1
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Van Doren SR, Scott BS, Koppisetti RK. SARS-CoV-2 fusion peptide sculpting of a membrane with insertion of charged and polar groups. Structure 2023; 31:1184-1199.e3. [PMID: 37625399 PMCID: PMC10592393 DOI: 10.1016/j.str.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike is essential for infection. How this charged and hydrophobic domain occupies and affects membranes needs clarification. Its depth in zwitterionic, bilayered micelles at pH 5 (resembling late endosomes) was measured by paramagnetic NMR relaxation enhancements used to bias molecular dynamics simulations. Asp830 inserted deeply, along with Lys825 or Lys835. Protonation of Asp830 appeared to enhance agreement of simulated and NMR-measured depths. While the fusion peptide occupied a leaflet of the DMPC bilayer, the opposite leaflet invaginated with influx of water and choline head groups in around Asp830 and bilayer-inserted polar side chains. NMR-detected hydrogen exchange found corroborating hydration of the backbone of Thr827-Phe833 inserted deeply in bicelles. Pinching of the membrane at the inserted charge and the intramembrane hydration of polar groups agree with theory. Formation of corridors of hydrated, inward-turned head groups was accompanied by flip-flop of head groups. Potential roles of the defects are discussed.
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Affiliation(s)
- Steven R Van Doren
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA.
| | - Benjamin S Scott
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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2
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Conformational space exploration of cryo-EM structures by variability refinement. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184133. [PMID: 36738875 DOI: 10.1016/j.bbamem.2023.184133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. In order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.
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3
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Špačková J, Goldberga I, Yadav R, Cazals G, Lebrun A, Verdié P, Métro TX, Laurencin D. Fast and Cost-Efficient 17 O-Isotopic Labeling of Carboxylic Groups in Biomolecules: From Free Amino Acids to Peptide Chains. Chemistry 2023; 29:e202203014. [PMID: 36333272 DOI: 10.1002/chem.202203014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 11/08/2022]
Abstract
17 O NMR spectroscopy is a powerful technique, which can provide unique information regarding the structure and reactivity of biomolecules. However, the low natural abundance of 17 O (0.04 %) generally requires working with enriched samples, which are not easily accessible. Here, we present simple, fast and cost-efficient 17 O-enrichment strategies for amino acids and peptides by using mechanochemistry. First, five unprotected amino acids were enriched under ambient conditions, consuming only microliter amounts of costly labeled water, and producing pure molecules with enrichment levels up to ∼40 %, yields ∼60-85 %, and no loss of optical purity. Subsequently, 17 O-enriched Fmoc/tBu-protected amino acids were produced on a 1 g/day scale with high enrichment levels. Lastly, a site-selective 17 O-labeling of carboxylic functions in peptide side-chains was achieved for RGD and GRGDS peptides, with ∼28 % enrichment level. For all molecules, 17 O ssNMR spectra were recorded at 14.1 T in reasonable times, making this an important step forward for future NMR studies of biomolecules.
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Affiliation(s)
| | | | - Rishit Yadav
- ICGM, CNRS, UM, ENSCM, 34293, Montpellier, France
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4
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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5
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022; 61:e202203319. [PMID: 35712982 PMCID: PMC9540533 DOI: 10.1002/anie.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 11/18/2022]
Abstract
Membrane proteins are known to exert many essential biological functions by forming complexes in cell membranes. An example refers to the β‐barrel assembly machinery (BAM), a 200 kDa pentameric complex containing BAM proteins A–E that catalyzes the essential process of protein insertion into the outer membrane of gram‐negative bacteria. While progress has been made in capturing three‐dimensional structural snapshots of the BAM complex, the role of the lipoprotein BamC in the complex assembly in functional lipid bilayers has remained unclear. We have devised a component‐selective preparation scheme to directly study BamC as part of the entire BAM complex in lipid bilayers. Combination with proton‐detected solid‐state NMR methods allowed us to probe the structure, dynamics, and supramolecular topology of full‐length BamC embedded in the entire complex in lipid bilayers. Our approach may help decipher how individual proteins contribute to the dynamic formation and functioning of membrane protein complexes in membranes.
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Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- MOE Key Lab for Cellular Dynamics School of Life Sciences University of Science and Technology of China 96 Jinzhai Road Hefei 230026 Anhui China
| | - Cecilia Pinto
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Current address: Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Van der Maasweg 9 2629 H. Z. Delft The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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6
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Roterman I, Stapor K, Fabian P, Konieczny L. Connexins and Pannexins—Similarities and Differences According to the FOD-M Model. Biomedicines 2022; 10:biomedicines10071504. [PMID: 35884807 PMCID: PMC9313468 DOI: 10.3390/biomedicines10071504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Connexins and pannexins are the transmembrane proteins of highly distinguished biological activity in the form of transport of molecules and electrical signals. Their common role is to connect the external environment with the cytoplasm of the cell, while connexin is also able to link two cells together allowing the transport from one to another. The analysis presented here aims to identify the similarities and differences between connexin and pannexin. As a comparative criterion, the hydrophobicity distribution in the structure of the discussed proteins was used. The comparative analysis is carried out with the use of a mathematical model, the FOD-M model (fuzzy oil drop model in its Modified version) expressing the specificity of the membrane’s external field, which in the case of the discussed proteins is significantly different from the external field for globular proteins in the polar environment of water. The characteristics of the external force field influence the structure of protein allowing the activity in a different environment.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland
- Correspondence:
| | - Katarzyna Stapor
- Department of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Piotr Fabian
- Department of Algorithmics and Software, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Leszek Konieczny
- Chair of Medical Biochemistry—Jagiellonian University—Medical College, Kopernika 7, 31-034 Kraków, Poland;
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7
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- ShengQi Xiang
- University of Science and Technology of China, Anhui, MOE Key lab for Cellular Dynamics CHINA
| | - Cecilia Pinto
- Delft University of Technology: Technische Universiteit Delft Department of Bionanoscience NETHERLANDS
| | - Marc Baldus
- Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 Utrecht NETHERLANDS
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8
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Pandit A. Structural dynamics of light harvesting proteins, photosynthetic membranes and cells observed with spectral editing solid-state NMR. J Chem Phys 2022; 157:025101. [DOI: 10.1063/5.0094446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photosynthetic light-harvesting complexes have a remarkable capacity to perform robust photo physics at ambient temperatures and in fluctuating environments. Protein conformational dynamics and membrane mobility are processes that contribute to the light-harvesting efficiencies and control photoprotective responses. This short review describes the application of Magic Angle Spinning (MAS) NMR spectroscopy for characterizing the structural dynamics of pigment, protein and thylakoid membrane components related to light harvesting and photoprotection. I will discuss the use of dynamics-based spectral editing solid-state NMR for distinguishing rigid and mobile components and assessing protein, pigment and lipid dynamics on sub-nanosecond to millisecond timescales. Dynamic spectral editing NMR has been applied to investigate Light-Harvesting Complex II (LHCII) protein conformational dynamics inside lipid bilayers and in native membranes. Furthermore, we used the NMR approach to assess thylakoid membrane dynamics. Finally, it is shown that dynamics-based spectral editing NMR, for reducing spectral complexity, by filtering motion-dependent signals, enabled us to follow processes in live photosynthetic cells.
