1
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Weber DK, Reddy UV, Robia SL, Veglia G. Pathological mutations in the phospholamban cytoplasmic region affect its topology and dynamics modulating the extent of SERCA inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184370. [PMID: 38986894 DOI: 10.1016/j.bbamem.2024.184370] [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: 04/10/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Phospholamban (PLN) is a 52 amino acid regulin that allosterically modulates the activity of the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) in the heart muscle. In its unphosphorylated form, PLN binds SERCA within its transmembrane (TM) domains, approximately 20 Å away from the Ca2+ binding site, reducing SERCA's apparent Ca2+ affinity (pKCa) and decreasing cardiac contractility. During the enzymatic cycle, the inhibitory TM domain of PLN remains anchored to SERCA, whereas its cytoplasmic region transiently binds the ATPase's headpiece. Phosphorylation of PLN at Ser16 by protein kinase A increases the affinity of its cytoplasmic domain to SERCA, weakening the TM interactions with the ATPase, reversing its inhibitory function, and augmenting muscle contractility. How the structural changes caused by pathological mutations in the PLN cytoplasmic region are transmitted to its inhibitory TM domain is still unclear. Using solid-state NMR spectroscopy and activity assays, we analyzed the structural and functional effects of a series of mutations and their phosphorylated forms located in the PLN cytoplasmic region and linked to dilated cardiomyopathy. We found that these missense mutations affect the overall topology and dynamics of PLN and ultimately modulate its inhibitory potency. Also, the changes in the TM tilt angle and cytoplasmic dynamics of PLN caused by these mutations correlate well with the extent of SERCA inhibition. Our study unveils new molecular determinants for designing variants of PLN that outcompete endogenous PLN to regulate SERCA in a tunable manner.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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2
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Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, Cotten ML. Antiviral activity of the host defense peptide piscidin 1: investigating a membrane-mediated mode of action. Front Chem 2024; 12:1379192. [PMID: 38988727 PMCID: PMC11233706 DOI: 10.3389/fchem.2024.1379192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Outbreaks of viral diseases are on the rise, fueling the search for antiviral therapeutics that act on a broad range of viruses while remaining safe to human host cells. In this research, we leverage the finding that the plasma membranes of host cells and the lipid bilayers surrounding enveloped viruses differ in lipid composition. We feature Piscidin 1 (P1), a cationic host defense peptide (HDP) that has antimicrobial effects and membrane activity associated with its N-terminal region where a cluster of aromatic residues and copper-binding motif reside. While few HDPs have demonstrated antiviral activity, P1 acts in the micromolar range against several enveloped viruses that vary in envelope lipid composition. Notably, it inhibits HIV-1, a virus that has an envelope enriched in cholesterol, a lipid associated with higher membrane order and stability. Here, we first document through plaque assays that P1 boasts strong activity against SARS-CoV-2, which has an envelope low in cholesterol. Second, we extend previous studies done with homogeneous bilayers and devise cholesterol-containing zwitterionic membranes that contain the liquid disordered (Ld; low in cholesterol) and ordered (Lo, rich in cholesterol) phases. Using dye leakage assays and cryo-electron microscopy on vesicles, we show that P1 has dramatic permeabilizing capability on the Lo/Ld, an effect matched by a strong ability to aggregate, fuse, and thin the membranes. Differential scanning calorimetry and NMR experiments demonstrate that P1 mixes the lipid content of vesicles and alters the stability of the Lo. Structural studies by NMR indicate that P1 interacts with the Lo/Ld by folding into an α-helix that lies parallel to the membrane surface. Altogether, these results show that P1 is more disruptive to phase-separated than homogenous cholesterol-containing bilayers, suggesting an ability to target domain boundaries. Overall, this multi-faceted research highlights how a peptide that interacts strongly with membranes through an aromatic-rich N-terminal motif disrupt viral envelope mimics. This represents an important step towards the development of novel peptides with broad-spectrum antiviral activity.
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Affiliation(s)
- Tristan Bepler
- New York Structural Biology Center, New York, NY, United States
| | - Michael D. Barrera
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mary T. Rooney
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, United States
| | - Evan Goodell
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
| | - Matthew J. Goodwin
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Elizabeth Harbron
- Department of Chemistry, William & Mary, Williamsburg, VA, United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Aarthi Narayanan
- Department of Biology, George Mason University, Manassas, VA, United States
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
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3
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Mori S, Shionyu M, Shimamoto K, Nomura K. Bacterial Glycolipid Acting on Protein Transport Across Membranes. Chembiochem 2024; 25:e202300808. [PMID: 38400776 DOI: 10.1002/cbic.202300808] [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: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
The process of protein transport across membranes involves a variety of factors and has been extensively investigated. Traditionally, proteinaceous translocons and chaperones have been recognized as crucial factors in this process. However, recent studies have highlighted the significant roles played by lipids and a glycolipid present in biological membranes in membrane protein transport. Membrane lipids can influence transport efficiency by altering the physicochemical properties of membranes. Notably, our studies have revealed that diacylglycerol (DAG) attenuates mobility in the membrane core region, leading to a dramatic suppression of membrane protein integration. Conversely, a glycolipid in Escherichia coli inner membranes, named membrane protein integrase (MPIase), enhances integration not only through the alteration of membrane properties but also via direct interactions with membrane proteins. This review explores the mechanisms of membrane protein integration mediated by membrane lipids, specifically DAG, and MPIase. Our results, along with the employed physicochemical analysis methods such as fluorescence measurements, nuclear magnetic resonance, surface plasmon resonance, and docking simulation, are presented to elucidate these mechanisms.
