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Related Concept Videos

Amino acids03:42

Amino acids

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...
Substituent Effects on Acidity of Carboxylic Acids01:31

Substituent Effects on Acidity of Carboxylic Acids

The acidity of carboxylic acids is influenced by the nature of the substituents bounded to the functional group. The acid strength is determined by the stability of the carboxylate anion—the conjugate base formed by dissociating the corresponding carboxylic acid.
Structures of Carboxylic Acid Derivatives01:28

Structures of Carboxylic Acid Derivatives

Structure of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
What are Proteins?01:28

What are Proteins?

Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight.  Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional structure...
What are Proteins?01:55

What are Proteins?

Overview
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

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Related Experiment Video

Updated: Jul 19, 2026

Determination of the Gas-phase Acidities of Oligopeptides
11:00

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Aspartic acid side chain effect-experimental and theoretical insight.

Marko Rozman1

  • 1Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruder Bosković Institute, Zagreb, Croatia.

Journal of the American Society for Mass Spectrometry
|October 20, 2006
PubMed
Summary

The aspartic acid effect involves side-chain proton transfer, initiating selective peptide bond cleavage. This study computationally investigates this mechanism, revealing a favorable one-step process.

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LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics

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Area of Science:

  • Computational Chemistry
  • Biochemistry
  • Physical Chemistry

Background:

  • The intrinsic reactivity of aspartic acid and glutamic acid side chains is crucial for understanding peptide chemistry.
  • The
  • aspartic acid effect
  • describes a unique reactivity pathway involving side-chain carboxylic groups.

Purpose of the Study:

  • To investigate the gas-phase H/D exchange and intrinsic reactivity of aspartic acid and glutamic acid side-chain carboxylic groups.
  • To computationally elucidate the mechanism of selective peptide bond cleavage initiated by aspartic acid.

Main Methods:

  • Density Functional Theory (DFT) calculations, including B3LYP/6-31G(d) and G3(MP2)//B3LYP.
  • Gas-phase H/D exchange experiments and site-specific theoretical treatments.
  • Construction of potential energy profiles for proposed cleavage mechanisms.

Main Results:

  • H/D exchange and theoretical calculations indicated that side-chain carboxylic groups can initiate proton transfer and bond formation.
  • A selective peptide bond cleavage mechanism, termed the
  • aspartic acid effect
  • , was identified.
  • Computational studies on a model system (CH3CO-Asp-NHCH3) revealed a favorable one-step mechanism.

Conclusions:

  • The study supports a complex one-step mechanism for peptide bond cleavage involving proton transfer, bond formation, and cleavage.
  • The findings provide insights into the intrinsic reactivity of aspartic acid and its role in peptide bond hydrolysis.