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9
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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10
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Paluch P, Augustyniak R, Org ML, Vanatalu K, Kaldma A, Samoson A, Stanek J. NMR Assignment of Methyl Groups in Immobilized Proteins Using Multiple-Bond 13C Homonuclear Transfers, Proton Detection, and Very Fast MAS. Front Mol Biosci 2022; 9:828785. [PMID: 35425812 PMCID: PMC9002630 DOI: 10.3389/fmolb.2022.828785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
In nuclear magnetic resonance spectroscopy of proteins, methyl protons play a particular role as extremely sensitive reporters on dynamics, allosteric effects, and protein–protein interactions, accessible even in high-molecular-weight systems approaching 1 MDa. The notorious issue of their chemical shift assignment is addressed here by a joint use of solid-state 1H-detected methods at very fast (nearly 100 kHz) magic-angle spinning, partial deuteration, and high-magnetic fields. The suitability of a series of RF schemes is evaluated for the efficient coherence transfer across entire 13C side chains of methyl-containing residues, which is key for establishing connection between methyl and backbone 1H resonances. The performance of ten methods for recoupling of either isotropic 13C–13C scalar or anisotropic dipolar interactions (five variants of TOBSY, FLOPSY, DIPSI, WALTZ, RFDR, and DREAM) is evaluated experimentally at two state-of-the-art magic-angle spinning (55 and 94.5 kHz) and static magnetic field conditions (18.8 and 23.5 T). Model isotopically labeled compounds (alanine and Met-Leu-Phe tripeptide) and ILV-methyl and amide-selectively protonated, and otherwise deuterated chicken α-spectrin SH3 protein are used as convenient reference systems. Spin dynamics simulations in SIMPSON are performed to determine optimal parameters of these RF schemes, up to recently experimentally attained spinning frequencies (200 kHz) and B0 field strengths (28.2 T). The concept of linearization of 13C side chain by appropriate isotope labeling is revisited and showed to significantly increase sensitivity of methyl-to-backbone correlations. A resolution enhancement provided by 4D spectroscopy with non-uniform (sparse) sampling is demonstrated to remove ambiguities in simultaneous resonance assignment of methyl proton and carbon chemical shifts.
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Affiliation(s)
- Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | | | - Mai-Liis Org
- Tallin University of Technology, Tallinn, Estonia
| | | | - Ats Kaldma
- Tallin University of Technology, Tallinn, Estonia
| | - Ago Samoson
- Tallin University of Technology, Tallinn, Estonia
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- *Correspondence: Jan Stanek,
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11
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Tan H, Zhao Y, Zhao W, Xie H, Chen Y, Tong Q, Yang J. Dynamics properties of membrane proteins in native cell membranes revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183791. [PMID: 34624277 DOI: 10.1016/j.bbamem.2021.183791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
Abstract
Cell membranes provide an environment that is essential to the functions of membrane proteins. Cell membranes are mainly composed of proteins and highly diverse phospholipids. The influence of diverse lipid compositions of native cell membranes on the dynamics of the embedded membrane proteins has not been examined. Here we employ solid-state NMR to investigate the dynamics of E. coli Aquaporin Z (AqpZ) in its native inner cell membranes, and reveal the influence of diverse lipid compositions on the dynamics of AqpZ by comparing it in native cell membranes to that in POPC/POPG bilayers. We demonstrate that the dynamic rigidity of AqpZ generally conserves in both native cell membranes and POPC/POPG bilayers, due to its tightly packed tetrameric structure. In the gel and the liquid crystal phases of lipids, our experimental results show that AqpZ is more dynamic in native cell membranes than that in POPC/POPG bilayers. In addition, we observe that phase transitions of lipids in native membranes are less sensitive to temperature variations compared with that in POPC/POPG bilayers, which results in that the dynamics of AqpZ is less affected by the phase transitions of lipids in native cell membranes than that in POPC/POPG bilayers. This study provides new insights into the dynamics of membrane proteins in native cell membranes.
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Affiliation(s)
- Huan Tan
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, PR China.