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Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
- Department of Chemistry Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
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4
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Nomura K, Mori S, Shimamoto K. Roles of a Glycolipid MPIase in Sec-Independent Membrane Protein Insertion. MEMBRANES 2024; 14:48. [PMID: 38392675 PMCID: PMC10890265 DOI: 10.3390/membranes14020048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Membrane protein integrase (MPIase), an endogenous glycolipid in Escherichia coli (E. coli) membranes, is essential for membrane protein insertion in E. coli. We have examined Sec-independent membrane protein insertion mechanisms facilitated by MPIase using physicochemical analytical techniques, namely solid-state nuclear magnetic resonance, fluorescence measurements, and surface plasmon resonance. In this review, we outline the physicochemical characteristics of membranes that may affect membrane insertion of proteins. Subsequently, we introduce our results verifying the effects of membrane lipids on insertion and estimate the impact of MPIase. Although MPIase is a minor component of E. coli membranes, it regulates insertion by altering the physicochemical properties of the membrane. In addition, MPIase promotes insertion by interacting with substrate proteins. We propose comprehensive mechanisms for the membrane insertion of proteins involving MPIase, which provide a physicochemical basis for understanding the roles of glycolipids in protein translocation.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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5
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Veeraprakash B, Kesava Reddy M, Das BB, Lobo NP, Ramanathan KV, Narasimhaswamy T. Effortless Extraction of Structural and Orientational Information from 13C- 1H Dipolar Couplings for Thiophene Mesogens. J Phys Chem B 2023; 127:10912-10922. [PMID: 38063349 DOI: 10.1021/acs.jpcb.3c06176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Five molecular mesogens containing phenyl rings and thiophene are subjected to a detailed 13C NMR investigation. The first mesogen contains only phenyl rings, while the other four have thiophene with substitution at position 2 or 3. Two of these also have a spacer inserted between the thiophene and the rest of the core unit. The mesophase properties evaluated by complementary techniques reveal an enantiotropic nematic phase for all the cases and smectic C as well as Crystal J for a few mesogens. In addition to solution 13C NMR, the samples were studied using 1D and 2D solid-state 13C NMR experiments in the liquid crystalline phase. The chemical shifts and 13C-1H dipolar couplings obtained in the mesophase provided cutting-edge information about the molecular structure and orientation of the thiophene mesogens. Accordingly, dramatic differences in these parameters are noted for the mesogens, and consequently, the identification of 2- and 3-substituted thiophene mesogens is accomplished by a simple visual examination of the 2D spectra. Furthermore, for mesogens with a spacer between thiophene and the rest of the core, 13C chemical shifts and 13C-1H dipolar couplings showed remarkable variation, which was directly reflected in the order parameters. For instance, the order parameter (Szz) of thiophene in 2- and 3-substituted mesogens in which the spacer is absent is ∼0.63 whereas for those with spacer, it is reduced to ∼0.14-0.18. In comparison, the mesogen in which the core unit is made up of phenyl rings alone that is used to benchmark the characteristics of thiophene ordering showed an order parameter of ∼0.85. The study unambiguously demonstrates the supremacy of 13C NMR in extracting the structural and orientational information on mesogens in which thiophene is a constituent of the core unit.
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Affiliation(s)
- Bathini Veeraprakash
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India
| | | | - Bibhuti B Das
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Nitin P Lobo
- Centre for Analysis, Testing, Evaluation & Reporting Services (CATERS), CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Tanneru Narasimhaswamy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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6
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Kim M, Kim Y. NMR Structural Study of Syndecan-4 Transmembrane Domain with Cytoplasmic Region. Molecules 2023; 28:7855. [PMID: 38067582 PMCID: PMC10708377 DOI: 10.3390/molecules28237855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Syndecan-4 (SDC4) consists of transmembrane heparan sulfate proteoglycan (HSPG) belonging to the syndecan family. It is present in most cell types of Mammalia. Its structure contains a heparan-sulfate-modified extracellular domain, a single transmembrane domain, and a short C-terminal cytoplasmic domain. Regarding the overall cellular function of SDC4, other cells or ligands can bind to its ecto-domain. In addition, 4,5-bisphosphate phosphatidylinositol (PIP2) or protein kinase Cα can bind to its cyto-domain to activate downstream signaling pathways. To understand the signal transduction mechanism of syndecan, it is important to know the interactions between their actual structure and function in vivo. Therefore, it is important to identify the structure of SDC4 to understand the ligand binding behavior of SDC4. In this study, expression and purification were performed to reveal structures of the short ecto-domain, the transmembrane domain, and the cytoplasmic domain of Syd4-eTC (SDC4). Solution-state NMR spectroscopy and solid-state NMR spectroscopy were used to study the structure of Syd4-eTC in membrane environments and to demonstrate the interaction between Syd4-eTC and PIP2.
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Affiliation(s)
| | - Yongae Kim
- Department of Chemistry, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon, Yongin 17035, Republic of Korea;
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7
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Veeraprakash B, Shanavas AKJ, Reddy GSM, Lobo NP, Ramanathan KV, Narasimhaswamy T. Molecular Conformations of Shape Anisometrically Variant Mesogens in Liquid Crystalline Phase Studied by 13 C NMR Spectroscopy. Chemphyschem 2023:e202300353. [PMID: 37725408 DOI: 10.1002/cphc.202300353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
Mesogens that vary in shape anisometry have been investigated by 13 C solid-state NMR in the liquid crystalline phase to inspect the conformations. The molecules examined comprise of (i) rod-like mesogen with three-phenyl ring core and terminal hexyloxy chains, (ii) three-ring core linked to the fourth phenyl ring via a spacer, and (iii) trimesic acid connected to three side arms core units through a spacer. The order parameter (Szz ) values for the phenyl rings of the rod-like mesogen are 0.65-0.68, while the mesogen with a three-ring core linked to a phenyl ring via spacer showed dissimilarity. Consequently, for the core unit phenyl rings, Szz is ~0.70, and the terminal phenyl ring showed a low value of 0.12. For the trimesic acid based mesogen, the Szz value for the side arm phenyl rings is ~0.53, and for the central phenyl ring, a very low value of 0.11 is witnessed. By considering the ordering of the rod-like mesogen as a yardstick and employing the ratios of Szz values of the phenyl rings, the average conformations of other mesogens are arrived. Accordingly, for the trimesic acid based mesogen, a tripod-like conformation instead of λ shape is proposed in the liquid crystalline phase.
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Affiliation(s)
- Bathini Veeraprakash
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
| | - Abdul K J Shanavas
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
| | - Goddeti S M Reddy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
| | - Nitin P Lobo
- Centre for Analysis, Testing, Evaluation & Reporting Services (CATERS), CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | | | - Tanneru Narasimhaswamy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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8
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Galiakhmetov AR, Davern CM, Esteves RJA, Awosanya EO, Guthrie QAE, Proulx C, Nevzorov AA. Aligned peptoid-based macrodiscs for structural studies of membrane proteins by oriented-sample NMR. Biophys J 2022; 121:3263-3270. [PMID: 35918898 PMCID: PMC9463639 DOI: 10.1016/j.bpj.2022.07.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 11/21/2022] Open
Abstract
Development of a robust, uniform, and magnetically orientable lipid mimetic will undoubtedly advance solid-state NMR of macroscopically aligned membrane proteins. Here, we report on a novel lipid membrane mimetic based on peptoid belts. The peptoids, composed of 15 residues, were synthesized by alternating N-(2-phenethyl)glycine with N-(2-carboxyethyl)glycine residues at a 2:1 molar ratio. The chemically synthesized peptoids possess a much lower degree of polydispersity versus styrene-maleic acid polymers, thus yielding uniform discs. Moreover, the peptoid oligomers are more flexible and do not require a specific folding, unlike lipoproteins, in order to wrap around the hydrophobic membrane core. The NMR spectra measured for the membrane-bound form of Pf1 coat protein incorporated in this new lipid mimetics demonstrate a higher order parameter and uniform linewidths compared with the conventional bicelles and peptide-based macrodiscs. Importantly, unlike bicelles, the peptoid-based macrodiscs are detergent free.
