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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 and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complex Assembly

Protein Complex Assembly

Structural Protein Function

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: Feb 6, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural

Gloria A A Saracino¹, Federico Fontana², Shehrazade Jekhmane³

¹Center for Nanomedicine and Tissue Engineering (CNTE) ASST Ospedale Niguarda Cà Granda Piazza dell'Ospedale Maggiore 3 20162 Milan Italy.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)

|August 22, 2018

Summary

A new software, Morphoscanner, identifies and visualizes beta-structuring and beta-sheet formation in proteins and peptides. This tool aids in understanding self-assembling peptides and molecular aggregation dynamics.

Keywords:

coarse‐grained molecular dynamics multilayer graph theory pattern recognition self‐assembling peptides β‐structures

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Area of Science:

Biomolecular dynamics and self-assembly.
Computational biophysics and structural biology.

Background:

Self-assembly and molecular folding are fundamental processes in nature, driving biological organization.
Understanding protein/peptide aggregation dynamics is crucial but lacks dedicated analytical tools.

Purpose of the Study:

To develop and validate an innovative software tool for analyzing beta-structuring and beta-sheet formation.
To provide intuitive visualization of molecular dynamics related to protein and peptide aggregation.

Main Methods:

Development of the Morphoscanner software suite.
Application of coarse-grained molecular dynamics simulations for self-assembling peptides (SAPs).
Analysis of simulated systems and crystal structures of proteins and peptides.

Main Results:

Morphoscanner successfully identifies and visualizes beta-structuring and beta-sheet formation.
The software reveals distinct beta-structuring schemes and kinetics for different SAP sequences.
Demonstrated versatility in analyzing various biomolecular simulations.

Conclusions:

Morphoscanner is a novel and versatile tool for probing aggregation dynamics.
The software aids in understanding the self-assembly of peptides and other biomolecules.
Facilitates the analysis of molecular dynamics trajectories and local order evolution.