbinolamine, a nucleophilic attack followed by several proton transfer reactions. The hydroxyl group of the carbinolamine is converted into water to make a better leaving group that can push the reaction forward by eliminating a water molecule. In enamine formation, the last step involves the abstraction of a proton from the α carbon to...
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Inorganic Nitrogen Assimilation01:22

Inorganic Nitrogen Assimilation

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Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme...
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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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Conformational gating in ammonia lyases.

Matteo Lambrughi1, Željka Sanader Maršić1, Veronica Saez-Jimenez2

  • 1Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.

Biochimica Et Biophysica Acta. General Subjects
|March 31, 2020
PubMed
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Understanding enzyme dynamics is key for ammonia lyase applications. This study reveals how regulatory loops in 3-methylaspartate ammonia lyase (MAL) control active site accessibility through conformational changes.

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Area of Science:

  • Enzymology
  • Structural Biology
  • Computational Biology

Background:

  • Ammonia lyases are crucial enzymes with significant industrial and biomedical potential.
  • Understanding the structure-dynamics-function relationship is vital for optimizing ammonia lyase applications.

Purpose of the Study:

  • To investigate conformational dynamics near the catalytic pocket of 3-methylaspartate ammonia lyase (MAL).
  • To elucidate the role of regulatory elements in modulating enzyme activity and substrate accessibility.

Main Methods:

  • Microsecond all-atom molecular dynamics simulations of MAL.
  • Analysis using dimensionality reduction techniques, contact networks, and correlated motion analysis.

Main Results:

  • Identified two key regulatory elements: the β5-α2 loop and the helix-hairpin-loop subdomain.
  • These elements switch between 'occluded' and 'open' states, altering active site accessibility.
  • Conformational changes create or modify tunnels, facilitating substrate entry.

Conclusions:

  • A sequential mechanism was revealed where the helix-hairpin-loop subdomain's interaction changes precede β5-α2 loop movement.
  • Coupled conformational changes in these elements dynamically regulate catalytic site access.
  • These findings are relevant for other ammonia lyases and emphasize protein dynamics in enzyme engineering.