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Affiliation(s)
| | - Carolynn M Davern
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Richard J A Esteves
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Quibria A E Guthrie
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Caroline Proulx
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina.
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9
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De Angelis A, Park SH, Opella SJ. Magnetically Aligned Lipid Bilayers with High Cholesterol for Solid-State NMR of Membrane Proteins. Biochemistry 2022; 61:1561-1571. [PMID: 35849647 DOI: 10.1021/acs.biochem.2c00262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phospholipid bicelles are valuable membrane model systems to study membrane proteins by NMR and other physicochemical techniques. The range of bicelle compositions that are compatible with uniaxial alignment of the lipid bilayers in a magnetic field is still limited with regard to the addition of large amounts (>20%) of cholesterol and/or sphingolipids. Here, we demonstrate that n-dodecyl-β-D-melibioside (DDMB), which was recently introduced as a detergent to produce sphingolipid-cholesterol-rich isotropic bicelles for solution NMR studies, can also be used to produce magnetically alignable lipid bilayers with high cholesterol content that are well suited for solid-state NMR of membrane proteins. Remarkably, DDMB enables the preparation of high q bicelles that contain 50% mol cholesterol while retaining their ability to form a stable, well-aligned liquid crystalline bilayer phase in a magnetic field. We show that the intact 46-residue membrane-bound form of Pf1 bacteriophage coat protein and a truncated construct of the membrane protein Vpu from HIV-1 (residues 2-30) in DDMB bicelles are well aligned and undergo fast and uniaxial rotational diffusion about the bilayer normal, similarly to what is observed in other bicelle and macrodisc systems. We also demonstrate a spectroscopic method that measures the increase in the thickness of DMPC bilayers that results from the addition of cholesterol, using the PISA-wheel spectral patterns of trans-membrane helices as a molecular goniometer. For example, we find that the hydrophobic thickness of DMPC bilayers is increased by approximately 2.5 Å in the presence of 35% mol cholesterol.
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Affiliation(s)
- Anna De Angelis
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, California 92093-0307 United States
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10
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Reddy UV, Weber DK, Wang S, Larsen EK, Gopinath T, De Simone A, Robia S, Veglia G. A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca 2+-ATPase. Structure 2022; 30:360-370.e6. [PMID: 34875216 PMCID: PMC8897251 DOI: 10.1016/j.str.2021.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/14/2021] [Accepted: 11/11/2021] [Indexed: 12/31/2022]
Abstract
SERCA is a P-type ATPase embedded in the sarcoplasmic reticulum and plays a central role in muscle relaxation. SERCA's function is regulated by single-pass membrane proteins called regulins. Unlike other regulins, dwarf open reading frame (DWORF) expressed in cardiac muscle has a unique activating effect. Here, we determine the structure and topology of DWORF in lipid bilayers using a combination of oriented sample solid-state NMR spectroscopy and replica-averaged orientationally restrained molecular dynamics. We found that DWORF's structural topology consists of a dynamic N-terminal domain, an amphipathic juxtamembrane helix that crosses the lipid groups at an angle of 64°, and a transmembrane C-terminal helix with an angle of 32°. A kink induced by Pro15, unique to DWORF, separates the two helical domains. A single Pro15Ala mutant significantly decreases the kink and eliminates DWORF's activating effect on SERCA. Overall, our findings directly link DWORF's structural topology to its activating effect on SERCA.
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Affiliation(s)
- U. Venkateswara Reddy
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel K. Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erik K. Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK,Department of Pharmacy, University of Naples “Federico II”, Naples, 80131, Italy
| | - Seth Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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11
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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12
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Wright AK, Paulino J, Cross TA. Emulating Membrane Protein Environments─How Much Lipid Is Required for a Native Structure: Influenza S31N M2. J Am Chem Soc 2022; 144:2137-2148. [PMID: 35089701 DOI: 10.1021/jacs.1c10174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This report investigates the homotetrameric membrane protein structure of the S31N M2 protein from Influenza A virus in the presence of a high molar ratio of lipid. The structured regions of this protein include a single transmembrane helix and an amphipathic helix. Two structures of the S31N M2 conductance domain from Influenza A virus have been deposited in the Protein Data Bank (PDB). These structures present different symmetries about the channel main axis. We present new magic angle spinning and oriented sample solid-state NMR spectroscopic data for S31N M2 in liquid crystalline lipid bilayers using protein tetramer:lipid molar ratios ranging from 1:120 to 1:240. The data is consistent with an essentially 4-fold-symmetric structure very similar to the M2 WT structure that also has a single conformation for the four monomers, except at the His37 and Trp41 functional sites when characterized in samples with a high molar ratio of lipid. While detergent solubilization is well recognized today as a nonideal environment for small membrane proteins, here we discuss the influence of a high lipid to protein ratio for samples of the S31N M2 protein to stabilize an essentially 4-fold-symmetric conformation of the M2 membrane protein. While it is generally accepted that the chemical and physical properties of the native environment of membrane proteins needs to be reproduced judiciously to achieve the native protein structure, here we show that not only the character of the emulated membrane environment is important but also the abundance of the environment is important for achieving the native structure. This is a critical finding as a membrane protein spectroscopist's goal is always to generate a sample with the highest possible protein sensitivity while obtaining spectra of the native-like structure.
