[ASAP] Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures

		BioNMR > Educational resources > Journal club
[ASAP] Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-19-2022, 10:43 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,187

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

[ASAP] Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures

[ASAP] Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures

Biochemistry
DOI: 10.1021/acs.biochem.2c00099

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Enhancing sensitivity of Double Electron-Electron Resonance (DEER) by using Relaxation-Optimized Acquisition Length Distribution (RELOAD) scheme Enhancing sensitivity of Double Electron-Electron Resonance (DEER) by using Relaxation-Optimized Acquisition Length Distribution (RELOAD) scheme Publication date: January 2019 Source: Journal of Magnetic Resonance, Volume 298 Author(s): Sergey Milikisiyants, Maxim A. Voinov, Antonin Marek, Morteza Jafarabadi, Jing Liu, Rong Han, Shenlin Wang, Alex I. Smirnov Abstract	nmrlearner	Journal club	0	01-07-2019 05:49 AM
[ASAP] g-Tensor Directions in the Protein Structural Frame of Hyperthermophilic Archaeal Reduced Rieske-Type Ferredoxin Explored by 13C Pulsed Electron Paramagnetic Resonance g-Tensor Directions in the Protein Structural Frame of Hyperthermophilic Archaeal Reduced Rieske-Type Ferredoxin Explored by 13C Pulsed Electron Paramagnetic Resonance https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00438/20180620/images/medium/bi-2018-00438r_0006.gif Biochemistry DOI: 10.1021/acs.biochem.8b00438 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/GfViSnJYGKs More...	nmrlearner	Journal club	0	06-21-2018 10:11 PM
Observation of strongly forbidden solid effect dynamic nuclear polarization transitions via electron-electron double resonance detected NMR From The DNP-NMR Blog: Observation of strongly forbidden solid effect dynamic nuclear polarization transitions via electron-electron double resonance detected NMR Smith, A.A., et al., Observation of strongly forbidden solid effect dynamic nuclear polarization transitions via electron-electron double resonance detected NMR. J Chem Phys, 2013. 139(21): p. 214201. http://www.ncbi.nlm.nih.gov/pubmed/24320373	nmrlearner	News from NMR blogs	0	05-06-2014 01:57 AM
[NMR paper] pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. J Phys Chem B. 2013 Apr 11;117(14):3689-706 Authors: Toal S, Meral D, Verbaro D, Urbanc B, Schweitzer-Stenner R Abstract...	nmrlearner	Journal club	0	09-24-2013 10:18 AM
[NMR paper] Detection of the water-binding sites of the oxygen-evolving complex of Photosystem II using W-band 17O electron-electron double resonance-detected NMR spectroscopy. Detection of the water-binding sites of the oxygen-evolving complex of Photosystem II using W-band 17O electron-electron double resonance-detected NMR spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Detection of the water-binding sites of the oxygen-evolving complex of Photosystem II using W-band 17O electron-electron double resonance-detected NMR spectroscopy. J Am Chem Soc. 2012 Oct 10;134(40):16619-34 Authors: Rapatskiy L, Cox N, Savitsky A, Ames WM, Sander J,...	nmrlearner	Journal club	0	03-02-2013 11:45 AM
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure Abstract Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utilityâ??using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterionsâ??by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5...	nmrlearner	Journal club	0	06-25-2012 04:41 AM
Effect of freezing conditions on distances and their distributions derived from Double Electron Electron Resonance (DEER): A study of doubly-spin-labeled T4 lysozyme Effect of freezing conditions on distances and their distributions derived from Double Electron Electron Resonance (DEER): A study of doubly-spin-labeled T4 lysozyme Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 216</br> Elka R. Georgieva, Aritro S. Roy, Vladimir M. Grigoryants, Petr P. Borbat, Keith A. Earle, Charles P. Scholes, Jack H. Freed</br> Pulsed dipolar ESR spectroscopy, DEER and DQC, require frozen samples. An important issue in the biological application of this technique is how the freezing rate and concentration of cryoprotectant...	nmrlearner	Journal club	0	03-13-2012 03:33 PM
Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 24 January 2012</br> Elka R.Georgieva, Aritro S.Roy, Vladimir M.Grigoryants, Petr P.Borbat, Keith A.*Earle, ...</br> Pulsed dipolar ESR spectroscopy, DEER and DQC, require frozen samples. An important issue in the biological application of this technique is how the freezing rate and concentration of cryoprotectant could possibly affect the...	nmrlearner	Journal club	0	01-25-2012 08:56 AM

« 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