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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12
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Abstract
Cell penetrating peptides (CPPs) are generally defined as short positively charged peptides, containing 5-30 amino acids. Based on their physicochemical properties, they are classified as three main groups, namely hydrophobic, amphipathic, and hydrophilic. They are capable of interacting with the cell membrane without inducing serious toxicity, and they can carry cargo molecules across the membrane. Cargo molecules could be different therapeutics which makes CPPs valuable in the field of drug delivery into living cells. Nowadays, CPPs are considered as potential parts of therapeutics against several diseases.Despite similarities in their primary structure, the interactions of CPPs with a cell membrane may vary a lot. This is even more complicated when the CPP is bound to the cargo molecule. The mechanism(s) of their cellular uptake and endosomal escape have not been completely resolved. Understanding the mechanism of membrane interaction will help us designing a CPP with enhanced, selective cargo delivery, hopefully resulting in better disease treatments. So far energy independent direct membrane penetration and energy-dependent endocytosis have been suggested as two main mechanisms of cellular entry for CPPs, and both may be applicable for the same CPP-complex, depending on the conditions.In order to understand which mechanism is associated with a particular CPP 's cellular uptake in a particular cell (sometimes including endosomal escape), different biological and biophysical methods and strategies have been applied. In this chapter, we will address several biophysical methods, such as fluorescence spectroscopy, circular dichroism (CD) spectroscopy, dynamic light scattering, and NMR .We also review different membrane model systems which are suitable for the biophysical studies. These include large unilamellar phospholipid vesicles (LUVs ), which are the most commonly used in the lipid-peptide interaction studies. Detergent micelles and mixed micelles (bicelles) are also suitable membrane model systems, particularly in high-resolution NMR studies.
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Affiliation(s)
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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13
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Lusky OS, Meir M, Goldbourt A. Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR. BIOPHYSICAL REPORTS 2021; 1:100027. [PMID: 36425459 PMCID: PMC9680805 DOI: 10.1016/j.bpr.2021.100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 05/14/2023]
Abstract
RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear 15N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous 1H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods.
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Affiliation(s)
| | - Moran Meir
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Faculty of Exact Sciences
- Corresponding author
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14
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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15
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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16
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Bohg C, Öster C, Utesch T, Bischoff S, Lange S, Shi C, Sun H, Lange A. A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor. Chem Sci 2021; 12:12754-12762. [PMID: 34703562 PMCID: PMC8494044 DOI: 10.1039/d1sc02146j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions. Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.![]()
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Affiliation(s)
- Claudia Bohg
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Tillmann Utesch
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Susanne Bischoff
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China Huangshan Road 443 Hefei 230027 People's Republic of China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Institut für Biologie, Humboldt-Universität zu Berlin Invalidenstraße 42 10115 Berlin Germany
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17
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Jodaitis L, van Oene T, Martens C. Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins. Int J Mol Sci 2021; 22:7267. [PMID: 34298884 PMCID: PMC8306737 DOI: 10.3390/ijms22147267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
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Affiliation(s)
| | | | - Chloé Martens
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (L.J.); (T.v.O.)
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18
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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19
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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20
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Gopinath T, Weber D, Wang S, Larsen E, Veglia G. Solid-State NMR of Membrane Proteins in Lipid Bilayers: To Spin or Not To Spin? Acc Chem Res 2021; 54:1430-1439. [PMID: 33655754 DOI: 10.1021/acs.accounts.0c00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Membrane proteins mediate a plethora of cellular functions and represent important targets for drug development. Unlike soluble proteins, membrane proteins require native-like environments to fold correctly and be active. Therefore, modern structural biology techniques have aimed to determine the structure and dynamics of these membrane proteins at physiological temperature and in liquid crystalline lipid bilayers. With the flourishing of new NMR methodologies and improvements in sample preparations, magic angle spinning (MAS) and oriented sample solid-state NMR (OS-ssNMR) spectroscopy of membrane proteins is experiencing a new renaissance. Born as antagonistic approaches, these techniques nowadays offer complementary information on the structural topology and dynamics of membrane proteins reconstituted in lipid membranes. By spinning biosolid samples at the magic angle (θ = 54.7°), MAS NMR experiments remove the intrinsic anisotropy of the NMR interactions, increasing spectral resolution. Internuclear spin interactions (spin exchange) are reintroduced by RF pulses, providing distances and torsion angles to determine secondary, tertiary, and quaternary structures of membrane proteins. OS-ssNMR, on the other hand, directly detects anisotropic NMR parameters such as dipolar couplings (DC) and anisotropic chemical shifts (CS), providing orientational constraints to determine the architecture (i.e., topology) of membrane proteins relative to the lipid membrane. Defining the orientation of membrane proteins and their interactions with lipid membranes is of paramount importance since lipid-protein interactions can shape membrane protein conformations and ultimately define their functional states.In this Account, we report selected studies from our group integrating MAS and OS-ssNMR techniques to give a comprehensive view of the biological processes occurring at cellular membranes. We focus on the main experiments for both techniques, with an emphasis on new implementation to increase both sensitivity and spectral resolution. We also describe how the structural constraints derived from both isotropic and anisotropic NMR parameters are integrated into dynamic structural modeling using replica-averaged orientational-restrained molecular dynamics simulations (RAOR-MD). We showcase small membrane proteins that are involved in Ca2+ transport and regulate cardiac and skeletal muscle contractility: phospholamban (PLN, 6 kDa), sarcolipin (SLN, 4 kDa), and DWORF (4 kDa). We summarize our results for the structures of these polypeptides free and in complex with the sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA, 110 kDa). Additionally, we illustrate the progress toward the determination of the structural topology of a six transmembrane protein associated with succinate and acetate transport (SatP, hexamer 120 kDa). From these examples, the integrated MAS and OS-ssNMR approach, in combination with modern computational methods, emerges as a way to overcome the challenges posed by studying large membrane protein systems.