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Affiliation(s)
- Anna K Wright
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Joana Paulino
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Timothy A Cross
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States.,National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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13
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Wang S, Gopinath T, Larsen EK, Weber DK, Walker C, Uddigiri VR, Mote KR, Sahoo SK, Periasamy M, Veglia G. Structural basis for sarcolipin's regulation of muscle thermogenesis by the sarcoplasmic reticulum Ca 2+-ATPase. SCIENCE ADVANCES 2021; 7:eabi7154. [PMID: 34826239 PMCID: PMC8626070 DOI: 10.1126/sciadv.abi7154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/06/2021] [Indexed: 06/10/2023]
Abstract
The sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA) plays a central role in muscle contractility and nonshivering thermogenesis. SERCA is regulated by sarcolipin (SLN), a single-pass membrane protein that uncouples Ca2+ transport from ATP hydrolysis, promoting futile enzymatic cycles and heat generation. The molecular determinants for regulating heat release by the SERCA/SLN complex are unclear. Using thermocalorimetry, chemical cross-linking, and solid-state NMR spectroscopy in oriented phospholipid bicelles, we show that SERCA’s functional uncoupling and heat release rate are dictated by specific SERCA/SLN intramembrane interactions, with the carboxyl-terminal residues anchoring SLN to the SR membrane in an inhibitory topology. Systematic deletion of the carboxyl terminus does not prevent the SERCA/SLN complex formation but reduces uncoupling in a graded manner. These studies emphasize the critical role of lipids in defining the active topology of SLN and modulating the heat release rate by the SERCA/SLN complex, with implications in fat metabolism and basal metabolic rate.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erik K. Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel K. Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Venkateswara Reddy Uddigiri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500046, India
| | - Sanjaya K. Sahoo
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Muthu Periasamy
- Department of Physiology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Department of Internal Medicine, College of Medicine, University of Central Florida, Orlando, FL 32827, 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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14
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Long Z, Ruthford J, Opella SJ. 3D printed sample tubes for solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106957. [PMID: 33798799 PMCID: PMC8141027 DOI: 10.1016/j.jmr.2021.106957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The availability of 3D printers and an assortment of polymers that can be fashioned into a wide variety of shapes provides opportunities to rethink the design and construction of probes for NMR spectroscopy. The direct interfacing of computer aided design (CAD) with precise 3D printing enables the simplification and optimization of probes through the rapid production of components. Here we demonstrate the use of 3D printing to fully integrate a permanent former for the radiofrequency (RF) coil with the sample chamber (equivalent to the sample tube). This simultaneously increases the sample volume and improves the filling factor within a fixed outer diameter (OD). It also reduces the space lost in dual coil arrangements where a high frequency resonator is positioned outside a solenoid coil tuned to one or more lower frequencies, making multiple-resonance experiments more efficient. The initial applications demonstrate the possibilities for future designs that reimagine the interface between resonators and the liquid, solid, and heterogeneous samples encountered in NMR studies of biomolecules, polymers, surfaces, and spectroscopy (MRS) and imaging (MRI) of biological organs and intact organisms.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Jamie Ruthford
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States.
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15
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Weber DK, Reddy UV, Wang S, Larsen EK, Gopinath T, Gustavsson MB, Cornea RL, Thomas DD, De Simone A, Veglia G. Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by Ca 2+ and phosphorylation. eLife 2021; 10:66226. [PMID: 33978571 PMCID: PMC8184213 DOI: 10.7554/elife.66226] [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: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023] Open
Abstract
Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca2+-transport response to β-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation by cAMP-dependent protein kinase A or increase in Ca2+ concentration reverses the inhibitory effects through an unknown mechanism. Using oriented-sample solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we reveal that phosphorylation of PLN's cytoplasmic regulatory domain signals the disruption of several inhibitory contacts at the transmembrane binding interface of the SERCA-PLN complex that are propagated to the enzyme's active site, augmenting Ca2+ transport. Our findings address long-standing questions about SERCA regulation, epitomizing a signal transduction mechanism operated by posttranslationally modified bitopic membrane proteins.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - U Venkateswara Reddy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Erik K Larsen
- Department of Chemistry, University of Minnesota, Minneapolis, United States
| | - Tata Gopinath
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Martin B Gustavsson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom.,Department of Pharmacy, University of Naples 'Federico II', Naples, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States.,Department of Chemistry, University of Minnesota, Minneapolis, United States
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16
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Lapin J, Awosanya EO, Esteves RJA, Nevzorov AA. 1H/ 13C/ 15N triple-resonance experiments for structure determinaton of membrane proteins by oriented-sample NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 111:101701. [PMID: 33260039 DOI: 10.1016/j.ssnmr.2020.101701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The benefits of triple-resonance experiments for structure determination of macroscopically oriented membrane proteins by solid-state NMR are discussed. While double-resonance 1H/15N experiments are effective for structure elucidation of alpha-helical domains, extension of the method of oriented samples to more complex topologies and assessing side-chain conformations necessitates further development of triple-resonance (1H/13C/15N) NMR pulse sequences. Incorporating additional spectroscopic dimensions involving 13C spin-bearing nuclei, however, introduces essential complications arising from the wide frequency range of the 1H-13C dipolar couplings and 13C CSA (>20 kHz), and the presence of the 13C-13C homonuclear dipole-dipole interactions. The recently reported ROULETTE-CAHA pulse sequence, in combination with the selective z-filtering, can be used to evolve the structurally informative 1H-13C dipolar coupling arising from the aliphatic carbons while suppressing the signals from the carbonyl and methyl regions. Proton-mediated magnetization transfer under mismatched Hartman-Hahn conditions (MMHH) can be used to correlate 13C and 15N nuclei in such triple-resonance experiments for the subsequent 15N detection. The recently developed pulse sequences are illustrated for n-acetyl Leucine (NAL) single crystal and doubly labeled Pf1 coat protein reconstituted in magnetically aligned bicelles. An interesting observation is that in the case of 15N-labeled NAL measured at 13C natural abundance, the triple (1H/13C/15N) MMHH scheme predominantly gives rise to long-range intermolecular magnetization transfers from 13C to 15N spins; whereas direct Hartmann-Hahn 13C/15N transfer is entirely intramolecular. The presented developments advance NMR of oriented samples for structure determination of membrane proteins and liquid crystals.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Richard J A Esteves
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204 USA.
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17
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Steger LME, Kohlmeyer A, Wadhwani P, Bürck J, Strandberg E, Reichert J, Grage SL, Afonin S, Kempfer M, Görner AC, Koch J, Walther TH, Ulrich AS. Structural and functional characterization of the pore-forming domain of pinholin S 2168. Proc Natl Acad Sci U S A 2020; 117:29637-29646. [PMID: 33154156 PMCID: PMC7703622 DOI: 10.1073/pnas.2007979117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pinholin S2168 triggers the lytic cycle of bacteriophage φ21 in infected Escherichia coli Activated transmembrane dimers oligomerize into small holes and uncouple the proton gradient. Transmembrane domain 1 (TMD1) regulates this activity, while TMD2 is postulated to form the actual "pinholes." Focusing on the TMD2 fragment, we used synchrotron radiation-based circular dichroism to confirm its α-helical conformation and transmembrane alignment. Solid-state 15N-NMR in oriented DMPC bilayers yielded a helix tilt angle of τ = 14°, a high order parameter (Smol = 0.9), and revealed the azimuthal angle. The resulting rotational orientation places an extended glycine zipper motif (G40xxxS44xxxG48) together with a patch of H-bonding residues (T51, T54, N55) sideways along TMD2, available for helix-helix interactions. Using fluorescence vesicle leakage assays, we demonstrate that TMD2 forms stable holes with an estimated diameter of 2 nm, as long as the glycine zipper motif remains intact. Based on our experimental data, we suggest structural models for the oligomeric pinhole (right-handed heptameric TMD2 bundle), for the active dimer (right-handed Gly-zipped TMD2/TMD2 dimer), and for the full-length pinholin protein before being triggered (Gly-zipped TMD2/TMD1-TMD1/TMD2 dimer in a line).
