Probing allosteric coupling in a constitutively open mutant of the ion channel KcsA using solid-state NMR [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
Probing allosteric coupling in a constitutively open mutant of the ion channel KcsA using solid-state NMR [Biophysics and Computational Biology]

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

04-01-2020, 12:01 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Probing allosteric coupling in a constitutively open mutant of the ion channel KcsA using solid-state NMR [Biophysics and Computational Biology]

Probing allosteric coupling in a constitutively open mutant of the ion channel KcsA using solid-state NMR [Biophysics and Computational Biology]

Zhiyu Sun, Yunyao Xu, Dongyu Zhang, Ann E. McDermott...
Date: 2020-03-31

Transmembrane allosteric coupling is a feature of many critical biological signaling events. Here we test whether transmembrane allosteric coupling controls the potassium binding affinity of the prototypical potassium channel KcsA in the context of C-type inactivation. Activation of KcsA is initiated by proton binding to the pH gate upon an... Read More

PNAS:
Number: 13
Volume: 117

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR [Biophysics and Computational Biology] An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR Siavash Vahidi, Zev A. Ripstein, Jordan B. Juravsky, Enrico Rennella, Alfred L. Goldberg, Anthony K. Mittermaier, John L. Rubinstein, Lewis E. Kay... Date: 2020-03-17 The 300-kDa ClpP1P2 protease from Mycobacterium tuberculosis collaborates with the AAA+ (ATPases associated with a variety of cellular activities) unfoldases, ClpC1 and ClpX, to degrade substrate proteins. Unlike in other bacteria, all of the components of the Clp system are essential for...	nmrlearner	Journal club	0	03-18-2020 10:42 AM
Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy [Biophysics and Computational Biology] Structural basis for the ethanol action on G-protein-activated inwardly rectifying potassium channel 1 revealed by NMR spectroscopy Yuki Toyama, Hanaho Kano, Yoko Mase, Mariko Yokogawa, Masanori Osawa, Ichio Shimada... Date: 2018-04-10 Ethanol consumption leads to a wide range of pharmacological effects by acting on the signaling proteins in the human nervous system, such as ion channels. Despite its familiarity and biological importance, very little is known about the molecular mechanisms underlying the ethanol action, due to extremely weak binding affinity and... Read More ...	nmrlearner	Journal club	0	04-11-2018 12:49 AM
Cholesterol-binding site of the influenza M2 protein in lipid bilayers from solid-state NMR [Biophysics and Computational Biology] Cholesterol-binding site of the influenza M2 protein in lipid bilayers from solid-state NMR Matthew R. Elkins, Jonathan K. Williams, Martin D. Gelenter, Peng Dai, Byungsu Kwon, Ivan V. Sergeyev, Bradley L. Pentelute, Mei Hong... Date: 2017-12-05 The influenza M2 protein not only forms a proton channel but also mediates membrane scission in a cholesterol-dependent manner to cause virus budding and release. The atomic interaction of cholesterol with M2, as with most eukaryotic membrane proteins, has long been elusive. We have now determined the cholesterol-binding site of... Read More ...	nmrlearner	Journal club	0	12-06-2017 08:02 AM
Zinc-binding structure of a catalytic amyloid from solid-state NMR [Biophysics and Computational Biology] Zinc-binding structure of a catalytic amyloid from solid-state NMR Myungwoon Lee, Tuo Wang, Olga V. Makhlynets, Yibing Wu, Nicholas F. Polizzi, Haifan Wu, Pallavi M. Gosavi, Jan Stohr, Ivan V. Korendovych, William F. DeGrado, Mei Hong... Date: 2017-06-13 Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive...	nmrlearner	Journal club	0	06-13-2017 09:46 PM
Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac [Biophysics and Computational Biology] Fluorine-19 NMR and computational quantification of isoflurane binding to the voltage-gated sodium channel NaChBac Monica N. Kinde, Vasyl Bondarenko, Daniele Granata, Weiming Bu, Kimberly C. Grasty, Patrick J. Loll, Vincenzo Carnevale, Michael L. Klein, Roderic G. Eckenhoff, Pei Tang, Yan Xu... Date: 2016-11-29 Voltage-gated sodium channels (NaV) play an important role in general anesthesia. Electrophysiology measurements suggest that volatile anesthetics such as isoflurane inhibit NaV by stabilizing the inactivated state or altering the inactivation kinetics. Recent computational...	nmrlearner	Journal club	0	11-29-2016 09:02 PM
Allosteric code of NMR chemical shifts [Biophysics and Computational Biology] Allosteric code of NMR chemical shifts VanSchouwen, B., Melacini, G.... Date: 2016-08-23 One of the broadest definitions of allostery is in terms of long-range couplings between remote sites within a molecular system (1–4). Allosteric couplings are critical to understand the molecular basis of physiological regulatory mechanisms as well as of pathological deregulation (1–4). Allostery is also opening new opportunities in drug design... Read More PNAS: Number: 34	nmrlearner	Journal club	0	08-24-2016 04:35 AM
Allosteric effects in c-Abl by solution NMR [Biophysics and Computational Biology] Allosteric effects in c-Abl by solution NMR Skora, L., Mestan, J., Fabbro, D., Jahnke, W., Grzesiek, S.... Date: 2013-11-19 Successful treatment of chronic myelogenous leukemia is based on inhibitors binding to the ATP site of the deregulated breakpoint cluster region (Bcr)–Abelson tyrosine kinase (Abl) fusion protein. Recently, a new type of allosteric inhibitors targeting the Abl myristoyl pocket was shown in preclinical studies to overcome ATP-site inhibitor resistance arising... Read More PNAS: Number: 47	nmrlearner	Journal club	0	11-20-2013 12:42 AM
Cu-SOD structure and dynamics by solid-state NMR [Biophysics and Computational Biology] Cu-SOD structure and dynamics by solid-state NMR Knight, M. J., Pell, A. J., Bertini, I., Felli, I. C., Gonnelli, L., Pierattelli, R., Herrmann, T., Emsley, L., Pintacuda, G.... Date: 2012-07-10 We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C nuclear relaxation rates. The system on which we demonstrate these methods is the...	nmrlearner	Journal club	0	07-10-2012 06:01 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off