Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit - pnas.org

		BioNMR > NMR community > Online News
Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit - pnas.org

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

10-12-2024, 03:04 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

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit - pnas.org

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit - pnas.org

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit pnas.org Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Tracking protein-protein interactions by NMR: conformational selection in human steroidogenic cytochrome P450 CYP17A1 induced by cytochrome b(5) Tracking protein-protein interactions by NMR: conformational selection in human steroidogenic cytochrome P450 CYP17A1 induced by cytochrome b(5) The human steroidogenic cytochrome P450 CYP17A1 catalyzes two types of reactions in the biosynthetic pathway leading from pregnenolone to testosterone and several other steroid hormones. The first is the hydroxylation of pregnenolone or progesterone to the corresponding 17?-hydroxy steroid, followed by a lyase reaction that converts these 17?-hydroxy intermediates to the androgens dehydroepiandrosterone and androstenedione, respectively....	nmrlearner	Journal club	0	06-06-2024 11:50 PM
[ASAP] Ligand- and pH-Induced Structural Transition of Gypsy Moth Lymantria dispar Pheromone-Binding Protein 1 (LdisPBP1) Ligand- and pH-Induced Structural Transition of Gypsy Moth Lymantria dispar Pheromone-Binding Protein 1 (LdisPBP1) https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.0c00592/20200911/images/medium/bi0c00592_0012.gif Biochemistry DOI: 10.1021/acs.biochem.0c00592 http://feeds.feedburner.com/~r/acs/bichaw/~4/Hl9whcZefp0 More...	nmrlearner	Journal club	0	09-13-2020 09:18 AM
[NMR paper] Ligand-induced conformational change of Plasmodium falciparum AMA1 detected using (19)F NMR. Ligand-induced conformational change of Plasmodium falciparum AMA1 detected using (19)F NMR. Related Articles Ligand-induced conformational change of Plasmodium falciparum AMA1 detected using (19)F NMR. J Med Chem. 2014 Jul 28; Authors: Ge X, MacRaild CA, Devine S, Debono CO, Wang G, Scammells PJ, Scanlon MJ, Anders RF, Foley M, Norton RS Abstract We established an efficient means of probing ligand-induced conformational change in the malaria drug target AMA1 using 19F NMR. AMA1 was labeled with 5-fluorotryptophan (5F-Trp) and...	nmrlearner	Journal club	0	07-30-2014 10:22 AM
[NMR paper] Ligand-Induced Conformational Changes of the Multidrug Resistance Transporter EmrE Probed by Oriented Solid-State NMR Spectroscopy. Ligand-Induced Conformational Changes of the Multidrug Resistance Transporter EmrE Probed by Oriented Solid-State NMR Spectroscopy. Ligand-Induced Conformational Changes of the Multidrug Resistance Transporter EmrE Probed by Oriented Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl. 2013 Aug 12; Authors: Gayen A, Banigan JR, Traaseth NJ Abstract An EmrE-ging market: Oriented solid-state NMR spectroscopy and biochemical cross-linking experiments were used to show that the ligand-free membrane protein transporter EmrE forms...	nmrlearner	Journal club	0	08-14-2013 05:24 PM
NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand...	nmrlearner	Journal club	0	07-13-2011 06:42 PM
NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi200067t/aop/images/medium/bi-2011-00067t_0002.gif Biochemistry DOI: 10.1021/bi200067t http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/sLQe7ipMThM More...	nmrlearner	Journal club	0	04-15-2011 01:40 AM
NMR analysis reveals 17?-estradiol induced conformational change in ER? ligand binding domain expressed in E. coli. NMR analysis reveals 17?-estradiol induced conformational change in ER? ligand binding domain expressed in E. coli. NMR analysis reveals 17?-estradiol induced conformational change in ER? ligand binding domain expressed in E. coli. Mol Biol Rep. 2010 Dec 12; Authors: Paramanik V, Thakur MK Nuclear magnetic resonance (NMR) spectroscopy is a useful biophysical technique to study the ligand-protein interaction. In this report, we have used bacterially produced ER? and its domains for studying the functional analysis of ligand-protein interaction....	nmrlearner	Journal club	0	12-15-2010 12:03 PM
[NMR paper] Ligand-induced structural changes to maltodextrin-binding protein as studied by solut Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. Related Articles Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J Mol Biol. 2001 Jun 15;309(4):961-74 Authors: Evenäs J, Tugarinov V, Skrynnikov NR, Goto NK, Muhandiram R, Kay LE Solution NMR studies on the physiologically relevant ligand-free and maltotriose-bound states of maltodextrin-binding protein (MBP) are presented. Together with existing data on MBP in complex with...	nmrlearner	Journal club	0	11-19-2010 08:32 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