Related Experiment Video
Updated: Oct 10, 2025
15:28
Mutagenesis and Functional Analysis of Ion Channels Heterologously Expressed in Mammalian Cells
Published on: October 1, 2010
17.6K
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain
Willow Coyote-Maestas1, David Nedrud1, Antonio Suma2
1Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
Nature Communications
|December 9, 2021
Summary
Domain recombination drives protein function evolution, but biophysical compatibility is key. This study models domain insertion in ion channels, revealing rules for designing functional protein variants.
Area of Science:
- Structural biology
- Biophysics
- Computational biology
- Ion channel research
Background:
- Protein domains are fundamental units of protein structure and function.
- Domain recombination is a known driver of multidomain protein evolution, but biophysical constraints on domain combination remain poorly understood.
- Understanding these constraints is crucial for predicting and designing novel protein functions.
Purpose of the Study:
- To investigate the biophysical mechanisms governing protein domain compatibility in the context of ion channel assembly.
- To develop a predictive model for domain insertion variants in the Inward Rectifier K+ channel (Kir2.1).
- To explore the relationship between domain insertion, protein folding, and cell surface expression.
Main Methods:
- Massively parallel insertional mutagenesis was employed to generate and test over 300,000 domain recombination variants of Kir2.1.
- Machine learning was utilized to build a quantitative biophysical model of domain compatibility.
- Insertional profiling was used to map functional responses to specific structural regions of the ion channel.
Main Results:
- Data suggest a concerted action of genomic and biophysical mechanisms favoring domain gain at protein termini during ion channel evolution.
- A machine learning model successfully predicted domain compatibility, providing rudimentary design rules for viable domain insertion variants.
- Positional responses to motif insertion clustered, correlating with distinct structural regions and biophysical properties (folding stability, gating) of Kir2.1.
Conclusions:
- Genomic and biophysical factors cooperatively shape domain evolution in ion channels.
- The developed biophysical model offers a framework for designing novel, functional ion channel variants.
- Insertional profiling serves as a high-throughput method for annotating functional roles of ion channel structural regions.
More Related Videos
11:55Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
Published on: August 16, 2016
11.8K
12:04Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
9.1K
Related Concept Videos
01:19Ion Channels
88.9K
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...
Ion channels are specialized integral membrane proteins on the plasma membrane that allow...
88.9K
01:24Non-gated Ion Channels
7.4K
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....
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism....
7.4K
01:19Ligand-gated Ion Channels
13.0K
Ligand-gated ion channels are transmembrane proteins with a channel for ions to pass through and a binding site for a ligand. The channel opens only when a ligand attaches to the binding site.
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that...
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that...
13.0K
01:12Mechanically-gated Ion Channels
6.9K
Mechanically-gated ion channels are proteins found in eukaryotic and prokaryotic cell membranes that open in response to mechanical stress. Tension, compression, swelling, and shear stress can alter the conformation of the protein, opening a transmembrane channel that allows the passage of ions for signal transmission. In eukaryotes, mechanically-gated channels are distributed in several regions like the neurons, lungs, skin, bladder, and heart, where they play critical roles in numerous...
6.9K
01:18Patch Clamp
5.8K
Many fundamental cell functions such as muscle contraction and nerve transmission rely on the electrical signals produced by the movement of positively and negatively charged ions across the cell membrane. One competent method to record current flowing across the whole cell or single ion channel is the patch-clamp technique.
In this method, a glass micropipette containing electrolyte solution is tightly sealed against a small portion of the cell membrane. As a result, a patch of the cell...
In this method, a glass micropipette containing electrolyte solution is tightly sealed against a small portion of the cell membrane. As a result, a patch of the cell...
5.8K
01:21Electrochemical Gradient and Channel Proteins: An Overview
3.2K
An electrochemical gradient is a fundamental concept in biology and chemistry. It regulates the movement of ions across cell membranes. This movement is influenced by two factors:
The electrical gradient: The electrical gradient across cell membranes refers to the difference in electric charge between the inside and outside of a cell. This difference drives the movement of ions towards or away from the cells. For instance, if the inside of the cell is more negatively charged relative to...
The electrical gradient: The electrical gradient across cell membranes refers to the difference in electric charge between the inside and outside of a cell. This difference drives the movement of ions towards or away from the cells. For instance, if the inside of the cell is more negatively charged relative to...
3.2K