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Piersanti E, Rezig L, Tranchida F, El-Houri W, Abagana SM, Campredon M, Shintu L, Yemloul M. Evaluation of the Rotating-Frame Relaxation ( T1ρ) Filter and Its Application in Metabolomics as an Alternative to the Transverse Relaxation ( T2) Filter. Anal Chem 2021; 93:8746-8753. [PMID: 34133140 DOI: 10.1021/acs.analchem.0c05251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nuclear magnetic resonance (NMR)-based metabolomic studies commonly involve the use of T2 filter pulse sequences to eliminate or attenuate the broad signals from large molecules and improve spectral resolution. In this paper, we demonstrate that the T1ρ filter-based pulse sequence represents an interesting alternative because it allows the stability and the reproducibility needed for statistical analysis. The integrity of the samples and the stability of the instruments were assessed for different filter durations and amplitudes. We showed that the T1ρ filter pulse sequence did not induce sample overheating for a filter duration of up to 500 ms. The reproducibility was evaluated and compared with the T2 filter in serum and liver samples. The implementation is relatively simple and provides the same statistical and analytical results as those obtained with the standard filters. Regarding tissues analysis, because the duration of the filter is the same as that of the spin-lock, the synchronization of the echo delays with the magic angle spinning (MAS) rate is no longer necessary as for T2 filter-based sequences. The results presented in this article aim at establishing a new protocol to improve metabolomic studies and pave the way for future developments on T1ρ alternative filters, in liquid and HR-MAS NMR experiments.
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Affiliation(s)
- Elena Piersanti
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Lamya Rezig
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Fabrice Tranchida
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Wael El-Houri
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Seidou M Abagana
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Mylène Campredon
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
| | - Mehdi Yemloul
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2,Marseille, France
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Javanainen M, Ollila OHS, Martinez-Seara H. Rotational Diffusion of Membrane Proteins in Crowded Membranes. J Phys Chem B 2020; 124:2994-3001. [PMID: 32188248 DOI: 10.1021/acs.jpcb.0c00884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Membrane proteins travel along cellular membranes and reorient themselves to form functional oligomers and protein-lipid complexes. Following the Saffman-Delbrück model, protein radius sets the rate of this diffusive motion. However, it is unclear how this model, derived for ideal and dilute membranes, performs under crowded conditions of cellular membranes. Here, we study the rotational motion of membrane proteins using molecular dynamics simulations of coarse-grained membranes and 2-dimensional Lennard-Jones fluids with varying levels of crowding. We find that the Saffman-Delbrück model captures the size-dependency of rotational diffusion under dilute conditions where protein-protein interactions are negligible, whereas stronger scaling laws arise under crowding. Together with our recent work on lateral diffusion, our results reshape the description of protein dynamics in native membrane environments: The translational and rotational motions of proteins with small transmembrane domains are rapid, whereas larger proteins or protein complexes display substantially slower dynamics.
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Affiliation(s)
- Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.,Computational Physics Laboratory, Tampere University, Tampere 33720, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic
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Vögele M, Köfinger J, Hummer G. Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. J Phys Chem B 2019; 123:5099-5106. [PMID: 31132280 PMCID: PMC6750896 DOI: 10.1021/acs.jpcb.9b01656] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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We investigate
system-size effects on the rotational diffusion of membrane proteins
and other membrane-embedded molecules in molecular dynamics simulations. We find that
the rotational diffusion coefficient slows down relative to the infinite-system
value by a factor of one minus the ratio of protein and box areas.
This correction factor follows from the hydrodynamics of rotational
flows under periodic boundary conditions and is rationalized in terms
of Taylor–Couette flow. For membrane proteins like transporters,
channels, or receptors in typical simulation setups, the protein-covered
area tends to be relatively large, requiring a significant finite-size
correction. Molecular dynamics simulations of the protein adenine
nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid
membranes show that the hydrodynamic finite-size correction for rotational
diffusion is accurate in standard-use cases. The dependence of the
rotational diffusion on box size can be used to determine the membrane
viscosity.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany.,Institute for Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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Gulyani A, Dey N, Bhattacharya S. Highly Responsive Fluorescent Assemblies Allow for Unique, Multiparametric Sensing of the Phospholipid Membrane Environment. Chemistry 2018; 25:1507-1514. [DOI: 10.1002/chem.201803627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Akash Gulyani
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
- Institute for Stem Cell Biology & Regenerative Medicine; GKVK Post, Bangalore 560065 India
| | - Nilanjan Dey
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
- Institute for Stem Cell Biology & Regenerative Medicine; GKVK Post, Bangalore 560065 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
- Present address: Indian Association for Cultivation of Science; Kolkata 700032 India
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