NMR spectroscopy charges into protein surface electrostatics [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
NMR spectroscopy charges into protein surface electrostatics [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

07-23-2021, 01:54 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

NMR spectroscopy charges into protein surface electrostatics [Biophysics and Computational Biology]

NMR spectroscopy charges into protein surface electrostatics [Biophysics and Computational Biology]

Frans A. A. Mulder...
Date: 2021-07-22

Life needs interaction. The current pandemic has made visible how much interaction, or lack thereof, means for the life of each and every one of us. The validity of this statement also extends to the tiny and invisible: Over the years, scientists have taken key steps to understand the interactions... Read More

PNAS:
Number: 30
Volume: 118

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
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
Probing the cooperativity of Thermoplasma acidophilum proteasome core particle gating by NMR spectroscopy [Biophysics and Computational Biology] Probing the cooperativity of Thermoplasma acidophilum proteasome core particle gating by NMR spectroscopy Rui Huang, Felipe Perez, Lewis E. Kay... Date: 2017-11-14 The 20S proteasome core particle (20S CP) plays an integral role in cellular homeostasis by degrading proteins no longer required for function. The process is, in part, controlled via gating residues localized to the ends of the heptameric barrel-like CP structure that occlude substrate entry pores, preventing unregulated degradation of... Read More PNAS: Number: 46	nmrlearner	Journal club	0	11-15-2017 08:36 AM
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
Protein NMR structures at >=100-kHz MAS [Biophysics and Computational Biology] Protein NMR structures at >=100-kHz MAS Andreas, L. B., Jaudzems, K., Stanek, J., Lalli, D., Bertarello, A., Le Marchand, T., Cala-De Paepe, D., Kotelovica, S., Akopjana, I., Knott, B., Wegner, S., Engelke, F., Lesage, A., Emsley, L., Tars, K., Herrmann, T., Pintacuda, G.... Date: 2016-08-16 Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that,...	nmrlearner	Journal club	0	08-16-2016 07:38 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
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology] Protein structure modeling using sparse NMR data Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D.... Date: 2012-06-19 While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...	nmrlearner	Journal club	0	06-20-2012 02:28 AM
Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology] Ultrahigh resolution protein structures using NMR chemical shift tensors Wylie, B. J., Sperling, L. J., Nieuwkoop, A. J., Franks, W. T., Oldfield, E., Rienstra, C. M.... Date: 2011-10-11 NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13C? and 15N (peptide backbone) groups in a protein, the ?1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13C? and...	nmrlearner	Journal club	0	10-12-2011 06:37 AM
Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy [Biophysics and Computational Biology] Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy Masterson, L. R., Shi, L., Metcalfe, E., Gao, J., Taylor, S. S., Veglia, G.... Date: 2011-04-26 Protein kinase A (PKA) is a ubiquitous phosphoryl transferase that mediates hundreds of cell signaling events. During turnover, its catalytic subunit (PKA-C) interconverts between three major conformational states (open, intermediate, and closed) that are dynamically and allosterically activated by nucleotide binding. We show that the structural transitions between these...	nmrlearner	Journal club	0	04-27-2011 04:16 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