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 11-24-2010, 09:16 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,813
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 Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD

Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.

Related Articles Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.

Biochemistry. 2003 Dec 2;42(47):13856-68

Authors: Hu H, Clarkson MW, Hermans J, Lee AL

To gain physical insights into how proteins respond to changes in pH, the picosecond to nanosecond time scale dynamics of the small serine protease inhibitor eglin c have been studied by NMR spin relaxation experiments and MD simulations under two pH solution conditions, pH 7 and 3. Like many proteins, eglin c is destabilized by a lowering of the pH, although it retains enough stability to maintain its native conformation at pH 3. Backbone (15)N relaxation results show comparable global tumbling times (tau(m)) and model-free order parameters (S(2)) under the two pH conditions, indicating that the molecule maintains its overall molecular shape and structure at low pH, although the backbone rigidity is slightly increased (/ = 0.6%). In contrast, the side-chain methyl dynamics, as measured from (2)H relaxation experiments, show a substantial increase in rigidity at lower pH (/ = 14.8%). Molecular dynamics simulations performed at these pH states produce results consistent with NMR measurements, showing that the two methods are in qualitative agreement. Although a full accounting of the physical basis for the concurrent conformational rigidification and destabilization at low pH requires further investigation, the high level of detail in the MD simulations provides a potential molecular mechanism: the breaking of the hydrogen bond between the side chains of Asp46 and Arg53, and changes in electrostatic interactions, appear to allow the binding loop to move closer to the core part of the protein, resulting in a more compact structure at low pH. This more compact structure may be responsible for the increased level of restriction of molecular motion. As these findings show, the stability of a molecular structure is distinct from its conformational rigidity, and the two can even change in opposite directions, against na´ve expectation.

PMID: 14636053 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Water proton spin saturation affects measured protein backboneN spin relaxation rates
Water proton spin saturation affects measured protein backboneN spin relaxation rates Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 1 October 2011</br> Kang*Chen, Nico*Tjandra</br> Protein backboneN NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses....
nmrlearner Journal club 0 10-02-2011 08:25 AM
[NMR tweet] Nuclear Spin Relaxation in Liquids: Nuclear Spin Relaxation in LiquidsNuclear magnetic resonance (NMR) is wide... http://bit.ly/hDdW99
Nuclear Spin Relaxation in Liquids: Nuclear Spin Relaxation in LiquidsNuclear magnetic resonance (NMR) is wide... http://bit.ly/hDdW99 Published by booksvariety (BooksVariety.com) on 2010-12-04T23:02:54Z Source: Twitter
nmrlearner Twitter NMR 0 12-04-2010 11:36 PM
[NMR paper] NMR chemical shift and relaxation measurements provide evidence for the coupled foldi
NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain. Related Articles NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain. Nucleic Acids Res. 2005;33(7):2061-77 Authors: Vise PD, Baral B, Latos AJ, Daughdrill GW The interaction between the acidic transactivation domain of the human tumor suppressor protein p53 (p53TAD) and the 70 kDa subunit of human replication protein A (hRPA70)...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] 15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth fa
15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor. Related Articles 15N NMR relaxation studies of free and ligand-bound human acidic fibroblast growth factor. J Biol Chem. 2000 Dec 15;275(50):39444-50 Authors: Chi Y, Kumar TK, Chiu IM, Yu C 15N NMR relaxation data have been used to characterize the backbone dynamics of the human acidic fibroblast growth factor (hFGF-1) in its free and sucrose octasulfate (SOS)-bound states. (15)N longitudinal (R(1)), transverse (R(2)) relaxation rates and (1H)-(15)N...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and
Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and magnetization transfer in the presence of an off-resonance irradiation field. Related Articles Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and magnetization transfer in the presence of an off-resonance irradiation field. J Magn Reson B. 1994 May;104(1):11-25 Authors: Kuwata K, Brooks D, Yang H, Schleich T The derivation of a generalized relaxation matrix equation for the off-resonance rotating-frame spin-lattice...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and
Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and magnetization transfer in the presence of an off-resonance irradiation field. Related Articles Relaxation-matrix formalism for rotating-frame spin-lattice proton NMR relaxation and magnetization transfer in the presence of an off-resonance irradiation field. J Magn Reson B. 1994 May;104(1):11-25 Authors: Kuwata K, Brooks D, Yang H, Schleich T The derivation of a generalized relaxation matrix equation for the off-resonance rotating-frame spin-lattice...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] 19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic bindi
19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic binding to proteins. Analysis of isoflurane binding to serum albumin. Related Articles 19F-NMR spin-spin relaxation (T2) method for characterizing volatile anesthetic binding to proteins. Analysis of isoflurane binding to serum albumin. Biochemistry. 1992 Aug 11;31(31):7069-76 Authors: Dubois BW, Evers AS This paper characterizes the low-affinity ligand binding interactions of a fluorinated volatile anesthetic, isoflurane (CHF2OCHClCF3), with bovine serum albumin...
nmrlearner Journal club 0 08-21-2010 11:45 PM
Protein flexibility and rigidity predicted from se
Protein flexibility and rigidity predicted from sequence http://cubic.bioc.columbia.edu/papers/2005_bvalue/paper.html
nmrlearner A test forum 0 05-07-2005 07:04 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 04:29 AM.


Map