Publication date: 23 May 2017 Source:Biophysical Journal, Volume 112, Issue 10
Author(s): Shenyuan Xu, Shuisong Ni, Michael A. Kennedy
At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by*N- and C-terminal ?-helices. PRP structures are dominated by four-sided right-handed ?-helices typically consisting of mixtures of type II and type IV ?-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II ?-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown. Given its unusual structure, we investigated the biophysical properties of At2g44920 as a representative of the ?-helix family to determine if it had exceptional global stability, backbone dynamics, or amide hydrogen exchange rates. Circular dichroism measurements yielded a melting point of 62.8°C, indicating unexceptional global thermal stability. Nuclear spin relaxation measurements indicated that the Rfr-fold core was rigid with order parameters ranging from 0.7 to 0.9. At2g44920 exhibited a striking range of amide hydrogen exchange rates spanning 10 orders of magnitude, with lifetimes ranging from minutes to several months. A weak correlation was found among hydrogen exchange rates, hydrogen bonding energies, and amino acid solvent-accessible areas. Analysis of contributions from fast (approximately picosecond to nanosecond) backbone dynamics to amide hydrogen exchange rates revealed that the average order parameter of amides undergoing fast exchange was significantly smaller compared to those undergoing slow exchange. Importantly, the activation energies for amide hydrogen exchange were found to be generally higher for the slowest exchanging amides in the central Rfr coil and decreased toward the terminal coils. This could be explained by assuming that the concerted motions of two preceding or following coils required for hydrogen bond disruption and amide hydrogen exchange have a higher activation energy compared to that required for displacement of a single coil to facilitate amide hydrogen exchange in either the terminal or penultimate coils.
[NMR paper] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates
Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates
Publication date: Available online 11 October 2013
Source:Journal of Magnetic Resonance</br>
Author(s): Mitsuhiro Takeda , Yohei Miyanoiri , Tsutomu Terauchi , Chin-Jiun Yang , Masatsune Kainosho</br>
Polar side-chains in proteins play important roles in formingand maintaining three-dimensional structures, and thus participate invarious biological functions. Until recently, most protein NMR studieshave focused onthe non-exchangeable protons of amino acid...
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Measurement of amide hydrogen exchange rates with the use of radiation damping
Measurement of amide hydrogen exchange rates with the use of radiation damping
Abstract A simple method for measuring amide hydrogen exchange rates is presented, which is based on the selective inversion of water magnetization with the use of radiation damping. Simulations show that accurate exchange rates can be measured despite the complications of radiation damping and cross relaxation to the exchange process between amide and water protons. This method cannot eliminate the contributions of the exchange-relayed NOE and direct NOE to the measured exchange rates, but minimize the...
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[NMR paper] Amide proton hydrogen exchange rates for sperm whale myoglobin obtained from 15N-1H N
Amide proton hydrogen exchange rates for sperm whale myoglobin obtained from 15N-1H NMR spectra.
Related Articles Amide proton hydrogen exchange rates for sperm whale myoglobin obtained from 15N-1H NMR spectra.
Protein Sci. 2000 Jan;9(1):186-93
Authors: Cavagnero S, Thériault Y, Narula SS, Dyson HJ, Wright PE
The hydrogen exchange behavior of exchangeable protons in proteins can provide important information for understanding the principles of protein structure and function. The positions and exchange rates of the slowly-exchanging amide...
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11-18-2010 09:15 PM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy
Abstract We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15Nâ??T 1 timescales). We observed chemical exchange for 6...
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10-27-2010 08:51 AM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
Related Articles Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
J Biomol NMR. 2010 Oct 20;
Authors: Del Amo JM, Fink U, Reif B
We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that...
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[NMR paper] Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mas
Human recombinant FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Human recombinant FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR.
Protein Sci. 1997 Oct;6(10):2203-17
...
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[NMR paper] Rapid amide proton exchange rates in peptides and proteins measured by solvent quench
Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR.
Protein Sci. 1995 Apr;4(4):804-14
Authors: Zhang YZ,...
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15NH/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: a
Abstract Amide solvent exchange rates are regarded as a valuable source of information on structure/dynamics of unfolded (disordered) proteins. Proton-based saturation transfer experiments, normally used to measure solvent exchange, are known to meet some serious difficulties. The problems mainly arise from the need to (1) manipulate water magnetization and (2) discriminate between multiple magnetization transfer pathways that occur within the proton pool. Some of these issues are specific to unfolded proteins. For example, the compensation scheme used to cancel the Overhauser effect in the...
NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A.*thaliana
Linear Mode
