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 05-17-2011, 06:21 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 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 changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding. RESULTS: In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces. CONCLUSIONS: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

PMID: 21569443 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
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 ... - 7thSpace Interactive (press release)
Exploring NMR ensembles of calcium binding proteins: perspectives to design ... - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> Exploring NMR ensembles of calcium binding proteins: perspectives to design ... 7thSpace Interactive (press release) We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein ... Read here
nmrlearner Online News 0 05-13-2011 07:41 AM
[NMR paper] Calcium-modulated S100 protein-phospholipid interactions. An NMR study of calbindin D
Calcium-modulated S100 protein-phospholipid interactions. An NMR study of calbindin D9k and DPC. Related Articles Calcium-modulated S100 protein-phospholipid interactions. An NMR study of calbindin D9k and DPC. Biochemistry. 2005 May 3;44(17):6502-12 Authors: Malmendal A, Vander Kooi CW, Nielsen NC, Chazin WJ The cellular functions of several S100 proteins involve specific interactions with phospholipids and the cell membrane. The interactions between calbindin D(9k) (S100D) and the detergent dodecyl phosphocholine (DPC) were studied using NMR...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] In silico and NMR identification of inhibitors of the IGF-I and IGF-binding protein-5
In silico and NMR identification of inhibitors of the IGF-I and IGF-binding protein-5 interaction. Related Articles In silico and NMR identification of inhibitors of the IGF-I and IGF-binding protein-5 interaction. J Med Chem. 2002 Dec 19;45(26):5655-60 Authors: Kamionka M, Rehm T, Beisel HG, Lang K, Engh RA, Holak TA Recently we have determined the crystal structure of the insulin-like growth factor-I (IGF-I) in complex with the N-terminal domain of the IGF-binding protein-5 (IGFBP-5). Here we report results of computer screening for...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Exploring the calcium-binding site in photosystem II membranes by solid-state (113)Cd
Exploring the calcium-binding site in photosystem II membranes by solid-state (113)Cd NMR. Related Articles Exploring the calcium-binding site in photosystem II membranes by solid-state (113)Cd NMR. Biochemistry. 2000 Jun 13;39(23):6751-5 Authors: Matysik J, Alia A, Nachtegaal G, van Gorkom HJ, Hoff AJ, de Groot HJ Calcium (Ca(2+)) is an essential cofactor for photosynthetic oxygen evolution. Although the involvement of Ca(2+) at the oxidizing side of photosystem II of plants has been known for a long time, its ligand interactions and mode of...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] NMR for the design of functional mimetics of protein-protein interactions: one key is
NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges. Related Articles NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges. Biochem Cell Biol. 1998;76(2-3):177-88 Authors: Song J, Ni F Using the design of bivalent and bridge-binding inhibitors of thrombin as an example, we review an NMR-based experimental approach for the design of functional mimetics of protein-protein interactions. The strategy includes: (i) identification...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with
Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR. Related Articles Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR. Biochemistry. 1993 Sep 14;32(36):9407-16 Authors: Folkers PJ, van Duynhoven JP, van Lieshout HT, Harmsen BJ, van Boom JH, Tesser GI, Konings RN, Hilbers CW The DNA binding domain of the single-stranded DNA binding protein...
nmrlearner Journal club 0 08-22-2010 03:01 AM


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 07:14 PM.


Map