Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Peptide Bonds02:43

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

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...
Protein Folding01:25

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...
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Amide isomerization pathways II: Tracing geometrical prerequisites of acid-catalyzed amide cis-trans isomerization in globular proteins.

The Journal of chemical physics·2026
Same author

Investigating transthyretin variants H88R and I107V in amyloid priming: From destabilization to complete dissociation.

The FEBS journal·2026
Same author

Improving Protein Structure Determination by Integrating Ensemble-Driven Molecular Dynamics with Chemical Shift-Based Restraints.

Journal of chemical information and modeling·2026
Same author

Light-Driven Competitive Selection in a Protein-Catalyzed Dissipative Peptide Replication.

Angewandte Chemie (International ed. in English)·2026
Same author

Physiologically relevant forms of Tc- and Re-pyrophosphate radioactive tracers and the basis of their transthyretin amyloid sensitivity.

Scientific reports·2026
Same author

Addressing Sustainability Challenges in Peptide Synthesis with Flow Chemistry and Machine Learning.

Chemistry (Weinheim an der Bergstrasse, Germany)·2025

Related Experiment Video

Updated: Jul 11, 2026

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
10:31

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

Prolylproline unit in model peptides and in fragments from databases.

Ilona Hudáky1, András Perczel

  • 1Laboratory of Structural Chemistry and Biochemistry, Institute of Chemistry, Eötvös Loránd University, Pázmány sétány 1/A, Budapest 1117, Hungary.

Proteins
|September 27, 2007
PubMed
Summary

The prolylproline sequence is crucial for protein structure and function. Computational analysis reveals elongated structures are most common, influencing protein dynamics.

More Related Videos

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
11:44

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jul 11, 2026

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
10:31

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
11:44

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Published on: February 21, 2018

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • The prolylproline (Pro-Pro) sequence is prevalent in peptides and proteins, including collagen and enzymes.
  • Its conformation is critical for biological activity, ranging from immunosuppression to enzymatic function.
  • Understanding Pro-Pro conformations is key to deciphering its versatile structural roles.

Purpose of the Study:

  • To analyze the fundamental conformational properties of the Pro-Pro sequence.
  • To investigate the influence of Pro-Pro conformation on biological function.
  • To compare computational predictions with experimental data for Pro-Pro units.

Main Methods:

  • Ab initio and density functional theory (DFT) calculations using the polarizable continuum model (PCM).
  • Investigation of cis-trans isomerism, backbone conformation, and ring puckering in a model peptide (HCO-L-Pro-L-Pro-NH2).
  • Systematic comparison of computational results with experimental data from the Protein Data Bank and Cambridge Structural Database.

Main Results:

  • PCM calculations showed good agreement with high-resolution X-ray crystallography data.
  • Energy calculations and statistical analysis predicted that 87% of Pro-Pro units adopt elongated structures, while 13% form beta-turns.
  • Six specific backbone folds, including Polyproline II and various beta-turns, account for 96% of observed Pro-Pro sequences.

Conclusions:

  • The Pro-Pro sequence predominantly adopts elongated conformations, significantly contributing to protein structure.
  • Specific backbone folds like Polyproline II and beta-turns are favored, dictating structural roles.
  • In disordered regions, Pro-Pro units can sample diverse conformers, impacting segmental motion and protein dynamics.