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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Aromatic Hydrocarbon Anions: Structural Overview01:18

Aromatic Hydrocarbon Anions: Structural Overview

Neutral hydrocarbons like cyclopentadiene with an odd number of carbon atoms and one intervening CH2 group in the ring are not aromatic. Cyclopentadiene with 4 π electrons does not satisfy the 4n + 2 π electron rule. Additionally, the intervening CH2 group is sp3 hybridized and lacks a vacant p orbital, thereby interrupting the overlap of p orbitals in a continuous manner and preventing the delocalization of π electrons throughout the ring.
Due to the absence of continuous overlap of p...
Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group with both...
¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene π orbitals.

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Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
06:45

Transmembrane Domain Oligomerization Propensity determined by ToxR Assay

Published on: May 26, 2011

Aromatic-aromatic interactions in proteins: beyond the dimer.

Esteban Lanzarotti1, Rolf R Biekofsky, Darío A Estrin

  • 1Departamento de Química Biológica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina.

Journal of Chemical Information and Modeling
|June 14, 2011
PubMed
Summary
This summary is machine-generated.

Aromatic residue clusters larger than dimers are prevalent in proteins, adopting specific structures that influence protein folding and interactions. These findings reveal the broader importance of aromatic interactions in protein function.

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Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
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Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Aromatic residues are crucial for protein structure, stability, and interactions.
  • Interactions between pairs of aromatic residues (dimers) are well-studied.
  • Aromatic molecules in isolation form higher-order clusters (trimers, tetramers).

Purpose of the Study:

  • To identify and characterize aromatic residue clusters larger than dimers in protein structures.
  • To investigate the structural motifs and prevalence of these larger clusters.
  • To explore the functional implications of aromatic clusters in proteins.

Main Methods:

  • Surveyed protein structures in the Protein Data Bank (PDB).
  • Identified and analyzed clusters of aromatic residues exceeding dimer size.
  • Examined cluster conformations, including trimers and tetramers.
  • Utilized calmodulin as a case study for functional analysis.

Main Results:

  • Larger aromatic clusters are found in approximately 50% of unique crystallized proteins.
  • Clusters adopt known trimer motifs observed in benzene clusters.
  • These clusters are nonlocal, connecting distant sites in the primary protein sequence.
  • Two main cluster types were identified: symmetric and extended ladder.
  • Aromatic clusters were shown to play a role in protein folding and interactions using calmodulin.

Conclusions:

  • Aromatic clusters beyond dimers are common and structurally conserved in proteins.
  • These clusters are nonlocal and adopt specific, well-defined conformations.
  • Aromatic clusters significantly contribute to protein function, stability, and ligand recognition.