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21
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Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020; 19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023] Open
Abstract
Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.
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Key Words
- CLEM, correlated light and electron microscopy
- Crosslinking mass spectrometry
- Cryo-electron microscopy
- Cryo-electron tomography
- EPR, electron paramagnetic resonance
- FRET, Forster resonance energy transfer
- ISB, Integrative structural biology
- Integrative structural biology
- ML, machine learning
- MR, molecular replacement
- MSAs, multiple sequence alignments
- MX, macromolecular crystallography
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Protein docking
- Protein structure prediction
- Quinary interactions
- SAD, single-wavelength anomalous dispersion
- SANS, small angle neutron scattering
- SAXS, small angle X-ray scattering
- X-ray crystallography
- XL-MS, cross-linking mass spectrometry
- cryo-EM SPA, cryo-EM single particle analysis
- cryo-EM, cryo-electron microscopy
- cryo-ET, cryo-electron tomography
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Affiliation(s)
- Samantha J. Ziegler
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Sam J.B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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22
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Miao Y, Lam D, Zhuang J, Zhu J, Poget SF, Tang M. Membrane Topology of an Ion Channel Detected by Solid-State Nuclear Magnetic Resonance and Paramagnetic Effects. J Phys Chem Lett 2020; 11:9795-9801. [PMID: 33151058 DOI: 10.1021/acs.jpclett.0c02014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion channels are often targeted by toxins or other ligands to modify their channel activities and alter ion conductance. Interactions between toxins and ion channels could result in changes in membrane insertion depth for residues close to the binding site. Paramagnetic solid-state nuclear magnetic resonance (SSNMR) has shown great potential in providing structural information on membrane samples. We used KcsA as a model ion channel to investigate how the paramagnetic effects of Mn2+ and Dy3+ ions with headgroup-modified chelator lipids would influence the SSNMR signals of membrane proteins in proteoliposomes. Spectral comparisons have shown significant changes of peak intensities for the residues in the loop or terminal regions due to paramagnetic effects corresponding to the close proximity to the membrane surface. Hence, these results demonstrate that paramagnetic SSNMR can be used to detect surface residues based on the topology and membrane insertion properties for integral membrane proteins.
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Affiliation(s)
- Yimin Miao
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Dennis Lam
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jianqin Zhuang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jing Zhu
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sebastien F Poget
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ming Tang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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23
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Weber DK, Veglia G. A theoretical assessment of structure determination of multi-span membrane proteins by oriented sample solid-state NMR spectroscopy. Aust J Chem 2020; 73:246-251. [PMID: 33162560 DOI: 10.1071/ch19307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Oriented sample solid state NMR (OS-ssNMR) spectroscopy allows direct determination of the structure and topology of membrane proteins reconstituted into aligned lipid bilayers. While OS-ssNMR theoretically has no upper size limit, its application to multi-span membrane proteins has not been established since most studies have been restricted to single or dual span proteins and peptides. Here, we present a critical assessment of the application of this method to multi-span membrane proteins. We used molecular dynamics simulations to back-calculate [15N-1H] separated local field (SLF) spectra from a G protein-coupled receptor (GPCR) and show that fully resolved spectra can be obtained theoretically for a multi-span membrane protein with currently achievable resonance linewidths.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Potnuru LR, Duong NT, Ahlawat S, Raran-Kurussi S, Ernst M, Nishiyama Y, Agarwal V. Accuracy of 1H- 1H distances measured using frequency selective recoupling and fast magic-angle spinning. J Chem Phys 2020; 153:084202. [PMID: 32872876 DOI: 10.1063/5.0019717] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Selective recoupling of protons (SERP) is a method to selectively and quantitatively measure magnetic dipole-dipole interaction between protons and, in turn, the proton-proton distance in solid-state samples at fast magic-angle spinning. We present a bimodal operator-based Floquet approach to describe the numerically optimized SERP recoupling sequence. The description calculates the allowed terms in the first-order effective Hamiltonian, explains the origin of selectivity during recoupling, and shows how different terms are modulated as a function of the radio frequency amplitude and the phase of the sequence. Analytical and numerical simulations have been used to evaluate the effect of higher-order terms and offsets on the polarization transfer efficiency and quantitative distance measurement. The experimentally measured 1H-1H distances on a fully protonated thymol sample are ∼10%-15% shorter than those reported from diffraction studies. A semi-quantitative model combined with extensive numerical simulations is used to rationalize the effect of the third-spin and the role of different parameters in the experimentally observed shorter distances. Measurements at high magnetic fields improve the match between experimental and diffraction distances. The measurement of 1H-1H couplings at offsets different from the SERP-offset has also been explored. Experiments were also performed on a perdeuterated ubiquitin sample to demonstrate the feasibility of simultaneously measuring multiple quantitative distances and to evaluate the accuracy of the measured distance in the absence of multispin effects. The estimation of proton-proton distances provides a boost to structural characterization of small pharmaceuticals and biomolecules, given that the positions of protons are generally not well defined in x-ray structures.
