BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 04-01-2020, 12:01 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,033
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default 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
Reply With Quote


Did you find this post helpful? Yes | No

Reply
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


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2020, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:26 PM.


Map