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Affiliation(s)
- Lena M E Steger
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Annika Kohlmeyer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Johannes Reichert
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Marin Kempfer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Anne C Görner
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Julia Koch
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Torsten H Walther
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany;
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany;
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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18
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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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19
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Reddy MG, Lobo NP, Roy A, Ramanathan KV, Narasimhaswamy T. Strikingly different molecular organization and molecular order of tetracatenar mesogens in columnar mesophases revealed by XRD and 13C NMR. Phys Chem Chem Phys 2020; 22:23986-23997. [PMID: 33073796 DOI: 10.1039/d0cp03933k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For a successful design of functional mesogens, it is paramount to understand factors that contribute to molecular organisation such as molecular shape, the non-covalent interactions of the constituent moieties as well as nanosegregation of incompatible molecular parts. In this study on four tetracatenar mesogens, we show that by a slight change in the length of the terminal chain, the molecular organization changes from lamellar to columnar phase and that the orientational order experiences profound change between the lamellar, the center rectangular columnar and the hexagonal columnar mesophases. We consider here, mesogens that exhibit lamellar and columnar mesophases with five phenyl rings in the central rod-like core which are subjected to XRD and high resolution solid state 13C NMR investigations in their mesophases. The XRD studies indicate that the lower homologs exhibit a lamellar mesophase while the higher homologs show either a centre rectangular columnar phase or a 2D hexagonal columnar mesophase. 13C NMR investigations reveal interesting and strikingly different molecular orientations in each of these phases. For example, values of order parameters of one of the phenyl rings in the core region of the mesogens vary from 0.75 and 0.77 for the lamellar mesogens to 0.45 and 0.17 for the centre rectangular columnar and the hexagonal columnar mesogens respectively. While these values indicate that the mesogenic molecules are oriented along the magnetic field as expected in the lamellar phases, the very low order parameter in the hexagonal columnar phase arises due to molecules distributed azimuthally in layers and undergoing motion about the columnar axis which itself is oriented orthogonal to the magnetic field. Such cutting edge information extracted from the combined use of XRD and 13C NMR studies on tetracatenar mesogens is expected to be of significant use for the study of π-conjugated polycatenar systems where functional properties depend on the molecular orientation and order.
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Affiliation(s)
- M Guruprasad Reddy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India.
| | - Nitin P Lobo
- Centre for Analysis, Testing, Evaluation & Reporting Services (CATERS), CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India
| | - Arun Roy
- Soft Condensed Matter, Raman Research Institute, Bangalore, 560080, India.
| | - K V Ramanathan
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India.
| | - T Narasimhaswamy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India.
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20
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Lobo NP, Ramanathan KV, Narasimhaswamy T. 13 C NMR investigations of molecular order of rod-like, bent-core, and thiophene mesogens. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:988-1009. [PMID: 31770458 DOI: 10.1002/mrc.4972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
In this review, methods to obtain the orientational order of topologically variant molecular mesogens using by one- and two-dimensional (2D) solid-state 13 C nuclear magnetic resonance (NMR) spectroscopy are described. Besides 13 C chemical shifts, the 13 C─1 H dipolar couplings measured from 2D-separated local field (SLF) technique are used for computing the order parameters of a variety of mesogens. The investigated molecules are composed of a variable number of rings in the core, that is, core ranging from simply one ring to five rings. Among the mesogens investigated, a special focus has been placed on mesogens with thiophene rings, which are gaining popularity as liquid crystalline organic semiconductors. The replacement of a phenyl ring by thiophene in the core has a dramatic influence on molecular topology, as observed from the measured order parameters. The review highlights the advantages of the 2D SLF method for understanding the local dynamics and for mapping the topology of mesogens through the measured order parameters. SLF NMR studies of as many as 24 molecular mesogens that vary in terms of the molecular structure as well as topology are covered in the review. Order parameters of the rings have been estimated from the 13 C─1 H dipolar couplings in the nematic, smectic A, smectic C, and tilted hexatic phases as well as in B1 and B2 mesophases of various mesogens. It is anticipated that, in the years to come, the 2D SLF method would provide advanced molecular information on structurally complex mesogens that are emerging in liquid crystal science through the incessant efforts of synthetic chemists. The mini review covers the orientational order of topologically variant molecular mesogens determined by 1D and 2D solid-state 13 C NMR spectroscopy. Accordingly, rod-like, bent-core, and thiophene mesogens were subjected to 2D SLF measurements to get the order parameters from which the topology was established. The replacement of phenyl ring by thiophene and its influence on order parameters as well as on molecular topology is also discussed.
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Affiliation(s)
- Nitin P Lobo
- Inorganic and Physical Chemistry, CSIR-Central Leather Research Institute, Chennai, India
| | - K V Ramanathan
- NMR Research Centre, Indian Institute of Science, Bangalore, India
| | - T Narasimhaswamy
- Polymer Science and Technology, CSIR-Central Leather Research Institute, Chennai, India
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21
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Applications of NMR in Drug:Cyclodextrin Complexes. Methods Mol Biol 2020. [PMID: 33113144 DOI: 10.1007/978-1-0716-0920-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
NMR spectroscopy is an effective technique, applicable for studying bioactive materials or drug delivery systems in order to obtain comprehensive details related to structural and dynamic characteristics at atomic resolution. The applications of NMR spectroscopy have been increased considerably as a result of the combination of advancement in technological NMR instrumentation and scientific knowledge. This chapter is dedicated to highlight the applications of NMR spectroscopy in drug:cyclodextrin complexes using both liquid- and solid-state NMR spectroscopy.
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22
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Long Z, Opella SJ. 1H detection of heteronuclear dipolar oscillations with water suppression in single crystal peptide and oriented protein samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106793. [PMID: 32827996 PMCID: PMC8132951 DOI: 10.1016/j.jmr.2020.106793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Oriented sample solid-state NMR is a complementary approach to protein structure determination with the distinct advantage that it can be applied to supramolecular assemblies, such as viruses and membrane proteins, under near-native conditions, which generally include high levels of hydration as found in living systems. Thus, in order to perform 1H detected versions of multi-dimensional experiments water suppression techniques must be integrated into the pulse sequences. For example, 1H-windowed detection of 1H-15N dipolar couplings enable multi-dimensional NMR experiments to be performed. Here we show that the addition of a solvent suppression pulse during the z-filter interval greatly improves the sensitivity of the experiments by suppressing the 1H signals from water present. This is demonstrated here with a crystal sample submerged in water and then extended to proteins. The combination of solvent-suppressed 1H detected PISEMO and the use of a strip shield-solenoid coil probe configuration provides a two-fold sensitivity enhancement in both the crystal sample and Pf1 coat protein sample compared to the 15N direct detection method. Here we also examine protein NMR line-widths and sensitivity enhancements in the context of window detected separated local field experiments for protein samples.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, United States.
