NMR paper Unbiased clustering of residues undergoing synchronous motions in proteins using NMR spin relaxation data

		BioNMR > Educational resources > Journal club
[NMR paper] Unbiased clustering of residues undergoing synchronous motions in proteins using NMR spin relaxation data

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

02-25-2025, 04:55 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,875

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

Unbiased clustering of residues undergoing synchronous motions in proteins using NMR spin relaxation data

Unbiased clustering of residues undergoing synchronous motions in proteins using NMR spin relaxation data

Biological macromolecules are dynamic entities that transition between various conformational states, often playing a vital role in biological functions. Their inherent flexibility spans a broad range of timescales. Motions occurring within the microsecond to millisecond range are especially important, as they are integral to processes such as enzyme catalysis, folding, ligand binding, and allostery. NMR Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are the preferred method...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations ... - Nature.com Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations ... - Nature.com Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations ... Nature.com Read here	nmrlearner	Online News	0	02-15-2024 07:41 AM
[NMR paper] NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins NMR screening methods based on ^(19)F spin-spin relaxation time (^(19)F-T(2)) were applied to fluorinated compounds bound to human serum albumin. Diflunisal and fleroxacin (the fluorinated compounds) contain two and three fluorine atoms per molecule, respectively, and are suitable as the model system for ^(19)F NMR analysis. It was shown that ^(19)F-T(2) was more sensitive in monitoring the binding affinity to the target protein than ^(19)F spin-lattice relaxation time...	nmrlearner	Journal club	0	10-17-2023 03:24 AM
[NMR paper] Explicit models of motions to analyze NMR relaxation data in proteins Explicit models of motions to analyze NMR relaxation data in proteins Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nanosecond motions, in particular, can be probed by nuclear spin relaxation rates, which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model-Free (MF) approach, which makes no assumption on the nature of motions and reports on the effective amplitude and... More...	nmrlearner	Journal club	0	10-02-2022 07:47 AM
[NMR paper] NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners The transient interactions of proteins and other molecules with much larger structures, such as synthetic or biological nanoparticles, lead to certain types of enhanced nuclear magnetic resonance (NMR) spin relaxation effects, which can be accurately measured by multidimensional solution NMR techniques. These relaxation effects provide new information about the nanostructures and the protein, their interactions, internal dynamics, and associated kinetic and thermodynamic...	nmrlearner	Journal club	0	03-23-2021 07:56 PM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. J Phys Chem B. 2014 Oct 28; Authors: Allnér O, Foloppe N, Nilsson L Abstract Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...	nmrlearner	Journal club	0	10-29-2014 03:51 PM
[NMR paper] Slow motions in microcrystalline proteins as observed by MAS-dependent 15N rotating-frame NMR relaxation Slow motions in microcrystalline proteins as observed by MAS-dependent 15N rotating-frame NMR relaxation Publication date: Available online 20 September 2014 Source:Journal of Magnetic Resonance</br> Author(s): Alexey Krushelnitsky , Tatiana Zinkevich , Bernd Reif , Kay Saalwächter</br> 15N NMR relaxation rate R 1? measurements reveal that a substantial fraction of residues in the microcrystalline chicken alpha-spectrin SH3 domain protein undergoes dynamics in the ?s - ms timescale range. On the basis of a comparison of 2D site-resolved with 1D integrated 15N...	nmrlearner	Journal club	0	09-20-2014 07:51 PM
[NMR paper] Local Isotropic Diffusion Approximation for Coupled Internal and Overall Molecular Motions in NMR Spin Relaxation. Local Isotropic Diffusion Approximation for Coupled Internal and Overall Molecular Motions in NMR Spin Relaxation. Related Articles Local Isotropic Diffusion Approximation for Coupled Internal and Overall Molecular Motions in NMR Spin Relaxation. J Phys Chem B. 2014 Aug 28; Authors: Gill ML, Palmer AG Abstract The present work demonstrates that NMR spin relaxation rate constants for molecules interconverting between states with different diffusion tensors can be modeled theoretically by combining orientational correlation...	nmrlearner	Journal club	0	08-29-2014 05:36 PM
[R] Clustering large data matrix Clustering large data matrix More...	nmrlearner	NMR bookmarks	0	08-19-2010 02:34 PM

« 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