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Related Concept Videos

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...
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...
Noncovalent Attractions in Biomolecules02:35

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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.
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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...
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Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...

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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
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Published on: February 6, 2020

Salt bridges: geometrically specific, designable interactions.

Jason E Donald1, Daniel W Kulp, William F DeGrado

  • 1Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.

Proteins
|February 3, 2011
PubMed
Summary
This summary is machine-generated.

Salt bridges in proteins show specific geometric preferences, influencing protein structure and function. Understanding these interactions aids in protein design and folding prediction.

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Area of Science:

  • Protein structure and dynamics
  • Biomolecular interactions
  • Computational biology

Background:

  • Salt bridges are crucial for protein conformational specificity, molecular recognition, and catalysis.
  • Previous studies have identified some geometric preferences of salt bridges.

Purpose of the Study:

  • To conduct a comprehensive analysis of salt bridge geometric preferences in protein structures.
  • To discover previously unrecognized salt bridge preferences and their roles.

Main Methods:

  • Surveying a large database of protein structures.
  • Analyzing geometric preferences, sequence separations, and spatial arrangements of salt bridges.
  • Developing quantitative methods for selecting crystal structure resolution and B-factor cutoffs.

Main Results:

  • Salt bridges between specific charged residues (Asp/Glu with His/Arg/Lys) exhibit well-defined geometric preferences.
  • Preferences were found for sequence and spatial separations, protein interfaces, and metal-binding sites.
  • Complex salt bridges involving three or more residues were discovered.
  • A strong relationship exists between salt bridge propensity and residue placement in protein sequences.

Conclusions:

  • Detailed knowledge of salt bridge geometry and sequence dependence aids de novo protein design and prediction algorithms.
  • Salt bridges may play a role in kinetically influencing protein folding and thermodynamically stabilizing native protein conformations.