NMR paper Using NMR diffusion data to validate MD models of disordered proteins: test case of N-terminal tail of histone H4

		BioNMR > Educational resources > Journal club
[NMR paper] Using NMR diffusion data to validate MD models of disordered proteins: test case of N-terminal tail of histone H4

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

11-22-2023, 06:46 PM

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

Using NMR diffusion data to validate MD models of disordered proteins: test case of N-terminal tail of histone H4

Using NMR diffusion data to validate MD models of disordered proteins: test case of N-terminal tail of histone H4

MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion D(tr), measurable by pulsed-field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP's conformational ensemble. Here we investigate, both experimentally and via the MD modeling, the translational diffusion of 25-residue N-terminal...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[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
A simple and sensitive detection of the binding ligands by using the receptor aggregation and NMR spectroscopy: a test case of the maltose binding protein A simple and sensitive detection of the binding ligands by using the receptor aggregation and NMR spectroscopy: a test case of the maltose binding protein Abstract Protein-ligand interaction is one of the highlights of molecular recognition. The most popular application of this type of interaction is drug development which requires a high throughput screening of a ligand that binds to the target protein. Our goal was to find a binding ligand with a simple detection, and once this type of ligand was found, other methods could then be used to measure...	nmrlearner	Journal club	0	09-15-2021 07:48 PM
[NMR paper] On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme. On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7388-69-wiley-full-text.png Related Articles On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme. Chembiochem. 2020 Nov 04;: Authors: Smith LJ, van Gunsteren WF, Hansen N Abstract Values of S2CH and S2NH order...	nmrlearner	Journal club	0	11-07-2020 03:20 PM
A CON-based NMR assignment strategy for pro-rich intrinsically disordered proteins with low signal dispersion: the C-terminal domain of histone H1.0 as a case study A CON-based NMR assignment strategy for pro-rich intrinsically disordered proteins with low signal dispersion: the C-terminal domain of histone H1.0 as a case study Abstract The C-terminal domain of histone H1.0 (C-H1.0) is involved in DNA binding and is a main determinant of the chromatin condensing properties of histone H1.0. Phosphorylation at the (S/T)-P-X-(K/R) motifs affects DNA binding and is crucial for regulation of C-H1.0 function. Since C-H1.0 is an intrinsically disordered domain, solution NMR is an excellent approach to characterize the...	nmrlearner	Journal club	0	11-25-2018 06:02 AM
[NMR paper] Liposcale: a novel advanced lipoprotein test based on 2D diffusion-ordered 1H NMR spectroscopy. Liposcale: a novel advanced lipoprotein test based on 2D diffusion-ordered 1H NMR spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jlr_final.gif Related Articles Liposcale: a novel advanced lipoprotein test based on 2D diffusion-ordered 1H NMR spectroscopy. J Lipid Res. 2015 Mar;56(3):737-46 Authors: Mallol R, Amigó N, Rodríguez MA, Heras M, Vinaixa M, Plana N, Rock E, Ribalta J, Yanes O, Masana L, Correig X Abstract Determination of...	nmrlearner	Journal club	0	11-17-2015 02:57 PM
[NMR tweet] Models of Scientific Development and the Case of Nuclear Magnetic Resonance (Synthese Library): http://amzn.to/kxbAwO Models of Scientific Development and the Case of Nuclear Magnetic Resonance (Synthese Library): http://amzn.to/kxbAwO Published by Staceeeygq (Stacee Quiller) on 2011-05-19T17:37:21Z Source: Twitter	nmrlearner	Twitter NMR	0	05-19-2011 05:40 PM
[NMR tweet] Models of Scientific Development and the Case of Nuclear Magnetic Resonance (Synthese Library): http://amzn.to/garj5l Models of Scientific Development and the Case of Nuclear Magnetic Resonance (Synthese Library): http://amzn.to/garj5l Published by Cassidykb02 (Cassidy Mcfatter) on 2011-04-27T12:14:02Z Source: Twitter	nmrlearner	Twitter NMR	0	04-27-2011 12:22 PM
[NMR paper] A systematic case study on using NMR models for molecular replacement: p53 tetrameriz A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited. Related Articles A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited. Acta Crystallogr D Biol Crystallogr. 2000 Dec;56(Pt 12):1535-40 Authors: Chen YW, Clore GM Molecular replacement using search models derived from nuclear magnetic resonance (NMR) spectroscopy has often proved problematic. It has been known for some time that the overall differences in atomic positions (r.m.s.d.)...	nmrlearner	Journal club	0	11-19-2010 08:29 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