Allosteric code of NMR chemical shifts [Biophysics and Computational Biology]

		BioNMR > Educational resources > Journal club
Allosteric code of NMR chemical shifts [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

08-24-2016, 04:35 AM

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

Allosteric code of NMR chemical shifts [Biophysics and Computational Biology]

Allosteric code of NMR chemical shifts [Biophysics and Computational Biology]

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
Volume: 113

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
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
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
Equilibrium simulations with NMR chemical shifts [Biophysics and Computational Biology] Equilibrium simulations with NMR chemical shifts Boomsma, W., Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, T., Lindorff-Larsen, K., Vendruscolo, M.... Date: 2014-09-23 Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with... Read...	nmrlearner	Journal club	0	09-24-2014 06:03 AM
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
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
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
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