Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cournia, Zoe; Allen, Toby W.; Andricioaei, Ioan; Antonny, Bruno; Baum, Daniel; Brannigan, Grace; Buchete, Nicolae‐Viorel; Deckman, Jason; Delemotte, Lucie; Val, Coral del; Friedman, Ran; Gkeka, Paraskevi; Hege, Hans‐Christian; Hénin, Jérôme; Kasimova, Marina A.; Kolocouris, Antonios; Klein, Michael L.; Khalid, Syma; Lemieux, M. Joanne; Lindow, Norbert; Roy, Mahua; Selent, Jana; Tarek, Mounir; Tofoleanu, Florentina; Vanni, Stefano; Urban, Siniša; Wales, David J.; Smith, Jeremy C.; Bondar, Ana‐Nicoleta

doi:10.1007/s00232-015-9802-0

Cited by 185 publications

(139 citation statements)

References 273 publications

(339 reference statements)

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“…demonstrated that the 1658 cm −1 peak is related to the unfolded state of proteins37. Recent numerical models have shown that pulsed electric fields can alter the folding of membrane proteins38. The evolution of the amide I band may be directly related to the structural modifications of proteins and especially to their folding state.…”

Section: Resultsmentioning

confidence: 99%

Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

Azan

Untereiner

Gobinet

et al. 2017

Sci Rep

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Confocal Raman microspectroscopy was used to study the interaction between pulsed electric fields and live cells from a molecular point of view in a non-invasive and label-free manner. Raman signatures of live human adipose-derived mesenchymal stem cells exposed or not to pulsed electric fields (8 pulses, 1 000 V/cm, 100 μs, 1 Hz) were acquired at two cellular locations (nucleus and cytoplasm) and two spectral bands (600–1 800 cm−1 and 2 800–3 100 cm−1). Vibrational modes of proteins (phenylalanine and amide I) and lipids were found to be modified by the electropermeabilization process with a statistically significant difference. The relative magnitude of four phenylalanine peaks decreased in the spectra of the pulsed group. On the contrary, the relative magnitude of the amide I band at 1658 cm−1 increased by 40% when comparing pulsed and control group. No difference was found between the control and the pulsed group in the high wavenumber spectral band. Our results reveal the modification of proteins in living cells exposed to pulsed electric fields by means of confocal Raman microspectroscopy.

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Section: Resultsmentioning

confidence: 99%

Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

Azan

Untereiner

Gobinet

et al. 2017

Sci Rep

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“…Molecular dynamics (MD) simulation is a widely used computational tool to explore relationships between structure, dynamics, and function of biomolecules [13-16]. It has been applied to a wide variety of biomolecules, in particular proteins [17-19], nucleic acids [20-22], biomembranes [23-26], glycans [27-29], and so on.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori

Miyashita²,

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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116

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This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov.

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“…Characterization of the structure and function of integral membrane proteins (IMPs) comes with major challenges due to the hydrophobicity and subsequent instability of IMPs in aqueous conditions. 1 Investigating IMPs while imbedded in native-like membrane environments 2 is a pragmatic approach to more accurately mimic their function in vivo. A number of approaches for sequestering IMPs within biomimetic lipids have advanced in recent years.…”

Section: Introductionmentioning

confidence: 99%

Enzyme‐mediated assembly of chimeric membrane proteins at phospholipid bilayers

Scott

Tullman

Kelman

et al. 2019

Engineering Reports

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Integral membrane proteins (IMPs) pose a challenge to study in vitro, as it is difficult to reproduce the membrane-imbedded context of their native state. In this study, we developed a generalized strategy for the assembly of chimeric IMPs within a phospholipid bilayer surface based on a two-step process that first imbeds the insoluble domain of the IMP into a phospholipid layer and then ligates the soluble part of the IMP to the imbedded portion under mild biochemical conditions using a mutant sortase A enzyme. The approach is demonstrated using the transmembrane domain of epidermal growth factor receptor (EGFR) and the soluble extracellular loop of the B-lymphocyte antigen CD20 protein in a POPC tethered bilayer membrane (tBLM). The conditions of the enzymatic reaction were optimized for peptide ligation at the tBLM surface and the role of Ca 2+ ions in ligation efficiency examined. Additionally, binding of the CD20/EGFR chimera in the context of a membrane environment by the rituximab antibody was measured to assess functionality. KEYWORDS CD20, EIS, rituximab, sortase A, SPR, TM domain of epidermal growth factorThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cited by 185 publications

References 273 publications

Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Enzyme‐mediated assembly of chimeric membrane proteins at phospholipid bilayers

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