NMR paper NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions

		BioNMR > Educational resources > Journal club
[NMR paper] NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions

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

03-18-2022, 12:01 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

NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions

NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions

A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (?R(2)) NMR methodology. Some limitations of the DEST/?R(2) methodology in applications to molecular systems with intermediate molecular...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Investigation of protein-ligand complexes by ligand-based NMR methods Investigation of protein-ligand complexes by ligand-based NMR methods Molecular recognition is at the base of all biological events and its knowledge at atomic level is pivotal in the development of new drug design approaches. NMR spectroscopy is one of the most widely used technique to detect and characterize transient ligand-receptor interactions in solution. In particular, ligand-based NMR approaches, including NOE-based NMR techniques, diffusion experiments and relaxation methods, are excellent tools to investigate how ligands interact with their receptors.... More...	nmrlearner	Journal club	0	04-18-2021 11:34 AM
[NMR paper] Exploring Weak Ligand-Protein Interactions by Long-Lived NMR States : Improved Contrast in Fragment-Based Drug Screening. Exploring Weak Ligand-Protein Interactions by Long-Lived NMR States : Improved Contrast in Fragment-Based Drug Screening. Related Articles Exploring Weak Ligand-Protein Interactions by Long-Lived NMR States : Improved Contrast in Fragment-Based Drug Screening. Angew Chem Int Ed Engl. 2014 Sep 4; Authors: Buratto R, Mammoli D, Chiarparin E, Williams G, Bodenhausen G Abstract Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long-lived states (LLS) in NMR...	nmrlearner	Journal club	0	09-10-2014 11:24 AM
[NMR paper] (19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2. (19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2. (19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2. Chem Biol Drug Des. 2014 May 9; Authors: Leung EW, Yagi H, Harjani JR, Mulcair MD, Scanlon MJ, Baell JB, Norton RS Abstract SPRY domain-containing SOCS box protein 2 (SPSB2) regulates inducible nitric oxide synthase (iNOS) by targeting it for proteasomal degradation. Inhibiting this interaction...	nmrlearner	Journal club	0	05-13-2014 03:11 PM
Research and Markets: Protein-Ligand Interactions. Methods and Principles in ... - Business Wire (press release) Research and Markets: Protein-Ligand Interactions. Methods and Principles in ... - Business Wire (press release) <img alt="" height="1" width="1" /> Research and Markets: Protein-Ligand Interactions. Methods and Principles in ... Business Wire (press release) The first part provides a basic understanding of the factors governing protein-ligand interaction, followed by a comparison of the four key experimental methods (calorimetry, surface plasmon resonance, NMR and X-ray crystallography) used in generating ... and more » Read here	nmrlearner	Online News	0	08-29-2012 04:31 PM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these interactions...	nmrlearner	Journal club	0	09-30-2011 06:00 AM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these...	nmrlearner	Journal club	0	09-30-2011 05:59 AM
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. BMC Struct Biol. 2011 May 12;11(1):24 Authors: Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA ABSTRACT: BACKGROUND: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural...	nmrlearner	Journal club	0	05-17-2011 06:21 PM
[NMR paper] Probing the binding entropy of ligand-protein interactions by NMR. Probing the binding entropy of ligand-protein interactions by NMR. Related Articles Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem. 2005 Sep;6(9):1585-91 Authors: Homans SW	nmrlearner	Journal club	0	12-01-2010 06:56 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