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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be bound by...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Jun 5, 2026

Nitropeptide Profiling and Identification Illustrated by Angiotensin II
07:31

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Published on: June 16, 2019

Factors influencing protein tyrosine nitration--structure-based predictive models.

Alexander S Bayden1, Vasily A Yakovlev, Paul R Graves

  • 1Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.

Free Radical Biology & Medicine
|December 22, 2010
PubMed
Summary

Researchers developed models to predict tyrosine nitration in proteins. These models use 3D structural features and identify factors like neighboring residues and environmental space that influence nitration sites.

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Detection of 3-Nitrotyrosine in Atmospheric Environments via a High-performance Liquid Chromatography-electrochemical Detector System
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Tyrosine nitration is a post-translational modification occurring under oxidative stress.
  • Understanding the structural determinants of tyrosine nitration is crucial for various biological processes.

Purpose of the Study:

  • To develop predictive models for site-specific tyrosine nitration based on protein structure.
  • To investigate structural factors influencing tyrosine nitration.

Main Methods:

  • Analysis of 3D structural features of 20 proteins with experimentally proven tyrosine nitration.
  • Quantitative assessment of factors like neighboring residue proximity and steric hindrance.
  • Development and validation of four structure-based predictive models.

Main Results:

  • Proximity to charged residues, forming hydrogen bond bridges, significantly influences nitration.
  • Buried tyrosines and those with insufficient space for the nitro group are generally not nitrated.
  • A top model accurately predicts 30 out of 35 known tyrosine nitrations, with a sensitivity of 60/71.

Conclusions:

  • Protein structure and local environment are key predictors of tyrosine nitration sites.
  • The developed models offer valuable tools for predicting tyrosine nitration in both in vitro and in vivo contexts.