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Affiliation(s)
- Lokeswara Rao Potnuru
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Sahil Ahlawat
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
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25
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The Droserasin 1 PSI: A Membrane-Interacting Antimicrobial Peptide from the Carnivorous Plant Drosera capensis. Biomolecules 2020; 10:biom10071069. [PMID: 32709016 PMCID: PMC7407137 DOI: 10.3390/biom10071069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
The Droserasins, aspartic proteases from the carnivorous plant Drosera capensis, contain a 100-residue plant-specific insert (PSI) that is post-translationally cleaved and independently acts as an antimicrobial peptide. PSIs are of interest not only for their inhibition of microbial growth, but also because they modify the size of lipid vesicles and strongly interact with biological membranes. PSIs may therefore be useful for modulating lipid systems in NMR studies of membrane proteins. Here we present the expression and biophysical characterization of the Droserasin 1 PSI (D1 PSI.) This peptide is monomeric in solution and maintains its primarily α-helical secondary structure over a wide range of temperatures and pH values, even under conditions where its three disulfide bonds are reduced. Vesicle fusion assays indicate that the D1 PSI strongly interacts with bacterial and fungal lipids at pH 5 and lower, consistent with the physiological pH of D. capensis mucilage. It binds lipids with a variety of head groups, highlighting its versatility as a potential stabilizer for lipid nanodiscs. Solid-state NMR spectra collected at a field strength of 36 T, using a unique series-connected hybrid magnet, indicate that the peptide is folded and strongly bound to the membrane. Molecular dynamics simulations indicate that the peptide is stable as either a monomer or a dimer in a lipid bilayer. Both the monomer and the dimer allow the passage of water through the membrane, albeit at different rates.
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26
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Membrane proteins in magnetically aligned phospholipid polymer discs for solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183333. [PMID: 32371072 DOI: 10.1016/j.bbamem.2020.183333] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Well-hydrated phospholipid bilayers provide a near-native environment for membrane proteins. They enable the preparation of chemically-defined samples suitable for NMR and other spectroscopic experiments that reveal the structure, dynamics, and functional interactions of the proteins at atomic resolution. The synthetic polymer styrene maleic acid (SMA) can be used to prepare detergent-free samples that form macrodiscs with diameters greater than 30 nm at room temperature, and spontaneously align in the magnetic field of an NMR spectrometer at temperatures above 35 °C. Here we show that magnetically aligned macrodiscs are particularly well suited for solid-state NMR experiments of membrane proteins because the SMA-lipid assembly both immobilizes the embedded protein and provides uniaxial order for oriented sample (OS) solid-state NMR studies. We show that aligned macrodiscs incorporating four different membrane proteins with a wide range of sizes and topological complexity yield high-resolution OS solid-state NMR spectra. The work is dedicated to Michelle Auger who made key contributions to the field of membrane and membrane protein biophysics.
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27
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Romero PR, Kobayashi N, Wedell JR, Baskaran K, Iwata T, Yokochi M, Maziuk D, Yao H, Fujiwara T, Kurusu G, Ulrich EL, Hoch JC, Markley JL. BioMagResBank (BMRB) as a Resource for Structural Biology. Methods Mol Biol 2020; 2112:187-218. [PMID: 32006287 DOI: 10.1007/978-1-0716-0270-6_14] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB), founded in 1988, serves as the archive for data generated by nuclear magnetic resonance (NMR) spectroscopy of biological systems. NMR spectroscopy is unique among biophysical approaches in its ability to provide a broad range of atomic and higher-level information relevant to the structural, dynamic, and chemical properties of biological macromolecules, as well as report on metabolite and natural product concentrations in complex mixtures and their chemical structures. BMRB became a core member of the Worldwide Protein Data Bank (wwPDB) in 2007, and the BMRB archive is now a core archive of the wwPDB. Currently, about 10% of the structures deposited into the PDB archive are based on NMR spectroscopy. BMRB stores experimental and derived data from biomolecular NMR studies. Newer BMRB biopolymer depositions are divided about evenly between those associated with structure determinations (atomic coordinates and supporting information archived in the PDB) and those reporting experimental information on molecular dynamics, conformational transitions, ligand binding, assigned chemical shifts, or other results from NMR spectroscopy. BMRB also provides resources for NMR studies of metabolites and other small molecules that are often macromolecular ligands and/or nonstandard residues. This chapter is directed to the structural biology community rather than the metabolomics and natural products community. Our goal is to describe various BMRB services offered to structural biology researchers and how they can be accessed and utilized. These services can be classified into four main groups: (1) data deposition, (2) data retrieval, (3) data analysis, and (4) services for NMR spectroscopists and software developers. The chapter also describes the NMR-STAR data format used by BMRB and the tools provided to facilitate its use. For programmers, BMRB offers an application programming interface (API) and libraries in the Python and R languages that enable users to develop their own BMRB-based tools for data analysis, visualization, and manipulation of NMR-STAR formatted files. BMRB also provides users with direct access tools through the NMRbox platform.
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Affiliation(s)
- Pedro R Romero
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Naohiro Kobayashi
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jonathan R Wedell
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Kumaran Baskaran
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Takeshi Iwata
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masashi Yokochi
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Dimitri Maziuk
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Hongyang Yao
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Toshimichi Fujiwara
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genji Kurusu
- PDBj-BMRB, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Eldon L Ulrich
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeffrey C Hoch
- BMRB, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - John L Markley
- BMRB, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
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Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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Gronnier J, Legrand A, Loquet A, Habenstein B, Germain V, Mongrand S. Mechanisms governing subcompartmentalization of biological membranes. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:114-123. [PMID: 31546133 DOI: 10.1016/j.pbi.2019.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Membranes show a tremendous variety of lipids and proteins operating biochemistry, transport and signalling. The dynamics and the organization of membrane constituents are regulated in space and time to execute precise functions. Our understanding of the molecular mechanisms that shape and govern membrane subcompartmentalization and inter-organelle contact sites still remains limited. Here, we review some reported mechanisms implicated in regulating plant membrane domains including those of plasma membrane, plastids, mitochondria and endoplasmic reticulum. Finally, we discuss several state-of-the-art methods that allow nowadays researchers to decipher the architecture of these structures at the molecular and atomic level.
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Affiliation(s)
- Julien Gronnier
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Anthony Legrand
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France; Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, All, Geoffroy Saint-Hilaire, Pessac, France
| | - Véronique Germain
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France
| | - Sébastien Mongrand
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire (LBM), UMR 5200, 33140 Villenave d'Ornon, France.
