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Related Concept Videos

Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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The trp operon in Escherichia coli exemplifies a repressible operon. It regulates the synthesis of tryptophan through repressor-mediated transcriptional control and attenuation. This dual regulatory mechanism ensures tryptophan biosynthesis occurs only when needed, conserving cellular resources.Structure of the trp OperonThe trp operon consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) that encode enzymes for tryptophan biosynthesis. These genes are transcribed as a single...
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Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
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Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
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Related Experiment Video

Updated: Sep 7, 2025

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase
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PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

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Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects.

Joseph W Schafer1, Xi Chen2, Steven D Schwartz1

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States.

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|June 20, 2022
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Summary

Directed evolution enhances enzyme stability but alters fast protein dynamics crucial for catalysis. This study contrasts allosteric and stand-alone enzyme functions at the femtosecond scale.

Keywords:
Markov chain Monte Carloallosteric effectcomputational chemistrydirected evolutionpromoting vibration

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Area of Science:

  • Biochemistry
  • Biophysics
  • Protein Engineering

Background:

  • Enzyme engineering aims to create stable, efficient catalysts for pharmaceutical and industrial applications.
  • Directed evolution can improve enzymes without detailed structure-activity knowledge.
  • Tryptophan synthase is a key enzyme studied for its catalytic mechanism.

Purpose of the Study:

  • To investigate the impact of directed evolution on tryptophan synthase's catalytic cycle.
  • To analyze the role of protein dynamics in enzyme catalysis.
  • To compare allosteric and stand-alone enzyme functions at the molecular level.

Main Methods:

  • Transition path sampling simulations were employed.
  • A key chemical transformation within the tryptophan synthase catalytic cycle was studied.
  • The dynamics of an engineered tryptophan synthase mutant were analyzed.

Main Results:

  • Directed evolution mimicked the natural allosteric effect on enzyme stability.
  • Fast protein dynamics critical for catalysis were significantly altered by directed evolution.
  • A contrast between allosteric and stand-alone functions was observed at the femtosecond timescale.

Conclusions:

  • Protein dynamics play a vital role in enzyme catalysis.
  • Mutations from protein engineering introduce complex, multifaceted changes.
  • Understanding enzyme dynamics is crucial for effective protein engineering.