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Related Concept Videos

Peptide Bonds02:43

Peptide Bonds

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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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Interfacial Electrochemical Methods: Overview01:06

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Interfacial electrochemical methods focus on the phenomena occurring at the boundary between an electrode and a solution, as opposed to bulk methods that concentrate on the solution's overall properties. These interfacial methods are classified as either static or dynamic based on the presence of a nonzero current in the electrochemical cell and the consistency of analyte concentrations. Static methods, such as potentiometry, measure the cell's potential without any significant current...
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Water and Mineral Acquisition02:34

Water and Mineral Acquisition

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Specialized tissues in plant roots have evolved to capture water, minerals, and some ions from the soil. Roots exhibit a variety of branching patterns that facilitate this process. The outermost root cells have specialized structures called root hairs that increase the root surface, thus increasing soil contact. Water can passively cross into roots, as the concentration of water in the soil is higher than that of the root tissue. Minerals, in contrast, are actively transported into root cells.
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Related Experiment Video

Updated: Feb 14, 2026

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy
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Facet selectivity in gold binding peptides: exploiting interfacial water structure.

Louise B Wright1, J Pablo Palafox-Hernandez2, P Mark Rodger1,3

  • 1Dept. of Chemistry , University of Warwick , Coventry , CV4 7AL , UK.

Chemical Science
|February 17, 2018
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Summary

Researchers used molecular simulations to understand how a gold-binding peptide (AuBP1) interacts with different gold surfaces. This peptide shows stronger binding to Au(111) than Au(100), with surface water structure being key for recognition.

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Protein Kinase C-delta Inhibitor Peptide Formulation using Gold Nanoparticles
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Area of Science:

  • Biomaterials science
  • Computational chemistry
  • Surface science

Background:

  • Peptide sequences can control the synthesis of gold nanoparticles.
  • Understanding peptide-surface interactions is crucial for bio-inspired materials.
  • Atomic-level insights into peptide-gold binding are challenging experimentally.

Purpose of the Study:

  • To link peptide sequence, conformation, and interfacial properties for gold nanoparticle synthesis.
  • To predict the adsorption free energy of the gold-binding peptide AuBP1 on different gold facets.
  • To elucidate the role of interfacial water structure in peptide-gold recognition.

Main Methods:

  • Utilized Replica Exchange with Solute Tempering with Metadynamics simulations.
  • Investigated the AuBP1 peptide at aqueous Au(111) and reconstructed Au(100) interfaces.
  • Analyzed peptide conformations and interfacial water structure.

Main Results:

  • Adsorption free energies were predicted for AuBP1 on Au(111), Au(100)(1 × 1), and Au(100)(5 × 1) surfaces.
  • Stronger adsorption of AuBP1 was observed on the Au(111) surface compared to Au(100) surfaces.
  • Predicted free energies correlated with interfacial water structuring, highlighting its importance.

Conclusions:

  • Surface hydration is a primary factor in peptide-gold recognition.
  • Simulation results align with experimental observations.
  • Findings can guide the use of AuBP1 with gold seed-nanocrystals to control gold nanoparticle morphology.