Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy
Literature Information
Alberto Collauto, Royi Kaufmann, William N. Zagotta, Daniella Goldfarb
Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron–electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3′,5′-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.
Recommended Journals

Russian Journal of Applied Chemistry

Saudi Pharmaceutical Journal

Russian Journal of Organic Chemistry

Organic Process Research & Development

Chemistry Education Research and Practice

Journal of Peptide Science

Current Opinion in Colloid & Interface Science

Journal of Natural Medicines

Acta Materialia

Russian Journal of Bioorganic Chemistry
Related Literature
SiC–Fe3O4 dielectric–magnetic hybrid nanowires: controllable fabrication, characterization and electromagnetic wave absorption
Caiyun Liang, Chenyu Liu, Huan Wang, Lina Wu, Zhaohua Jiang, Yongjun Xu, Baozhong Shen, Zhijiang Wang
DOI: 10.1039/C4TA02907K
ZnO nanorods on reduced graphene sheets with excellent field emission, gas sensor and photocatalytic properties
Rujia Zou, Guanjie He, Kaibing Xu, Qian Liu, Zhenyu Zhang, Junqing Hu
DOI: 10.1039/C3TA11490B
Chitosan/rectorite nanocomposite with injectable functionality for skin hemostasis
Xiaoyun Li, Yi-Chen Li, Mingjie Chen, Qingshan Shi, Runcang Sun, Xiaoying Wang
DOI: 10.1039/C8TB01085D
Advanced nanoparticle generation and excitation by lasers in liquids
Stephan Barcikowski, Giuseppe Compagnini
DOI: 10.1039/C2CP90132C
Barrierless photoisomerisation of the “simplest cyanine”: Joining computational and femtosecond optical spectroscopies to trace the full reaction path
Alexander Weigel, Matthias Pfaffe, Mohsen Sajadi, Rainer Mahrwald, Roberto Improta, Vincenzo Barone, Dario Polli, Giulio Cerullo, Nikolaus P. Ernsting, Fabrizio Santoro
DOI: 10.1039/C2CP41522D
Tailor-made compositional gradient copolymer by a many-shot RAFT emulsion polymerization method
Yunlong Guo, Jianhua Zhang, Peile Xie, Xiang Gao, Yingwu Luo
DOI: 10.1039/C4PY00003J
Simultaneous and controlled release of two different bioactive small molecules from nature inspired single material
Adil M. Rather, Arpita Shome, Bibhas K. Bhunia, Aparna Panuganti, Biman B. Mandal, Uttam Manna
DOI: 10.1039/C8TB02406E
Practical metal- and additive-free methods for radical-mediated reduction and cyclization reactions
Hao Jiang, Jesper R. Bak, Francisco Javier López-Delgado, Karl Anker Jørgensen
DOI: 10.1039/C3GC41520A
Non-precious Ir–V bimetallic nanoclusters assembled on reduced graphenenanosheets as catalysts for the oxygen reduction reaction
Wei Chen
DOI: 10.1039/C3TA12067H
You might also like
Are there alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3848-36-0) in synthesis?
When considering alternatives to 1-(4-Chlorophenyl)-N-hydroxymethanimine (CAS: 3...
How should (1R,9S,10S,12S,14E,16S,19R,20R,21S,22R)-3,9,21-Trihydroxy-5,10,12,14,16,20,22-heptamethyl-23,24-dioxatetracyclo[17.3.1.1~6,9~.0~2,7~]tetracosa-2,5,7,14-tetraen-4-one (CAS: 183202-73-5) be stored?
This compound should be stored in a cool, dry place away from direct sunlight. I...
How is 3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole (CAS: 419553-16-5) typically synthesized?
3-(4-Bromophenyl)-5-(2-fluorophenyl)-1,2,4-oxadiazole is synthesized through a m...
How is 5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS: 1639220-19-1) typically synthesized?
5-Chloro-2-(4-chlorophenyl)-4-methyl-6-[3-(1-piperidinyl)propoxy]pyrimidine (CAS...
What industries use 2-Chloro-4-(difluoromethoxy)pyridine (CAS: 1206978-15-5)?
2-Chloro-4-(difluoromethoxy)pyridine is used in the pharmaceutical industry for ...
What regulatory guidelines apply to 3-Chloro-6-methylpyridazine (CAS: 1121-79-5)?
3-Chloro-6-methylpyridazine (CAS: 1121-79-5) is classified under the Globally Ha...
Are there alternatives to Methyl 4,5-dimethyl-2-nitrobenzoate in synthesis?
Several alternatives can be used in the synthesis of Methyl 4,5-dimethyl-2-nitro...
Are there alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde in synthesis?
Alternatives to (2E,2'E)-3,3'-(1,4-Phenylene)bisacrylaldehyde include other acry...
What is 3-Amino-5-chloropyridin-2-ol hydrochloride (CAS: 1261906-29-9)?
3-Amino-5-chloropyridin-2-ol hydrochloride is an organic compound with the CAS n...
What precautions should be taken when handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one (CAS: 1092349-93-3)?
When handling 6,7-Difluoro-2,3-dihydro-4H-chromen-4-one, it is essential to wear...
Source Journal
Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.
![6-Bromo-2,3-dihydro-1H-pyrido[2,3-b][1,4]oxazine structure 6-Bromo-2,3-dihydro-1H-pyrido[2,3-b][1,4]oxazine structure](https://static.chemtradehub.com/structs/120/1203499-17-5-b4d1.webp)


![4-[(3-Chloro-2-fluorophenyl)amino]-7-methoxy-6-quinazolinyl acetate structure 4-[(3-Chloro-2-fluorophenyl)amino]-7-methoxy-6-quinazolinyl acetate structure](https://static.chemtradehub.com/structs/740/740081-22-5-f58f.webp)
