BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-01-2015, 01:52 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Thermodynamic and NMR analyses of NADPH binding to lipocalin-type prostaglandin D synthase.

Thermodynamic and NMR analyses of NADPH binding to lipocalin-type prostaglandin D synthase.

Related Articles Thermodynamic and NMR analyses of NADPH binding to lipocalin-type prostaglandin D synthase.

Biochem Biophys Res Commun. 2015 Oct 27;

Authors: Qin S, Shimamoto S, Maruno T, Kobayashi Y, Kawahara K, Yoshida T, Ohkubo T

Abstract
Lipocalin-type prostaglandin D synthase (L-PGDS) is one of the most abundant proteins in human cerebrospinal fluid (CSF) with dual functions as a prostaglandin D2 (PGD2) synthase and a transporter of lipophilic ligands. Recent studies revealed that L-PGDS plays important roles in protecting against various neuronal diseases induced by reactive oxygen species (ROS). However, the molecular mechanisms of such protective actions of L-PGDS remain unknown. In this study, we conducted thermodynamic and nuclear magnetic resonance (NMR) analyses, and demonstrated that L-PGDS binds to nicotinamide coenzymes, including NADPH, NADP(+), and NADH. Although a hydrophilic ligand is not common for L-PGDS, these ligands, especially NADPH showed specific interaction with L-PGDS at the upper pocket of its ligand-binding cavity with an unusually bifurcated shape. The binding affinity of L-PGDS for NADPH was comparable to that previously reported for NADPH oxidases and NADPH in vitro. These results suggested that L-PGDS potentially attenuates the activities of NADPH oxidases through interaction with NADPH. Given that NADPH is the substrate for NADPH oxidases that play key roles in neuronal cell death by generating excessive ROS, these results imply a novel linkage between L-PGDS and ROS.


PMID: 26518650 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase
Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase Abstract Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 310-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as...
nmrlearner Journal club 0 01-09-2015 03:58 PM
[NMR paper] Thermodynamic and solution state NMR characterization of the binding of secondary and conjugated bile acids to STARD5.
Thermodynamic and solution state NMR characterization of the binding of secondary and conjugated bile acids to STARD5. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Thermodynamic and solution state NMR characterization of the binding of secondary and conjugated bile acids to STARD5. Biochim Biophys Acta. 2013 Jul 16; Authors: Létourneau D, Lorin A, Lefebvre A, Cabana J, Lavigne P, Lehoux JG Abstract STARD5 is a member of the STARD4 sub-family...
nmrlearner Journal club 0 07-23-2013 09:52 PM
[NMR paper] Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments.
Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments. Related Articles Solution NMR analyses of the C-type carbohydrate recognition domain of DC-SIGNR reveal different binding modes for HIV-derived oligosaccharides and smaller glycan fragments. J Biol Chem. 2013 Jun 20; Authors: Probert F, Whittaker SB, Crispin M, Mitchell DA, Dixon AM Abstract The C-type lectin DC-SIGNR (Dendritic Cell-Specific ICAM-3-Grabbing...
nmrlearner Journal club 0 06-25-2013 12:17 AM
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
Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase.
Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase. Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase. Bioorg Med Chem. 2010 Dec 15;18(24):8485-92 Authors: Batruch I, Javasky E, Brown ED, Organ MG, Johnson PE Isothermal titration calorimetry (ITC) was used to determine the thermodynamic driving force for inhibitor binding to the enzyme dihydrofolate reductase (DHFR) from Escherichia coli. 1,4-Bis-{sulfanylmethyl}-3,6-dimethyl-benzene (1) binds DHFR:NADPH with a K(d) of 13±5 nM while the...
nmrlearner Journal club 0 03-09-2011 02:20 PM
NMR assignment of 1H, 13C, and 15N resonances of rat lipocalin-type prostaglandin D synthase.
NMR assignment of 1H, 13C, and 15N resonances of rat lipocalin-type prostaglandin D synthase. NMR assignment of 1H, 13C, and 15N resonances of rat lipocalin-type prostaglandin D synthase. Biomol NMR Assign. 2010 Oct;4(2):223-5 Authors: Liu J, Lv Y, Guo C, Lin D Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD(2)-synthesizing enzyme and an extracellular transporter for small lipophilic molecules. Here we report the backbone and side-chain resonance assignments of uniformly (15)N, (13)C labeled rat L-PGDS.
nmrlearner Journal club 0 03-05-2011 01:02 PM
NMR analyses of the G{beta}{gamma} binding and conformational rearrangements of the c
NMR analyses of the G{beta}{gamma} binding and conformational rearrangements of the cytoplasmic pore of G protein-activated inwardly rectifying potassium channel 1 (GIRK1). Related Articles NMR analyses of the G{beta}{gamma} binding and conformational rearrangements of the cytoplasmic pore of G protein-activated inwardly rectifying potassium channel 1 (GIRK1). J Biol Chem. 2010 Nov 12; Authors: Yokogawa M, Osawa M, Takeuchi K, Mase Y, Shimada I G protein-activated inwardly rectifying potassium channel (GIRK) plays crucial roles in regulating heart...
nmrlearner Journal club 0 11-16-2010 04:13 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 12:28 PM.


Map