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23
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Jeong JH, Kim M, Kim Y. NMR structural studies and mechanism of action of Lactophoricin analogs as antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183469. [PMID: 32871115 DOI: 10.1016/j.bbamem.2020.183469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs) are effective alternatives to conventional antibiotics. They protect the host from the constant invasion of a broad range of infectious microorganisms. AMPs have been at the forefront of the response to multidrug-resistant microbial strains and appear to be ideal drug candidates. Lactophoricin (LPcin), naturally produced from bovine milk, is a typical cationic antimicrobial peptide. Three analog peptides, including LPcin-YK5, LPcin-YK8, and LPcin-YK11, with enhanced antimicrobial activity compared to the wild-type LPcin, were designed and expressed in our laboratory. We investigated the structure and antimicrobial mechanisms of action of the three novel antimicrobial peptide analogs derived from LPcin using solution NMR and solid-state NMR spectroscopy in membrane environments. Our results revealed that the three LPcin analogs exhibited helical structures with different tilt angles on the phospholipid membrane surface. We proposed three-dimensional conformations and antibacterial mechanisms of action of the three peptide analogs in the phospholipid bilayers using two-dimensional solid-state separated local field NMR experiments.
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Affiliation(s)
- Ji-Ho Jeong
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In 17035, Republic of Korea
| | - Minseon Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In 17035, Republic of Korea
| | - Yongae Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In 17035, Republic of Korea.
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24
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Lapin J, Nevzorov AA. Computer-generated pulse sequences for 1H- 15N and 1H α- 13C α separated local-field experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 317:106794. [PMID: 32717619 DOI: 10.1016/j.jmr.2020.106794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
High-resolution separated local field (SLF) experiments are employed in oriented-sample solid state NMR to measure angular-dependent heteronuclear dipolar couplings for structure determination. While traditionally these experiments have been designed analytically by determining cycles of pulses with specific phases and durations to achieve cancellation of the homonuclear dipolar terms in the average Hamiltonian, recent work has introduced a computational approach to optimizing linewidths of the 1H-15N dipolar resonances. Accelerated by GPU processors, a computer algorithm searches for the optimal parameters by simulating numerous 1H-15N NMR spectra. This approach, termed ROULETTE, showed promising results by developing a new pulse sequence (ROULETTE-1.0) exhibiting 18% sharper mean linewidths than SAMPI4 for an N-acetyl Leucine (NAL) crystal. Herein, we expand on this previous work to improve the performance of the 1H-15N SLF experiment and extend the work beyond the original approach to new SLF experiments. The new algorithm, in addition to finding pulse durations and phases, now searches for the optimal on/off application scheme of radio frequency irradiation on each channel. This constitutes true de novo optimization, effectively optimizing every aspect of a pulse sequence instead of just phases and durations. With an improved ROULETTE algorithm, we have found a new 1H-15N pulse sequence, termed ROULETTE-2.0, yielding 32% sharper mean linewidths than SAMPI4 for NAL crystal at 500 MHz 1H frequency. Whereas both SAMPI4 and ROULETTE-1.0 have a window where the rf power on the I-channel is turned off, the new pulse sequence is entirely windowless. Furthermore, the reliability of the algorithm has been greatly improved in terms of avoiding false positives, i.e. well-performing pulse sequences in silica that fail to render narrow resonances in experiment. The program has been extended to the 13Cα-1Hα SLF experiments, using a 6 subdwell architecture similar to the 1H-15N optimization. Compared to the PISEMA pulse sequence, the mean 13Cα-1Hα linewidth is 17% sharper for the new pulse sequence, termed ROULETTE-CAHA. In addition to superior performance, the work demonstrates the broad applicability of the algorithm and its adaptability to different NMR experiments and spin systems.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, USA.
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25
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Weber DK, Wang S, Markley JL, Veglia G, Lee W. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinformatics 2020; 36:2915-2916. [PMID: 31930377 PMCID: PMC7203746 DOI: 10.1093/bioinformatics/btaa019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/04/2020] [Accepted: 01/09/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Two-dimensional [15N-1H] separated local field solid-state nuclear magnetic resonance (NMR) experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for α-helical segments using Polar Index Slant Angle (PISA)-wheel models. No integrated software has been made available for data analysis and visualization. RESULTS We have developed the PISA-SPARKY plugin to seamlessly integrate PISA-wheel modeling into the NMRFAM-SPARKY platform. The plugin performs basic simulations, exhaustive fitting against experimental spectra, error analysis and dipolar and chemical shift wave plotting. The plugin also supports PyMOL integration and handling of parameters that describe variable alignment and dynamic scaling encountered with magnetically aligned media, ensuring optimal fitting and generation of restraints for structure calculation. AVAILABILITY AND IMPLEMENTATION PISA-SPARKY is freely available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers of the SBGrid (https://sbgrid.org). The pisa.py script is available and documented on GitHub (https://github.com/weberdak/pisa.py) along with a tutorial video and sample data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel K Weber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, 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
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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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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Awosanya EO, Lapin J, Nevzorov AA. NMR "Crystallography" for Uniformly ( 13 C, 15 N)-Labeled Oriented Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3554-3557. [PMID: 31887238 DOI: 10.1002/anie.201915110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/29/2019] [Indexed: 01/01/2023]
Abstract
In oriented-sample (OS) solid-state NMR of membrane proteins, the angular-dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only 1 H-15 N dipolar couplings and 15 N chemical shifts have been routinely assessed in oriented 15 N-labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple-resonance NMR technique, which was applied to uniformly doubly (15 N, 13 C)-labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible 1 Hα -13 Cα dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α-helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α-helical transmembrane structure for Pf1 protein.
