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 01-09-2015, 03:58 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,926
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 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 development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment.
Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment. Related Articles Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment. J Biol Phys. 2013 Jan;39(1):131-44 Authors: Ba Y, Mao Y, Galdino L, Gnsen Z Abstract The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR...
nmrlearner Journal club 0 07-19-2013 09:20 PM
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR. Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR. Solid State Nucl Magn Reson. 2011 Mar 23; Authors: Mao Y, Jeong M, Wang T, Ba Y Antifreeze proteins (AFPs) provide survival mechanism for species living in subzero environments by lowering the freezing points of their...
nmrlearner Journal club 0 04-08-2011 10:00 AM
NMR characterizations of the ice binding surface of an antifreeze protein.
NMR characterizations of the ice binding surface of an antifreeze protein. NMR characterizations of the ice binding surface of an antifreeze protein. PLoS One. 2010;5(12):e15682 Authors: Hong J, Hu Y, Li C, Jia Z, Xia B, Jin C Antifreeze protein (AFP) has a unique function of reducing solution freezing temperature to protect organisms from ice damage. However, its functional mechanism is not well understood. An intriguing question concerning AFP function is how the high selectivity for ice ligand is achieved in the presence of free water of...
nmrlearner Journal club 0 01-07-2011 11:21 PM
[NMR paper] Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicat
Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicated by amide proton NMR chemical shifts. Related Articles Hydrogen bonding on the ice-binding face of a beta-helical antifreeze protein indicated by amide proton NMR chemical shifts. Biochemistry. 2004 Oct 19;43(41):13012-7 Authors: Daley ME, Graether SP, Sykes BD The dependence of amide proton chemical shifts on temperature is used as an indication of the hydrogen bonding properties in a protein. The amide proton temperature coefficients of the beta-helical...
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Characterization of threonine side chain dynamics in an antifreeze protein using natu
Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy. Related Articles Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy. J Biomol NMR. 2004 Jun;29(2):139-50 Authors: Daley ME, Sykes BD The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance (13)C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible...
nmrlearner Journal club 0 11-24-2010 09:51 PM
Protein-ice interaction of an antifreeze protein observed with solid-state NMR [Chemi
Protein-ice interaction of an antifreeze protein observed with solid-state NMR Siemer, A. B., Huang, K.-Y., McDermott, A. E.... Date: 2010-10-12 NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed NMR methods to study the interactions of proteins with their hydration shell and the ice lattice in frozen solution. We applied these methods to compare solvent interaction of an ice-binding...
nmrlearner Journal club 0 10-13-2010 04:10 AM
Protein-ice interaction of an antifreeze protein observed with solid-state NMR.
Protein-ice interaction of an antifreeze protein observed with solid-state NMR. Related Articles Protein-ice interaction of an antifreeze protein observed with solid-state NMR. Proc Natl Acad Sci U S A. 2010 Sep 30; Authors: Siemer AB, Huang KY, McDermott AE NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed NMR methods to study the interactions...
nmrlearner Journal club 0 10-05-2010 12:11 PM
Antifreeze Glycoprotein Activity Correlates with Long-Range Protein-Water Dynamics
Antifreeze Glycoprotein Activity Correlates with Long-Range Protein-Water Dynamics Simon Ebbinghaus et al http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1051632/aop/images/medium/ja-2010-051632_0004.gifJournal of the American Chemical Society, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable). Source: Journal of the American Chemical Society
nmrlearner Journal club 0 08-17-2010 05:52 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 10:47 AM.


Map