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 06-13-2018, 05:09 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,793
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 Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies.

Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies.

Related Articles Binding mode of AIF(370-394) peptide to CypA: insights from NMR, label-free and molecular docking studies.

Biochem J. 2018 Jun 11;:

Authors: Farina B, Sturlese M, Mascanzoni F, Caporale A, Monti A, Di Sorbo G, Fattorusso R, Ruvo M, Doti N

Abstract
The complex formation between the proteins Apoptosis Inducing Factor (AIF) and Cyclophilin A (CypA) following oxidative stress in neuronal cells has been suggested as a main target for reverting ischemia-stroke damage. Recently, a peptide encompassing AIF residues 370-394 has been developed to target the AIF-binding site on CypA, to prevent the association between the two proteins and suppress glutamate-induced cell death in neuronal cells. Using a combined approach based on NMR spectroscopy, synthesis and in vitro testing of all Ala-scan mutants of the peptide and molecular docking/molecular dynamics, we have generated a detailed model of the AIF(370-394)/CypA complex. The model suggests that the central region of the peptide spanning residues V374-K384 mostly interacts with the protein and that for efficient complex inhibition and preservation of CypA activity, it is bent around amino acids F46-G75 of the protein. The model is consistent with experimental data also from previous works and supports the concept that the peptide does not interfere with other CypA activities unrelated to AIF activation, therefore it may serve as an ideal template for generating future non-peptidic antagonists.


PMID: 29891613 [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
[NMR paper] Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.
Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Related Articles Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Phys Chem Chem Phys. 2018 Apr 26;: Authors: Špa?ková N, Trošanová Z, Šebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Žídek L, Kozelka J Abstract Water molecules can interact with aromatic moieties using either their O-H bonds or their lone-pairs of electrons. In...
nmrlearner Journal club 0 04-27-2018 10:26 PM
[NMR paper] Binding investigation between M2-1protein from hRSV and acetylated quercetin derivatives: 1H NMR, fluorescence spectroscopy, and molecular docking.
Binding investigation between M2-1protein from hRSV and acetylated quercetin derivatives: 1H NMR, fluorescence spectroscopy, and molecular docking. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Binding investigation between M2-1protein from hRSV and acetylated quercetin derivatives: 1H NMR, fluorescence spectroscopy, and molecular docking. Int J Biol Macromol. 2017 Dec 29;: Authors: Guimarăes GC, Piva HRM, Araújo GC, Lima CS, Regasini LO, de Melo FA, Fossey...
nmrlearner Journal club 0 01-04-2018 08:45 AM
[NMR paper] Insight to the binding mode of triazole RGD-peptidomimetics to integrin-rich cancer cells by NMR and molecular modeling.
Insight to the binding mode of triazole RGD-peptidomimetics to integrin-rich cancer cells by NMR and molecular modeling. Related Articles Insight to the binding mode of triazole RGD-peptidomimetics to integrin-rich cancer cells by NMR and molecular modeling. Bioorg Med Chem. 2016 Jan 14; Authors: Vasile F, Menchi G, Lenci E, Guarna A, Potenza D, Trabocchi A Abstract The binding features of a novel class of 'click chemistry'-derived RGD mimics with integrin ligand capability were studied toward ?v?3 integrin using STD-NMR...
nmrlearner Journal club 0 01-29-2016 04:20 PM
Hyperpolarized Xenon-Based Molecular Sensors for Label-Free Detection of analytes
From The DNP-NMR Blog: Hyperpolarized Xenon-Based Molecular Sensors for Label-Free Detection of analytes Garimella, P.D., et al., Hyperpolarized Xenon-Based Molecular Sensors for Label-Free Detection of analytes. J. Am. Chem. Soc., 2013. 136(1): p. 164-168. http://pubs.acs.org/doi/abs/10.1021/ja406760r
nmrlearner News from NMR blogs 0 02-28-2014 07:08 PM
[NMR paper] Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking.
Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking. J Med Chem. 2013 Aug 8;56(15):6146-55 Authors: Weidel E, de Jong JC, Brengel...
nmrlearner Journal club 0 11-12-2013 03:52 PM
[NMR paper] Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase.
Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase. Biochem Biophys Res Commun. 2013 Jan 4;430(1):313-9 Authors: Boonsri P, Neumann TS, Olson AL, Cai S, Herdendorf TJ, Miziorko HM, Hannongbua S, Sem DS Abstract Phosphomevalonate kinase (PMK)...
nmrlearner Journal club 0 05-15-2013 03:12 PM
[NMR paper] NMR dynamics-derived insights into the binding properties of a peptide interacting wi
NMR dynamics-derived insights into the binding properties of a peptide interacting with an SH2 domain. Related Articles NMR dynamics-derived insights into the binding properties of a peptide interacting with an SH2 domain. Biochemistry. 2005 Jan 18;44(2):694-703 Authors: Finerty PJ, Mittermaier AK, Muhandiram R, Kay LE, Forman-Kay JD The signal transduction protein phospholipase C-gamma1 (PLC-gamma1) is activated when its C-terminal SH2 domain (PLCC) binds the phosphorylated Tyr-1021 site (pTyr-1021) in the beta-platelet-derived growth factor...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR studies of the mode of binding of corepressors and inducers to Escherichia coli t
NMR studies of the mode of binding of corepressors and inducers to Escherichia coli trp repressor. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles NMR studies of the mode of binding of corepressors and inducers to Escherichia coli trp repressor. Eur J Biochem. 1996 Feb 1;235(3):804-13 Authors: Ramesh V, Syed SE, Frederick RO, Sutcliffe MJ, Barnes M, Roberts GC The binding of the corepressors tryptophan and 5-methyltryptophan and...
nmrlearner Journal club 0 08-22-2010 02:27 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 - 2018, 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 02:28 PM.


Map