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Affiliation(s)
- Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC, 27695-8204, USA
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Awosanya EO, Lapin J, Nevzorov AA. NMR “Crystallography” for Uniformly (
13
C,
15
N)‐Labeled Oriented Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Emmanuel O. Awosanya
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
| | - Joel Lapin
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
| | - Alexander A. Nevzorov
- Department of Chemistry North Carolina State University 2620 Yarbrough Drive Raleigh NC 27695-8204 USA
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Lapin J, Nevzorov AA. De novo NMR pulse sequence design using Monte-Carlo optimization techniques. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 310:106641. [PMID: 31734619 DOI: 10.1016/j.jmr.2019.106641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Separated Local Field (SLF) experiments have been routinely used for measuring 1H-15N heteronuclear dipolar couplings in oriented-sample solid-state NMR for structure determination of proteins. In the on-going pursuit of designing better-performing SLF pulse sequences (e.g. by increasing the number of subdwells, and varying the rf amplitudes and phases), analytical treatment of the relevant average Hamiltonian terms may become cumbersome and/or nearly impossible. Numerical simulations of NMR experiments using GPU processors can be employed to rapidly calculate spectra for moderately sized spin systems, which permit an efficient numeric optimization of pulse sequences by the Monte Carlo Simulated Annealing protocol. In this work, a computational strategy was developed to find the optimal phases and timings that substantially improve the 1H-15N dipolar linewidths over a broad range of dipolar couplings as compared to SAMPI4. More than 100 pulse sequences were developed de novo and tested on an N-acetyl Leucine crystal. Seventeen distinct pulse sequences were shown to produce sharper mean linewidths than SAMPI4. Overall, these pulse sequences have more variable parameters (involving non-quadrature phases) and do not involve symmetry between the odd and even dwells, which would likely preclude their rigorous analytical treatment. The top performing pulse sequence, termed ROULETTE-1, has 18% sharper mean linewidths than SAMPI4 when run on an N-acetyl Leucine crystal. This sequence was also shown to be robust over a broad range of 1H carrier frequencies and various crystal orientations. The performance of such an optimized pulse sequence was also illustrated on 15N Leucine-labeled Pf1 coat protein reconstituted in magnetically aligned bicelles. For the optimized pulse sequence the mean peak width was 14% sharper than SAMPI4, which in turn yielded a better signal to noise ratio, 20:1 vs. 17:1. This method is potentially extendable to de novo development of a variety of NMR experiments.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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Long Z, Park SH, Opella SJ. Effects of deuteration on solid-state NMR spectra of single peptide crystals and oriented protein samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 309:106613. [PMID: 31677452 PMCID: PMC7326366 DOI: 10.1016/j.jmr.2019.106613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Extensive deuteration can be used to simplify NMR spectra by "diluting" and minimizing the effects of the abundant 1H nuclei. In solution-state NMR and magic angle spinning solid-state NMR of proteins, perdeuteration has been widely applied and its effects are well understood. Oriented sample solid-state NMR of proteins, however, is at a much earlier stage of development. In spite of the promise of the approach, the effects of sample deuteration are largely unknown. Here we map out the effects of perdeuteration on solid-state NMR spectra of aligned samples by closely examining differences in results obtained on fully protiated and perdeuterated samples, where all of the carbon sites have either 1H or 2H bonded to them, respectively. The 2H and 15N labeled samples are back-exchanged in 1H2O solution so that the amide 15N sites have a bonded 1H. Line-widths in the 15N chemical shift, 1H chemical shift, and 1H-15N dipolar coupling frequency dimensions were compared for peptide single crystals as well as membrane proteins aligned along with the phospholipids in bilayers with their normals perpendicular to the direction of the magnetic field. Remarkably, line-width differences were not found between fully protiated and perdeuterated samples. However, in the absence of effective 1H-1H homonuclear decoupling, the line-widths in the 1H-15N heteronuclear dipolar coupling frequency dimension were greatly narrowed in the perdeuterated samples. In proton-driven spin diffusion (PDSD) experiments, no effects of perdeuteration were observed. In contrast, in mismatched Hartmann-Hahn experiments, perdeuteration enhances cross-peak intensities by allowing more efficient spin-exchange with less polarization transfer back to the carbon-bound 1H. Here we show that in oriented sample solid-state NMR, the effects of perdeuteration can be exploited in experiments where 1H-1H homonuclear decoupling cannot be applied. These data also provide evidence for the possible contribution of direct 15N-15N dilute-spin mixing mechanism in proton-driven spin diffusion experiments.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States.
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Wang S, Gopinath T, Veglia G. Improving the quality of oriented membrane protein spectra using heat-compensated separated local field experiments. JOURNAL OF BIOMOLECULAR NMR 2019; 73:617-624. [PMID: 31463642 PMCID: PMC6861693 DOI: 10.1007/s10858-019-00273-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/21/2019] [Indexed: 05/03/2023]
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is a powerful technique to determine the topology of membrane proteins in oriented lipid bilayers. Separated local field (SLF) experiments are central to this technique as they provide first-order orientational restraints, i.e., dipolar couplings and anisotropic chemical shifts. Despite the use of low-E (or E-free) probes, the heat generated during the execution of 2D and 3D SLF pulse sequences causes sizeable line-shape distortions. Here, we propose a new heat-compensated SE-SAMPI4 (hcSE-SAMPI4) pulse sequence that holds the temperature constant for the duration of the experiment. This modification of the SE-SAMPI4 results in sharper and more intense resonances without line-shape distortions. The spectral improvements are even more apparent when paramagnetic relaxation agents are used to speed up data collection. We tested the hcSE-SAMPI4 pulse sequence on a single-span membrane protein, sarcolipin (SLN), reconstituted in magnetically aligned lipid bicelles. In addition to eliminating peak distortions, the hcSE-SAMPI4 experiment increased the average signal-to-noise ratio by 20% with respect to the original SE-SAMPI4.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - T Gopinath
- 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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32
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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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33
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Boopathi AA, Janani K, Lobo NP, Narasimhaswamy T. 13C NMR Investigations of Hairy-Rod-Like π-Conjugated Mesogens. J Phys Chem B 2019; 123:5651-5664. [DOI: 10.1021/acs.jpcb.9b04282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- A. A. Boopathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | | | - Nitin P. Lobo
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - T. Narasimhaswamy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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34
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Lapin J, Nevzorov AA. Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:104-114. [PMID: 29920407 DOI: 10.1016/j.jmr.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on 15N-15N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space. The output from the program consists of a list of top-score main peak assignments, which can be subjected to further scoring criteria until a consensus solution is found. The algorithm has first been tested on a synthetic spectrum with randomly generated chemical shifts and dipolar couplings for the main peaks. The original assignments have been successfully recovered for as many as 100 main peaks when residue-type information was used even in the presence of substantial spectral peak overlap. The algorithm was then applied to assigning two sets of experimental spectra to recover and confirm the previously established assignments in an automated fashion. For the 20-residue transmembrane domain of Pf1 coat protein reconstituted in magnetically aligned bicelles, the original assignment by Park et al. (2010) was recovered by the automated algorithm with additional input from 5 selectively labeled amino acid spectra. The second case considered was the 46 residue Pf1 bacteriophage from Thiriot et al. (2005) and Knox et al. (2010), of which 38 residues were fit. Automated fitting resulted in several possible assignments but not exactly the original assignment. By using a post-fitting filtering procedure based on the number of missed cross peaks and Pf1 helical structure, a consensus spectroscopic assignment is proposed covering 84% of the original assignment. While the automated assignment works best in spectra with well-resolved crosspeaks, it also tolerates substantial spectral crowding to yield reasonable assignments in the cases where ambiguity and degeneracy of possible assignment solutions are inevitable.