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30
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Tang M, Lam D. Paramagnetic solid-state NMR of proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 103:9-16. [PMID: 31585788 DOI: 10.1016/j.ssnmr.2019.101621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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31
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Legrand A, Martinez D, Grélard A, Berbon M, Morvan E, Tawani A, Loquet A, Mongrand S, Habenstein B. Nanodomain Clustering of the Plant Protein Remorin by Solid-State NMR. Front Mol Biosci 2019; 6:107. [PMID: 31681795 PMCID: PMC6803476 DOI: 10.3389/fmolb.2019.00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/30/2019] [Indexed: 11/24/2022] Open
Abstract
Nanodomains are dynamic membrane subcompartments, enriched in specific lipid, and protein components that act as functional platforms to manage an abundance of cellular processes. The remorin protein of plants is a well-established nanodomain marker and widely serves as a paradigm to study nanodomain clustering. Located at the inner leaflet of the plasma membrane, remorins perform essential functions during signaling. Using deuterium and phosphorus solid-state NMR, we inquire on the molecular determinants of the lipid-protein and protein-protein interactions driving nanodomain clustering. By monitoring thermotropism properties, lipid acyl chain order and membrane thickness, we report the effects of phosphoinositides and sterols on the interaction of various remorin peptides and protein constructs with the membrane. We probed several critical residues involved in this interaction and the involvement of the coiled-coil homo-oligomerisation domain into the formation of remorin nanodomains. We trace the essential role of the pH in nanodomain clustering based on anionic lipids such as phosphoinositides. Our results reveal a complex interplay between specific remorin residues and domains, the environmental pH and their resulting effects on the lipid dynamics for phosphoinositide-enriched membranes.
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Affiliation(s)
- Anthony Legrand
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France.,Laboratoire de Biogenèse Membranaire - UMR 5200 - CNRS, Université de Bordeaux, Villenave-d'Ornon, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Melanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Estelle Morvan
- European Institute of Chemistry and Biology - UMS3033/US001, Pessac, France
| | - Arpita Tawani
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire - UMR 5200 - CNRS, Université de Bordeaux, Villenave-d'Ornon, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique Bordeaux, Pessac, France
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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McKay MJ, Fu R, Greathouse DV, Koeppe RE. Breaking the Backbone: Central Arginine Residues Induce Membrane Exit and Helix Distortions within a Dynamic Membrane Peptide. J Phys Chem B 2019; 123:8034-8047. [PMID: 31483653 DOI: 10.1021/acs.jpcb.9b06034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane domains of membrane proteins sometimes contain conserved charged or ionizable residues which may be essential for protein function and regulation. This work examines the molecular interactions of single Arg residues within a highly dynamic transmembrane peptide helix. To this end, we have modified the GW4,20ALP23 (acetyl-GGAW4(AL)7AW20AGA-amide) model peptide framework to incorporate Arg residues near the center of the peptide. Peptide helix formation, orientation and dynamics were analyzed by means of solid-state NMR spectroscopy to monitor specific 2H- or 15N-labeled residues. GW4,20ALP23 itself adopts a tilted orientation within lipid bilayer membranes. Nevertheless, the GW4,20ALP23 helix exhibits moderate to high dynamic averaging of NMR observables, such as 2H quadrupolar splittings or 15N-1H dipolar couplings, due to competition between the interfacial Trp residues on opposing helix faces. Here we examine how the helix dynamics are impacted by the introduction of a single Arg residue at position 12 or 14. Residue R14 restricts the helix to low dynamic averaging and a well-defined tilt that varies inversely with the lipid bilayer thickness. To compensate for the dominance of R14, the competing Trp residues cause partial unwinding of the helix at the C-terminal. By contrast, R12GW4,20ALP23 exits the DOPC bilayer to an interfacial surface-bound location. Interestingly, multiple orientations are exhibited by a single residue, Ala-9. Quadrupolar splittings generated by 2H-labeled residues A3, A5, A7, and A9 do not fit to the α-helical quadrupolar wave plot defined by residues A11, A13, A15, A17, A19, and A21. The discontinuity at residue A9 implicates a helical swivel distortion and an apparent 310-helix involving the N-terminal residues preceding A11. These molecular features suggest that, while arginine residues are prominent factors controlling transmembrane helix dynamics, the influence of interfacial tryptophan residues cannot be ignored.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University , Tallahassee , Florida 32310 , United States
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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Solid-state NMR spectroscopy based atomistic view of a membrane protein unfolding pathway. Nat Commun 2019; 10:3867. [PMID: 31455771 PMCID: PMC6711998 DOI: 10.1038/s41467-019-11849-8] [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] [Received: 05/13/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
Membrane protein folding, structure, and function strongly depend on a cell membrane environment, yet detailed characterization of folding within a lipid bilayer is challenging. Studies of reversible unfolding yield valuable information on the energetics of folding and on the hierarchy of interactions contributing to protein stability. Here, we devise a methodology that combines hydrogen-deuterium (H/D) exchange and solid-state NMR (SSNMR) to follow membrane protein unfolding in lipid membranes at atomic resolution through detecting changes in the protein water-accessible surface, and concurrently monitoring the reversibility of unfolding. We obtain atomistic description of the reversible part of a thermally induced unfolding pathway of a seven-helical photoreceptor. The pathway is visualized through SSNMR-detected snapshots of H/D exchange patterns as a function of temperature, revealing the unfolding intermediate and its stabilizing factors. Our approach is transferable to other membrane proteins, and opens additional ways to characterize their unfolding and stabilizing interactions with atomic resolution.
