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Peptide Bonds

Peptide Bonds

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...

Protein Folding

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...

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Updated: Sep 30, 2025

Constructing Thioether/Vinyl Sulfide-tethered Helical Peptides Via Photo-induced Thiol-ene/yne Hydrothiolation

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Molecular Simulation of Stapled Peptides.

Victor Ovchinnikov¹, Aravinda Munasinghe², Martin Karplus^3,4

¹Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. ovchinnv@georgetown.edu.

Methods in Molecular Biology (Clifton, N.J.)

|March 17, 2022

Summary

Hydrocarbon-stapled peptides offer therapeutic advantages over traditional drugs. Molecular dynamic (MD) simulations, accelerated by GPUs, enable detailed analysis of peptide behavior and binding affinity changes, aiding drug design.

Keywords:

Binding free energy MDM2 MMGBSA Molecular dynamics Peptide design p53

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Last Updated: Sep 30, 2025

Constructing Thioether/Vinyl Sulfide-tethered Helical Peptides Via Photo-induced Thiol-ene/yne Hydrothiolation

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Published on: August 1, 2018

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Published on: September 28, 2022

Construction of Cyclic Cell-Penetrating Peptides for Enhanced Penetration of Biological Barriers

Construction of Cyclic Cell-Penetrating Peptides for Enhanced Penetration of Biological Barriers

Published on: September 19, 2022

Area of Science:

Biologic therapeutics
Computational chemistry
Molecular modeling

Background:

Constrained peptides are an emerging class of therapeutics with potential advantages over small-molecule drugs and antibodies.
Their small size makes them suitable for rational design using computational methods.
Advances in hardware, like graphical processing units (GPUs), now permit large-scale molecular dynamic (MD) simulations.

Purpose of the Study:

To outline methods for performing and analyzing MD simulations of hydrocarbon-stapled peptides.
To investigate the conformational properties of these peptides in isolation and when bound to a partner.
To calculate changes in binding affinity following peptide mutation.

Main Methods:

Utilizing the CHARMM energy function for MD simulations.
Performing simulations on hydrocarbon-stapled peptides, both alone and complexed with a binding partner.
Analyzing simulation data to determine conformational dynamics and binding affinity alterations.

Main Results:

Established procedures for conducting and interpreting MD simulations of stapled peptides.
Characterized the conformational landscape of stapled peptides.
Quantified the impact of mutations on peptide-protein binding affinity.

Conclusions:

MD simulations are a powerful tool for understanding constrained peptide therapeutics.
These simulations facilitate the rational design and optimization of stapled peptides for drug development.
The described methods enable the investigation of structure-activity relationships in peptide therapeutics.