NMR paper Temperature-dependence of protein hydrogen bond properties as studied by high-resolut

		BioNMR > Educational resources > Journal club
[NMR paper] Temperature-dependence of protein hydrogen bond properties as studied by high-resolut

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-24-2010, 08:49 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Temperature-dependence of protein hydrogen bond properties as studied by high-resolut

Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.

Related Articles Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR.

J Mol Biol. 2002 Apr 12;317(5):739-52

Authors: Cordier F, Grzesiek S

The temperature-dependence of a large number of NMR parameters describing hydrogen bond properties in the protein ubiquitin was followed over a range from 5 to 65 degrees C. The parameters comprise hydrogen bond (H-bond) scalar couplings, h3JNC', chemical shifts, amide proton exchange rates, 15N relaxation parameters as well as covalent 1JNC' and 1JNH couplings. A global weakening of the h3JNC' coupling with increasing temperature is accompanied by a global upfield shift of the amide protons and a decrease of the sequential 1JNC' couplings. If interpreted as a linear increase of the N...O distance, the change in h3JNC' corresponds to an average linear thermal expansion coefficient for the NH-->O hydrogen bonds of 1.7 x 10(-4)/K, which is in good agreement with overall volume expansion coefficients observed for proteins. A residue-specific analysis reveals that not all hydrogen bonds are affected to the same extent by the thermal expansion. The end of beta-sheet beta1/beta5 at hydrogen bond E64-->Q2 appears as the most thermolabile, whereas the adjacent hydrogen bond I3-->L15 connecting beta-strands beta1 and beta2 is even stabilized slightly at higher temperatures. Additional evidence for the stabilization of the beta1/beta2 beta-hairpin at higher temperatures is found in reduced hydrogen exchange rates for strand end residue V17. This reduction corresponds to a stabilizing change in free energy of 9.7 kJ/mol for the beta1/beta2 hairpin. The result can be linked to the finding that the beta1/beta2 hairpin behaves as an autonomously folding unit in the A-state of ubiquitin under changed solvent conditions. For several amide groups the temperature-dependencies of the amide exchange rates and H-bond scalar couplings are uncorrelated. Therefore, amide exchange rates are not a sole function of the hydrogen bond "strength" as given by the electronic overlap of donors and acceptors, but are clearly dependent on other blocking mechanisms.

PMID: 11955021 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[Question from NMRWiki Q&A forum] bulk water relaxation dependence on temperature bulk water relaxation dependence on temperature Is liquid water's relaxation rate strongly dependent on temperature, and does anyone have a link to a good online article with the dependency equation?Thanks! Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	12-23-2011 10:21 AM
Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain Abstract Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13Câ?² longitudinal rate, and two cross-correlated rates involving dipolar and...	nmrlearner	Journal club	0	03-20-2011 07:14 PM
[NMR paper] Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. Related Articles Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J Magn Reson. 2005 May;174(1):43-53 Authors: Chang SL, Tjandra N The NMR spin-lattice relaxation rate (R1) and the rotating-frame spin-lattice relaxation rate (R1rho) of amide 15N and carbonyl 13C (13C') of the uniformly 13C- and 15N-labeled ubiquitin were measured at different temperatures and field strengths to investigate the...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar c Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints. Related Articles Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints. J Biomol NMR. 2004 Jan;28(1):31-41 Authors: Jensen PR, Axelsen JB, Lerche MH, Poulsen FM We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics. Temperature dependence of NMR order parameters and protein dynamics. Related Articles Temperature dependence of NMR order parameters and protein dynamics. J Am Chem Soc. 2003 Sep 17;125(37):11158-9 Authors: Massi F, Palmer AG The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Metabolic assessment of a neuron-enriched fraction of rat cerebrum using high-resolut Metabolic assessment of a neuron-enriched fraction of rat cerebrum using high-resolution 1H and 13C NMR spectroscopy. Related Articles Metabolic assessment of a neuron-enriched fraction of rat cerebrum using high-resolution 1H and 13C NMR spectroscopy. Magn Reson Med. 1993 Nov;30(5):559-67 Authors: Petroff OA, Pleban L, Prichard JW This study explored the utility of 1H and 13C magnetic resonance spectroscopy to study a neuron-enriched preparation made from rat cerebrum. The preparation contained high concentrations of N-acetylaspartate and...	nmrlearner	Journal club	0	08-22-2010 03:01 AM
[NMR paper] Effect of antibody binding on protein motions studied by hydrogen-exchange labeling a Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Related Articles Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Biochemistry. 1992 Nov 10;31(44):10678-85 Authors: Mayne L, Paterson Y, Cerasoli D, Englander SW We have used hydrogen-exchange labeling detected by 2D NMR to study antibody-protein interactions for two monoclonal antibodies raised against horse cytochrome c. The data show that these antibodies bind mainly to the...	nmrlearner	Journal club	0	08-21-2010 11:45 PM
[NMR paper] Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--arjournals.annualreviews.org-images-AnnualReviews100x25.gif Related Articles Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct. 1992;21:243-65 Authors: Englander SW, Mayne L HX-labeling experiments in the pH-pulse mode show that protein folding can be remarkably fast. A near-native form can be reached within milliseconds. Experimental analysis of...	nmrlearner	Journal club	0	08-21-2010 11:41 PM

« Previous Thread | Next 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