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35
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Aladin V, Corzilius B. Methyl dynamics in amino acids modulate heteronuclear cross relaxation in the solid state under MAS DNP. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 99:27-35. [PMID: 30865870 DOI: 10.1016/j.ssnmr.2019.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 05/09/2023]
Abstract
Dynamic Nuclear Polarization (DNP) is a wide-spread technique for sensitivity enhancement of MAS NMR. During a typical MAS DNP experiment, several mechanisms resulting in polarization transfer may be active at the same time. One such mechanism which is most commonly active but up to now mostly disregarded is SCREAM-DNP (Specific Cross Relaxation Enhancement by Active Motions under DNP). This effect is generally observed in direct DNP experiments if molecular dynamics are supporting heteronuclear cross relaxation similar to the nuclear Overhauser effect. We investigate this effect for the CH3 groups of all methyl-bearing amino acids (i.e., alanine, valine, leucine, isoleucine, threonine, and methionine). At the typical DNP temperature of ∼110 K the three-fold reorientation dynamics are still active, and efficient SCREAM-DNP is observed. We discuss variations in enhancement factors obtained by this effect in context of sample temperature and sterical hindrance of the methyl group. Next to the direct transfer to the methyl carbon, we also find evidence for much weaker transfer from the methyl protons directly to other carbons in the amino acid molecule and succeed to correlate build-up dynamics with the CH dipole coupling which is modulated by the CH3 orientation. Besides methyl dynamics we also identify ring dynamics within proline as a source of SCREAM-DNP. Our results are the first step towards utilization of this effect as a specific probing techniqueusing methyl groups in protein systems.
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Affiliation(s)
- Victoria Aladin
- Institute of Physical Chemistry, Institute of Biophysical Chemistry, Biomolecular Magnetic Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438, Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical Chemistry, Institute of Biophysical Chemistry, Biomolecular Magnetic Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438, Frankfurt, Germany.
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36
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Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR. Sci Rep 2019; 9:3995. [PMID: 30850624 PMCID: PMC6408475 DOI: 10.1038/s41598-019-40264-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/11/2019] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli diacylglycerol kinase (DGK) is an integral membrane protein, which catalyses the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatic acid (PA). It is a unique trimeric enzyme, which does not share sequence homology with typical kinases. It exhibits a notable complexity in structure and function despite of its small size. Here, chemical shift assignment of wild-type DGK within lipid bilayers was carried out based on 3D MAS NMR, utilizing manual and automatic analysis protocols. Upon nucleotide binding, extensive chemical shift perturbations could be observed. These data provide evidence for a symmetric DGK trimer with all of its three active sites concurrently occupied. Additionally, we could detect that the nucleotide substrate induces a substantial conformational change, most likely directing DGK into its catalytic active form. Furthermore, functionally relevant interprotomer interactions are identified by DNP-enhanced MAS NMR in combination with site-directed mutagenesis and functional assays.
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37
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Türková A, Zdrazil B. Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science. Comput Struct Biotechnol J 2019; 17:390-405. [PMID: 30976382 PMCID: PMC6438991 DOI: 10.1016/j.csbj.2019.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/18/2023] Open
Abstract
Organic anion and cation transporting proteins (OATs, OATPs, and OCTs), as well as the Multidrug and Toxin Extrusion (MATE) transporters of the Solute Carrier (SLC) family are playing a pivotal role in the discovery and development of new drugs due to their involvement in drug disposition, drug-drug interactions, adverse drug effects and related toxicity. Computational methods to understand and predict clinically relevant transporter interactions can provide useful guidance at early stages in drug discovery and design, especially if they include contemporary data science approaches. In this review, we summarize the current state-of-the-art of computational approaches for exploring ligand interactions and selectivity for these drug (uptake) transporters. The computational methods discussed here by highlighting interesting examples from the current literature are ranging from semiautomatic data mining and integration, to ligand-based methods (such as quantitative structure-activity relationships, and combinatorial pharmacophore modeling), and finally structure-based methods (such as comparative modeling, molecular docking, and molecular dynamics simulations). We are focusing on promising computational techniques such as fold-recognition methods, proteochemometric modeling or techniques for enhanced sampling of protein conformations used in the context of these ADMET-relevant SLC transporters with a special focus on methods useful for studying ligand selectivity.
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Affiliation(s)
- Alžběta Türková
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Barbara Zdrazil
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
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38
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Salnikov ES, Aisenbrey C, Anantharamaiah G, Bechinger B. Solid-state NMR structural investigations of peptide-based nanodiscs and of transmembrane helices in bicellar arrangements. Chem Phys Lipids 2019; 219:58-71. [DOI: 10.1016/j.chemphyslip.2019.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 02/08/2023]
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Lam D, Zhuang J, Cohen LS, Arshava B, Naider FR, Tang M. Effects of chelator lipids, paramagnetic metal ions and trehalose on liposomes by solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 94:1-6. [PMID: 30096558 DOI: 10.1016/j.ssnmr.2018.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
The effects of various lipid bound paramagnetic metal ions on liposomes prepared in the presence of trehalose and chelator lipids are evaluated to observe site-specific signal changes on liposome samples with optimal resolution in solid-state NMR spectroscopy. We found that Mn2+, Gd3+ and Dy3+ have different influences on the lipid 13C sites depending on their penetration depths into the bilayer, which can be extracted as distance information. The trehalose-liposome mixture is efficiently packed into solid-state NMR rotors and provides optimal resolution at reasonable instrument temperatures (10-50 °C). The effectiveness and convenience of the trehalose preparation for studying a membrane protein in liposomes are demonstrated by a membrane sample with a model membrane peptide to show that trehalose is useful to prepare consistent and stable membrane protein liposome samples for solid-state NMR.
