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

Detergent Purification of Membrane Proteins01:18

Detergent Purification of Membrane Proteins

Detergents are used to purify the integral proteins of the membrane. The hydrophobic portion of the detergent can replace membrane phospholipids while solubilizing the membrane proteins. When detergent monomers reach a specific concentration in a solution called critical micelle concentration (CMC), they form micelles. Above CMC, the concentration of the detergent monomers remains in equilibrium with the micelle. The number of detergent monomers present in the CMC varies for each detergent, and...

You might also read

Related Articles

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

Sort by
Same author

Improving the Estimation of p<i>K</i><sub>a</sub> Values for All Titratable Amino Acids at the Water/Membrane Interface.

The journal of physical chemistry. B·2026
Same author

Force Field and Membrane Patch Size Effects on Atomistic Models of Aquaporin-7.

Journal of chemical information and modeling·2026
Same author

Constant-pH Molecular Dynamics of Cationic Peptide Dendrimers Binding to siRNA.

Journal of chemical information and modeling·2026
Same author

<i>In Silico</i> Structural Analysis of the Grapevine Serine Protease VviSBT4.19 Involved in Defense against <i>P. viticola</i>.

Journal of agricultural and food chemistry·2025
Same author

Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.

Journal of chemical theory and computation·2025
Same author

PLUMED Tutorials: A collaborative, community-driven learning ecosystem.

The Journal of chemical physics·2025

Related Experiment Video

Updated: Jun 21, 2026

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions
10:58

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

Published on: July 27, 2017

9.6K

Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides.

Tomás F D Silva1, Diogo Vila-Viçosa1,2, Miguel Machuqueiro1

  • 1Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal.

Journal of Chemical Theory and Computation
|June 11, 2021
PubMed
Summary

A new pH-replica exchange method accurately predicts the pKa of the pH (low) insertion peptide (pHLIP) by overcoming sampling limitations in molecular dynamics simulations. Large membrane sizes are crucial for stable and realistic peptide/membrane interactions.

More Related Videos

Single Liposome Measurements for the Study of Proton-Pumping Membrane Enzymes Using Electrochemistry and Fluorescent Microscopy
12:15

Single Liposome Measurements for the Study of Proton-Pumping Membrane Enzymes Using Electrochemistry and Fluorescent Microscopy

Published on: February 21, 2019

7.6K
PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays
15:04

PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays

Published on: November 2, 2019

11.1K

Related Experiment Videos

Last Updated: Jun 21, 2026

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions
10:58

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

Published on: July 27, 2017

9.6K
Single Liposome Measurements for the Study of Proton-Pumping Membrane Enzymes Using Electrochemistry and Fluorescent Microscopy
12:15

Single Liposome Measurements for the Study of Proton-Pumping Membrane Enzymes Using Electrochemistry and Fluorescent Microscopy

Published on: February 21, 2019

7.6K
PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays
15:04

PeptiQuick, a One-Step Incorporation of Membrane Proteins into Biotinylated Peptidiscs for Streamlined Protein Binding Assays

Published on: November 2, 2019

11.1K

Area of Science:

  • Biophysics
  • Computational Biology
  • Membrane Biophysics

Background:

  • Membrane-interacting peptides and proteins are vital for biological pathways, influencing cell membrane properties through adsorption or insertion.
  • Atomistic simulations, including force-field refinements and enhanced sampling, are used to study these peptide/membrane interactions.
  • pH significantly impacts membrane interfaces, and peptides like the pH (low) insertion peptide (pHLIP) exhibit pH-dependent membrane insertion.

Purpose of the Study:

  • To address sampling limitations in simulating pH-dependent peptide/membrane interactions, particularly for the pHLIP.
  • To develop and apply a novel pH-replica exchange method for enhanced sampling of protonation and conformational states.
  • To accurately calculate the Asp14 pKa profile of wild-type pHLIP and understand its insertion mechanism.

Main Methods:

  • Development and application of a novel pH-replica exchange molecular dynamics method.
  • Simulation of wild-type pHLIP interacting with various sizes of 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (OPPC) membranes.
  • Analysis of Asp14 pKa variability, conformational heterogeneity, and electrostatic interactions with lipid phosphate groups.

Main Results:

  • The pH-replica exchange method provided enhanced sampling and more complete Asp14 pKa profiles.
  • Conformational heterogeneity due to electrostatic interactions between Asp14 and lipid phosphates caused pKa variability.
  • Calculated pKa values (6.0-6.2) in deeper membrane regions accurately predicted the experimental insertion pKa (6.0).
  • Smaller membrane systems (fewer lipids) induced deformations and lost stability, highlighting the need for large membrane patches (≥256 lipids).

Conclusions:

  • The developed pH-replica exchange method is a powerful tool for predicting pKa values and analyzing peptide/membrane electrostatic effects.
  • Accurate simulation of pHLIP insertion requires large membrane patches to avoid artifacts from membrane deformations.
  • The study provides confidence in the method's capabilities for future investigations of similar complex peptide/membrane systems.