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Related Concept Videos

Amino acids03:42

Amino acids

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Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
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Amino Acid Catabolism01:18

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Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
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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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Water: A Bronsted-Lowry Acid and Base02:30

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The reaction between a Brønsted-Lowry acid and water is called acid ionization. For example, when hydrogen fluoride dissolves in water and ionizes, protons are transferred from hydrogen fluoride molecules to water molecules, yielding hydronium ions and fluoride ions:
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Phase II Reactions: Sulfation and Conjugation with α-Amino Acids01:19

Phase II Reactions: Sulfation and Conjugation with α-Amino Acids

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Sulfation and α-amino acid conjugation are two critical biotransformation reactions in drug metabolism. Sulfation, a phase II biotransformation reaction, involves adding a polar sulfate group to a drug, enhancing its water solubility and promoting excretion. This process can either co-occur with or occur independently of glucuronidation. Nonmicrosomal sulfotransferase enzymes catalyze the process. The reaction involves 3'-phosphoadenosine-5'-phosphosulfate or PAPS coenzyme...
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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Topological Water Network Analysis Around Amino Acids.

Kwang-Eun Choi1, Eunkyoung Chae1, Anand Balupuri1

  • 1Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.

Molecules (Basel, Switzerland)
|July 25, 2019
PubMed
Summary

Topological water network (TWN) analysis offers a new method to study protein hydration without complex free energy calculations. This approach reveals insights into the surrounding environment of amino acids, aiding drug discovery.

Keywords:
amino acidsmolecular dynamics simulationtopological water networkwater

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Water molecules are crucial for protein stability, folding, function, and ligand binding.
  • Traditional methods for studying protein hydration often involve computationally intensive free energy perturbation algorithms.
  • An alternative approach is needed to study protein hydration without complex calculations.

Purpose of the Study:

  • To investigate protein hydration using topological water network (TWN) analysis as an alternative to free energy calculations.
  • To explore the hydration patterns of 20 amino acids in aqueous solution.
  • To compare simulation results with experimental observations.

Main Methods:

  • Molecular dynamics (MD) simulations were employed to explore water networks around 20 amino acids.
  • Topological water network (TWN) analysis was performed on the simulation data.
  • Results from MD simulations were compared with experimental data and structures from the Protein Data Bank.

Main Results:

  • TWN analysis successfully characterized water networks around amino acids.
  • Simulation-derived TWN patterns closely matched those observed in experimental data and Protein Data Bank structures.
  • The study demonstrated that TWNs are influenced by the surrounding environment.

Conclusions:

  • TWN analysis provides a viable alternative to free energy calculations for studying protein hydration.
  • TWNs offer valuable insights into the local environment of amino acid residues within proteins.
  • This methodology has potential applications in TWN-based drug discovery and development.