Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization [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

05-16-2017, 10:27 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization [Biophysics and Computational Biology]

Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization [Biophysics and Computational Biology]

Ivan V. Sergeyev, Boris Itin, Rivkah Rogawski, Loren A. Day, Ann E. McDermott...
Date: 2017-05-16

An experimental strategy has been developed to increase the efficiency of dynamic nuclear polarization (DNP) in solid-state NMR studies. The method makes assignments simpler, faster, and more reliable via sequential correlations of both side-chain and C? resonances. The approach is particularly suited to complex biomolecules and systems with significant chemical-shift... Read More

PNAS:
Number: 20
Volume: 114

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization. Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization. Related Articles Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization. Proc Natl Acad Sci U S A. 2017 May 01;: Authors: Sergeyev IV, Itin B, Rogawski R, Day LA, McDermott AE Abstract	nmrlearner	Journal club	0	05-04-2017 07:19 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
Structure of CAP-Gly on microtubules by MAS NMR [Biophysics and Computational Biology] Structure of CAP-Gly on microtubules by MAS NMR Yan, S., Guo, C., Hou, G., Zhang, H., Lu, X., Williams, J. C., Polenova, T.... Date: 2015-11-24 Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant... Read More PNAS: Number: 47	nmrlearner	Journal club	0	11-24-2015 09:32 PM
DNP MAS NMR on channelrhodopsin-2 [Biophysics and Computational Biology] DNP MAS NMR on channelrhodopsin-2 Becker-Baldus, J., Bamann, C., Saxena, K., Gustmann, H., Brown, L. J., Brown, R. C. D., Reiter, C., Bamberg, E., Wachtveitl, J., Schwalbe, H., Glaubitz, C.... Date: 2015-08-11 Channelrhodopsin-2 from Chlamydomonas reinhardtii is a light-gated ion channel. Over recent years, this ion channel has attracted considerable interest because of its unparalleled role in optogenetic applications. However, despite considerable efforts, an understanding of how molecular events during the photocycle, including the retinal trans-cis isomerization and the...	nmrlearner	Journal club	0	08-12-2015 08:58 AM
[NMR paper] NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). Related Articles NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). Biomol NMR Assign. 2014 Oct 8; Authors: Makrynitsa GI, Ntonti D, Marousis KD, Tsika AC, Lichière J, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA Abstract Macro...	nmrlearner	Journal club	0	10-09-2014 07:31 PM
[NMR paper] NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). Related Articles NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). Biomol NMR Assign. 2014 Sep 13; Authors: Melekis E, Tsika AC, Lichière J, Chasapis CT, Margiolaki I, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA Abstract Macro domains are ADP-ribose-binding modules present...	nmrlearner	Journal club	0	09-14-2014 02:26 PM
Protein dynamics from X-ray and NMR [Biophysics and Computational Biology] Protein dynamics from X-ray and NMR Fenwick, R. B., van den Bedem, H., Fraser, J. S., Wright, P. E.... Date: 2014-01-28 Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray... Read More PNAS: Number: 4	nmrlearner	Journal club	0	01-29-2014 12:50 AM
Mapping allostery through the covariance analysis of NMR chemical shifts [Biophysics and Computational Biology] Mapping allostery through the covariance analysis of NMR chemical shifts Selvaratnam, R., Chowdhury, S., VanSchouwen, B., Melacini, G.... Date: 2011-04-12 Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical...	nmrlearner	Journal club	0	04-13-2011 01:15 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