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 05-13-2017, 02:08 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,617
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 Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

Related Articles Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A.

Biophys J. 2017 May 09;112(9):1820-1828

Authors: Kawamura T, Wakamoto T, Kitazawa S, Sakuraba S, Kameda T, Kitahara R

Abstract
Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O2-binding sites by O2-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer surface protein A contains a nonglobular single-layer ?-sheet that connects the N- and C-terminal globular domains. Several cavities have been observed in both domains of the crystallized protein structure. The receptor-binding sites are occluded and line the largest cavity of the C-terminal domain. We observed significant O2-induced PREs for amide protons located around the largest cavity and at the central ?-sheet. We suggested three potential O2-accessible sites in the protein based on the 1/r(6) distance dependence of the PRE. Two sites were in or close to the largest cavity and the third site was in the surface crevice of the central ?-sheet. These results provide, to our knowledge, the first evidence of ligand binding to the surface crevice and cavity of the protein in solution. Because O2 generally binds more specifically to hydrophobic rather than hydrophilic cavities within a protein, the results also indicated that the receptor-binding sites lining the largest cavity were in the hydrophobic environment in the ground-state conformation. Molecular dynamics simulations permitted the visualization of the rotational and translational motions of O2 within the largest cavity, egress of O2 from the cavity, and ingress of O2 in the surface crevice of the ?-sheet. These molecular dynamics simulation results qualitatively explained the O2-induced changes in NMR observations. Exploring cavities that are sufficiently dynamic to enable access by small molecules can be a useful strategy for the design of stable proteins and their ligands.


PMID: 28494953 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A
Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A Publication date: 9 May 2017 Source:Biophysical Journal, Volume 112, Issue 9</br> Author(s): Takahiro Kawamura, Takuro Wakamoto, Soichiro Kitazawa, Shun Sakuraba, Tomoshi Kameda, Ryo Kitahara</br> Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O2-binding sites by O2-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer...
nmrlearner Journal club 0 05-10-2017 06:52 AM
[NMR paper] Using (15) N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy.
Using (15) N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy. Related Articles Using (15) N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy. Chembiochem. 2014 Feb 12; Authors: Werbeck ND, Kirkpatrick J, Reinstein J, Hansen DF Abstract A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic...
nmrlearner Journal club 0 02-13-2014 03:35 PM
[NMR paper] Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy.
Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. J Biochem. 2013 Oct 4; Authors: Yuasa N, Koyama T, Subedi GP, Yamaguchi Y, Matsushita M, Fujita-Yamaguchi Y Abstract T-antigen (Gal?1-3GalNAc?-1-Ser/Thr), also known as...
nmrlearner Journal club 0 10-08-2013 02:04 PM
Small-Molecule Binding Sites on Proteins Establishedby Paramagnetic NMR Spectroscopy
Small-Molecule Binding Sites on Proteins Establishedby Paramagnetic NMR Spectroscopy Jia-Ying Guan, Peter H. J. Keizers, Wei-Min Liu, Frank Lo?hr, Simon P. Skinner, Edwin A. Heeneman, Harald Schwalbe, Marcellus Ubbink and Gregg Siegal http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja401323m/aop/images/medium/ja-2013-01323m_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja401323m http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/ZukfjIRmQq8
nmrlearner Journal club 0 04-05-2013 11:03 PM
[NMR paper] Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy.
Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy. Related Articles Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy. J Am Chem Soc. 2013 Mar 20; Authors: Guan JY, Keizers PH, Liu WM, Loehr F, Skinner SP, Heeneman EA, Schwalbe H, Ubbink M, Siegal GD Abstract Determining the three dimensional structure of a small molecule-protein complex with weak affinity can be a significant challenge. We present a paramagnetic NMR method to determine intermolecular structure...
nmrlearner Journal club 0 03-21-2013 02:58 PM
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A 22 February 2012 Publication year: 2012 Source:Biophysical Journal, Volume 102, Issue 4</br> </br> Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the...
nmrlearner Journal club 0 02-03-2013 10:13 AM
Nature and Structure of Aluminum Surface Sites Grafted on Silica from a Combination of High-Field Aluminum-27 Solid-State NMR Spectroscopy and First-Principles Calculations
Nature and Structure of Aluminum Surface Sites Grafted on Silica from a Combination of High-Field Aluminum-27 Solid-State NMR Spectroscopy and First-Principles Calculations Rachel Nathaniel Kerber, Anthony Kermagoret, Emmanuel Callens, Pierre Florian, Dominique Massiot, Anne Lesage, Christophe Cope?ret, Franc?oise Delbecq, Xavier Rozanska and Philippe Sautet http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja3008566/aop/images/medium/ja-2012-008566_0006.gif Journal of the American Chemical Society DOI: 10.1021/ja3008566 ...
nmrlearner Journal club 0 04-10-2012 02:44 AM
Engineering [Ln(DPA)3]3â?? binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions
Engineering 3â?? binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions Abstract Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and...
nmrlearner Journal club 0 07-26-2011 11:11 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 10:08 AM.


Map