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Affiliation(s)
- Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jianqin Zhuang
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Leah S Cohen
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Boris Arshava
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Fred R Naider
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
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40
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Jamin N, Garrigos M, Jaxel C, Frelet-Barrand A, Orlowski S. Ectopic Neo-Formed Intracellular Membranes in Escherichia coli: A Response to Membrane Protein-Induced Stress Involving Membrane Curvature and Domains. Biomolecules 2018; 8:biom8030088. [PMID: 30181516 PMCID: PMC6163855 DOI: 10.3390/biom8030088] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/31/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
Bacterial cytoplasmic membrane stress induced by the overexpression of membrane proteins at high levels can lead to formation of ectopic intracellular membranes. In this review, we report the various observations of such membranes in Escherichia coli, compare their morphological and biochemical characterizations, and we analyze the underlying molecular processes leading to their formation. Actually, these membranes display either vesicular or tubular structures, are separated or connected to the cytoplasmic membrane, present mono- or polydispersed sizes and shapes, and possess ordered or disordered arrangements. Moreover, their composition differs from that of the cytoplasmic membrane, with high amounts of the overexpressed membrane protein and altered lipid-to-protein ratio and cardiolipin content. These data reveal the importance of membrane domains, based on local specific lipid⁻protein and protein⁻protein interactions, with both being crucial for local membrane curvature generation, and they highlight the strong influence of protein structure. Indeed, whether the cylindrically or spherically curvature-active proteins are actively curvogenic or passively curvophilic, the underlying molecular scenarios are different and can be correlated with the morphological features of the neo-formed internal membranes. Delineating these molecular mechanisms is highly desirable for a better understanding of protein⁻lipid interactions within membrane domains, and for optimization of high-level membrane protein production in E. coli.
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Affiliation(s)
- Nadège Jamin
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Manuel Garrigos
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Christine Jaxel
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
| | - Annie Frelet-Barrand
- Institut FEMTO-ST, UMR CNRS 6174, Université Bourgogne Franche-Comté, 15B avenue des Montboucons, 25030 Besançon CEDEX, France.
| | - Stéphane Orlowski
- Institute for Integrative Biology of the Cell (I2BC), CEA/Institut des Sciences du Vivant Fréderic-Joliot/SB2SM, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91191 Gif sur Yvette CEDEX, France.
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41
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Bielytskyi P, Gräsing D, Mote KR, Sai Sankar Gupta KB, Vega S, Madhu PK, Alia A, Matysik J. 13C → 1H transfer of light-induced hyperpolarization allows for selective detection of protons in frozen photosynthetic reaction center. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:82-91. [PMID: 29909081 DOI: 10.1016/j.jmr.2018.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 05/14/2023]
Abstract
In the present study, we exploit the light-induced hyperpolarization occurring on 13C nuclei due to the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect to boost the NMR signal intensity of selected protons via inverse cross-polarization. Such hyperpolarization transfer is implemented into 1H-detected two-dimensional 13C-1H correlation magic-angle-spinning (MAS) NMR experiment to study protons in frozen photosynthetic reaction centers (RCs). As a first trial, the performance of such an experiment is tested on selectively 13C labeled RCs from the purple bacteria of Rhodobacter sphaeroides. We observed response from the protons belonging to the photochemically active cofactors in their native protein environment. Such an approach is a potential heteronuclear spin-torch experiment which could be complementary to the classical heteronuclear correlation (HETCOR) experiments for mapping proton chemical shifts of photosynthetic cofactors and to understand the role of the proton pool around the electron donors in the electron transfer process occurring during photosynthesis.
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Affiliation(s)
- Pavlo Bielytskyi
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Daniel Gräsing
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500107, India
| | | | - Shimon Vega
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500107, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - A Alia
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2301 RA Leiden, The Netherlands; Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103 Leipzig, Germany.
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Supramolecular Organization of Apolipoprotein-A-I-Derived Peptides within Disc-like Arrangements. Biophys J 2018; 115:467-477. [PMID: 30054032 DOI: 10.1016/j.bpj.2018.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Apolipoprotein A-I is the major protein component of high-density lipoproteins and fulfils important functions in lipid metabolism. Its structure consists of a chain of tandem domains of amphipathic helices. Using this protein as a template membrane scaffolding protein, class A amphipathic helical peptides were designed to support the amphipathic helix theory and later as therapeutic tools in biomedicine. Here, we investigated the lipid interactions of two apolipoprotein-A-I-derived class A amphipathic peptides, 14A (Ac-DYLKA FYDKL KEAF-NH2) and 18A (Ac-DWLKA FYDKV AEKLK EAF- NH2), including the disc-like supramolecular structures they form with phospholipids. Thus, the topologies of 14A and 18A in phospholipid bilayers have been determined by oriented solid-state NMR spectroscopy. Whereas at a peptide-to-lipid ratio of 2 mol% the peptides align parallel to the bilayer surface, at 7.5 mol% disc-like structures are formed that spontaneously orient in the magnetic field of the NMR spectrometer. From a comprehensive data set of four 15N- or 2H-labeled positions of 14A, a tilt angle, which deviates from perfectly in-planar by 14°, and a model for the peptidic rim structure have been obtained. The tilt and helical pitch angles are well suited to cover the hydrophobic chain region of the bilayer when two peptide helices form a head-to-tail dimer. Thus, the detailed topology found in this work agrees with the peptides forming the rim of nanodiscs in a double belt arrangement.
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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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Auger M. Membrane solid-state NMR in Canada: A historical perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1483-1489. [PMID: 28652206 DOI: 10.1016/j.bbapap.2017.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/17/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Michèle Auger
- Département de chimie, PROTEO, CERMA, CQMF, Université Laval, Québec, Québec G1V 0A6, Canada.
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