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 11-17-2020, 07:53 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,403
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 All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy.

All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy.

Related Articles All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy.

Nat Commun. 2020 Nov 13;11(1):5760

Authors: Köhn B, Kovermann M

Abstract
The high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.


PMID: 33188202 [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
[ASAP] Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore
Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.0c00474/20200903/images/medium/bi0c00474_0009.gif Biochemistry DOI: 10.1021/acs.biochem.0c00474 http://feeds.feedburner.com/~r/acs/bichaw/~4/tn0G9nsz91w More...
nmrlearner Journal club 0 09-13-2020 09:18 AM
[NMR paper] Insights into protein stability in cell lysate by 19F NMR spectroscopy.
Insights into protein stability in cell lysate by 19F NMR spectroscopy. Related Articles Insights into protein stability in cell lysate by 19F NMR spectroscopy. Chembiochem. 2020 Aug 12;: Authors: Welte H, Kovermann M Abstract In living organisms, protein folding and function take place in an inhomogeneous, highly crowded environment possessing a concentration of diverse macromolecules of up to 400*g/L. It has been shown that the intracellular environment has a pronounced effect on the stability, dynamics and function of the...
nmrlearner Journal club 0 08-15-2020 05:51 AM
[NMR paper] Human plasma stability during handling and storage: impact on NMR metabolomics.
Human plasma stability during handling and storage: impact on NMR metabolomics. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Human plasma stability during handling and storage: impact on NMR metabolomics. Analyst. 2014 Mar 7;139(5):1168-77 Authors: Pinto J, Domingues MR, Galhano E, Pita C, Almeida Mdo C, Carreira IM, Gil AM Abstract This work contributes to fill in some existing gaps in the knowledge of human plasma degradability...
nmrlearner Journal club 0 08-29-2014 05:36 PM
[NMR paper] Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils.
Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Related Articles Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys. 2013 Mar 22; Authors: Comellas G, Rienstra CM Abstract Protein structure determination methods using magic-angle spinning solidstate nuclear magnetic resonance (MAS SSNMR) have experienced a remarkable...
nmrlearner Journal club 0 03-27-2013 03:33 PM
Superconducting Magnets Used to Observe Proteins, Atom-by-Atom - Azom.com
Superconducting Magnets Used to Observe Proteins, Atom-by-Atom - Azom.com http://www.bionmr.com//nt3.ggpht.com/news/tbn/t4dz7XpX589ZcM/6.jpg Azom.com <img alt="" height="1" width="1" /> Superconducting Magnets Used to Observe Proteins, Atom-by-Atom Azom.com â??This is a very specialized facility,â?? says Stanley Opella, professor of chemistry and biochemistry and director of the Center for NMR Spectroscopy and Imaging of Proteins, the organization that operates this building. The purpose of the facility is to ...
nmrlearner Online News 0 10-27-2012 03:04 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 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
[NMR paper] Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational
Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. Related Articles Insights into the determinants of beta-sheet stability: 1H and 13C NMR conformational investigation of three-stranded antiparallel beta-sheet-forming peptides. J Pept Res. 2003 Apr;61(4):177-88 Authors: Santiveri CM, Rico M, Jiménez MA, Pastor MT, Pérez-Payá E In a previous study we designed a 20-residue peptide able to adopt a significant population of a three-stranded...
nmrlearner Journal club 0 11-24-2010 09:01 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 - 2020, 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 08:20 AM.


Map