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Ion Channels

Ion Channels

The movement of ions like sodium, potassium, and calcium into and out of the cell is essential to maintain the electrochemical gradient in living cells. The ion channels—a class of membrane transport proteins—help maintain this ionic gradient for the smooth functioning of physiological activities such as maintaining cell size and volume, conducting nerve impulses, and gas and nutrient exchange.
Ion channels are specialized integral membrane proteins on the plasma membrane that allow specific...

Facilitated Transport

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...

Non-gated Ion Channels

Non-gated Ion Channels

Ion channels are specialized proteins on the plasma membrane that allow charged ions to pass down their electrochemical gradient. Their main function is to maintain the membrane potential which is critical for cell viability. These channels are either gated or non-gated and can transport more than a thousand ions within milliseconds for the cellular event to occur.
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.

Non-gated Ion Channels

Non-gated Ion Channels

Ion channels are specialized proteins on the plasma membrane that allow charged ions to pass down their electrochemical gradient. Their main function is to maintain the membrane potential which is critical for cell viability. These channels are either gated or non-gated and can transport more than a thousand ions within milliseconds for the cellular event to occur.
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.

Fast Reactions

Fast Reactions

Fast reactions occurring in times shorter than the time needed to mix reactants pose a unique challenge for investigation. In a liquid-phase continuous-flow system, reactants A and B are swiftly pushed into the mixing chamber, where mixing occurs within 1 ms. The reaction mixture then flows through an observation tube, and one measures light absorption to determine species concentrations at various points of the tube. This method is most appropriate when relatively large volumes of reactants...

Facilitated Diffusion

Facilitated Diffusion

The plasma membrane, a critical structure in cellular biology, houses an array of transporters, or carrier proteins, interspersed within its lipid bilayer. These proteins play a crucial role in solute transport through facilitated diffusion, a form of passive diffusion that uses transporters to move the molecules across the membrane.
In this process, substrates such as organic compounds and ions interact with a transporter on one side, triggering conformational changes in proteins that enable...

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Related Experiment Video

Updated: May 25, 2026

High-resolution Spatiotemporal Analysis of Receptor Dynamics by Single-molecule Fluorescence Microscopy

High-resolution Spatiotemporal Analysis of Receptor Dynamics by Single-molecule Fluorescence Microscopy

Published on: July 25, 2014

Gated Diffusion-controlled Reactions.

J Andrew McCammon¹

¹Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365, USA. jmccammon@ucsd.edu.

|May 21, 2011

Summary

This summary is machine-generated.

Predicting protein ligand binding and reactivity is challenging due to dynamic protein site occlusion. This review covers computational methods, including protein-centric and full dynamical simulations, and their biological implications.

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Last Updated: May 25, 2026

High-resolution Spatiotemporal Analysis of Receptor Dynamics by Single-molecule Fluorescence Microscopy

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Published on: July 25, 2014

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Measuring Nucleotide Binding to Intact, Functional Membrane Proteins in Real Time

Measuring Nucleotide Binding to Intact, Functional Membrane Proteins in Real Time

Published on: March 11, 2021

Area of Science:

Computational biology
Biophysics
Protein dynamics

Background:

Protein binding and active sites are frequently blocked by polypeptide motion.
Predicting ligand binding and reactivity requires accounting for these dynamic occlusions.

Purpose of the Study:

To review recent theoretical and computational methods for predicting ligand binding and reactivity in dynamically occluded protein sites.
To discuss the biological implications of these methods.

Main Methods:

Protein-centric approaches: Explicitly simulate only the protein target.
Dynamical simulation approaches: Explicitly simulate both the protein target and the ligand.

Main Results:

Recent advancements in computational methods offer improved prediction of ligand binding and reactivity rates.
Comparison of protein-centric versus full dynamical simulation approaches highlights their respective strengths and applications.

Conclusions:

Understanding protein dynamics is crucial for accurate prediction of molecular interactions.
These computational strategies have significant implications for drug discovery and understanding biological processes.