Related Experiment Video
Updated: Jul 3, 2026
15:05
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
Published on: May 20, 2020
Structural and energetic analysis of activation by a cyclic nucleotide binding domain
Stephen L Altieri1, Gina M Clayton, William R Silverman
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Journal of Molecular Biology
|July 16, 2008
Summary
MlotiK1, a cyclic nucleotide-binding domain (CNB) protein, reveals structural insights into ligand-dependent channel activation. New crystal structures illuminate how cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) binding influences protein conformation and function.
Area of Science:
- Structural Biology
- Biophysics
- Molecular Biology
Background:
- MlotiK1 is a prokaryotic cyclic-nucleotide-dependent ion channel.
- It possesses an intracellular C-terminal cyclic nucleotide binding (CNB) domain.
- Previous studies solved X-ray structures of the CNB domain in apo and cAMP-bound states.
Purpose of the Study:
- To determine new X-ray structures of the MlotiK1 CNB domain in apo, cGMP-bound, and second cAMP-bound states.
- To analyze structural differences between apo and ligand-bound states, and structural variability within states.
- To probe nucleotide selectivity and the role of specific residues in ligand binding and channel activation.
Main Methods:
- X-ray crystallography
- Protein expression and purification
- Structural analysis and comparison
Main Results:
- Three new MlotiK1 CNB domain structures were determined: a second apo configuration, a cGMP-bound structure, and a second cAMP-bound structure.
- Analysis of five structures revealed conformational changes upon ligand binding and structural plasticity.
- Nucleotide selectivity and key residue interactions for ligand binding and activation were identified.
Conclusions:
- Structural data provide a framework for understanding ligand-dependent activation in MlotiK1.
- Identified ligand-protein interactions are crucial for MlotiK1's functional modulation.
- Findings contribute to a broader understanding of nucleotide-dependent protein classes.
Related Concept Videos
01:22Activation and Inactivation of G Proteins
Heterotrimeric G proteins are guanine nucleotide-binding proteins. As the name suggests, heterotrimeric G proteins are composed of three subunits: alpha, beta, and gamma. They remain GDP-bound or GTP-bound inside the cells and switch between inactive/active states. The Gα subunit possesses the nucleotide-binding pocket that binds guanine nucleotides and switches between GDP or GTP-bound states. In contrast, the Gꞵ and Gγ subunits are always bound together with high affinity and are together...
01:16Calmodulin-dependent Signaling
Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
01:30Assembly of Signaling Complexes
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
01:18ATP Synthase: Structure
ATP synthase or ATPase is among the most conserved proteins found in bacteria, mammals, and plants. This enzyme can catalyze a forward reaction in response to the electrochemical gradient, producing ATP from ADP and inorganic phosphate. ATP synthase can also work in a reverse direction by hydrolyzing ATP and generating an electrochemical gradient. Different forms of ATP synthases have evolved special features to meet the specific demands of the cell. Based on their specific feature, ATP...
01:24Intracellular Signaling Cascades
Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. The continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors, which cannot interact with most components of the cell, such as DNA. Only internal receptors can interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the...
01:09GPCRs Regulate Adenylyl Cylase Activity
Some GPCRs transmit signals through adenylyl cyclase (AC), a transmembrane enzyme. AC helps synthesize second messenger cyclic adenosine monophosphate (cAMP). AC catalyzes cyclization reaction and converts ATP to cAMP by releasing a pyrophosphate. The pyrophosphate is further hydrolyzed to phosphate by the enzyme pyrophosphatase, which drives cAMP synthesis to completion. However, cAMP is rapidly degraded to 5′ AMP by the enzymes phosphodiesterase (PDE), preventing overstimulation of cells.
Two...
Two...