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Affiliation(s)
- Joel Lapin
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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McKay MJ, Martfeld AN, De Angelis AA, Opella SJ, Greathouse DV, Koeppe RE. Control of Transmembrane Helix Dynamics by Interfacial Tryptophan Residues. Biophys J 2018; 114:2617-2629. [PMID: 29874612 PMCID: PMC6129553 DOI: 10.1016/j.bpj.2018.04.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 01/12/2023] Open
Abstract
Transmembrane protein domains often contain interfacial aromatic residues, which may play a role in the insertion and stability of membrane helices. Residues such as Trp or Tyr, therefore, are often found situated at the lipid-water interface. We have examined the extent to which the precise radial locations of interfacial Trp residues may influence peptide helix orientation and dynamics. To address these questions, we have modified the GW5,19ALP23 (acetyl-GGALW5(LA)6LW19LAGA-[ethanol]amide) model peptide framework to relocate the Trp residues. Peptide orientation and dynamics were analyzed by means of solid-state nuclear magnetic resonance (NMR) spectroscopy to monitor specific 2H- and 15N-labeled residues. GW5,19ALP23 adopts a defined, tilted orientation within lipid bilayer membranes with minimal evidence of motional averaging of NMR observables, such as 2H quadrupolar or 15N-1H dipolar splittings. Here, we examine how peptide dynamics are impacted by relocating the interfacial Trp (W) residues on both ends and opposing faces of the helix, for example by a 100° rotation on the helical wheel for positions 4 and 20. In contrast to GW5,19ALP23, the modified GW4,20ALP23 helix experiences more extensive motional averaging of the NMR observables in several lipid bilayers of different thickness. Individual and combined Gaussian analyses of the 2H and 15N NMR signals confirm that the extent of dynamic averaging, particularly rotational "slippage" about the helix axis, is strongly coupled to the radial distribution of the interfacial Trp residues as well as the bilayer thickness. Additional 2H labels on alanines A3 and A21 reveal partial fraying of the helix ends. Even within the context of partial unwinding, the locations of particular Trp residues around the helix axis are prominent factors for determining transmembrane helix orientation and dynamics within the lipid membrane environment.
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Affiliation(s)
- Matthew J McKay
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Anna A De Angelis
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas.
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36
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Awosanya EO, Nevzorov AA. Protein Rotational Dynamics in Aligned Lipid Membranes Probed by Anisotropic T 1ρ NMR Relaxation. Biophys J 2018; 114:392-399. [PMID: 29401436 DOI: 10.1016/j.bpj.2017.11.3740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/07/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
A membrane-bound form of Pf1 coat protein reconstituted in magnetically aligned DMPC/DHPC bicelles was used as a molecular probe to quantify for the viscosity of the lipid membrane interior by measuring the uniaxial rotational diffusion coefficient of the protein. Orientationally dependent 15N NMR relaxation times in the rotating frame, or T1ρ, were determined by fitting individually the decay of the resolved NMR peaks corresponding to the transmembrane helix of Pf1 coat protein as a function of the spin-lock time incorporated into the 2D SAMPI4 pulse sequence. The T1ρ relaxation mechanism was modeled by uniaxial rotational diffusion on a cone, which yields a linear correlation with respect to the bond factor sin4θB, where θB is the angle that the NH bond forms with respect to the axis of rotation. Importantly, the bond factors can be independently measured from the dipolar couplings in the separated local-field SAMPI4 spectra. From this dependence, the value of the diffusion coefficient D|| = 8.0 × 105 s-1 was inferred from linear regression of the experimental T1ρ data even without any spectroscopic assignment. Alternatively, a close value of D|| = 7.7 × 105 s-1 was obtained by fitting the T1ρ relaxation data for the assigned NMR peaks of the transmembrane domain of Pf1 to a wavelike pattern as a function of residue number. The method illustrates the use of single-helix transmembrane peptides as molecular probes to assess the dynamic parameters of biological membranes by NMR relaxation in oriented lipid bilayers.
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Affiliation(s)
- Emmanuel O Awosanya
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina.
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Santhosh Kumar Reddy Y, Lobo NP, Narasimhaswamy T. Effect of alkyl chain and linking units on mesophase transitions and molecular order of rod-like thiophene mesogens:13C NMR investigation. NEW J CHEM 2018. [DOI: 10.1039/c7nj03525j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This study provides insight into the influence of alkyl chains and linking units on the mesophase properties of thiophene-based mesogens and on the orientational constraints of the core and terminal alkyl chain.
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Affiliation(s)
| | - Nitin P. Lobo
- Inorganic & Physical Chemistry
- CSIR-Central Leather Research Institute
- Chennai 600020
- India
| | - T. Narasimhaswamy
- Polymer Science & Technology
- CSIR-Central Leather Research Institute
- Chennai 600020
- India
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Ridone P, Grage SL, Patkunarajah A, Battle AR, Ulrich AS, Martinac B. "Force-from-lipids" gating of mechanosensitive channels modulated by PUFAs. J Mech Behav Biomed Mater 2017; 79:158-167. [PMID: 29304430 DOI: 10.1016/j.jmbbm.2017.12.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/15/2022]
Abstract
The level of fatty acid saturation in phospholipids is a crucial determinant of the biophysical properties of the lipid bilayer. Integral membrane proteins are sensitive to changes of their bilayer environment such that their activities and localization can be profoundly affected. When incorporated into phospholipids of mammalian cells, poly-unsaturated fatty acids (PUFAs) determine the mechanical properties of the bilayer thereby affecting several membrane-associated functions such as endo- and exo-cytosis and ion channel/membrane receptor signalling cascades. In order to understand how membrane tension is propagated through poly-unsaturated bilayers, we characterized the effect of lipid saturation on liposome reconstituted MscS and MscL, the two bacterial mechanosensitive ion channels that have for many years served as models of ion- channel-mediated mechanotransduction. The combination of NMR and patch clamp experiments in this study demonstrate that bilayer thinning is the main responsible factor for the modulation of the MscL threshold of activation while a change in transbilayer pressure profile is indicated as the main factor behind the observed modulation of the MscS kinetics. Together, our data offer a novel insight into how the structural shape differences between the two types of mechanosensitive channels determine their differential modulation by poly-unsaturated phospholipids and thus lay the foundation for future functional studies of eukaryotic ion channels involved in the physiology of mechanosensory transduction processes in mammalian cells. SUMMARY Mechanosensitive channels MscL and MscS are differentially modulated by poly-unsaturated fatty acids in lipid bilayers. MscL becomes sensitized because of increased hydrophobic mismatch while MscS open state is stabilized due to changes in the bilayer lateral pressure profile determined by NMR.
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Affiliation(s)
- Pietro Ridone
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Stephan L Grage
- Institute for Biological Interfaces IBG-2, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrutha Patkunarajah
- School of Medical Sciences, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Andrew R Battle
- Translational Research Institute (TRI) and Institute of Health and Biomedical Innovation (IHBI), School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
| | - Anne S Ulrich
- Institute for Biological Interfaces IBG-2, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia.
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Gan Z, Hung I, Wang X, Paulino J, Wu G, Litvak IM, Gor'kov PL, Brey WW, Lendi P, Schiano JL, Bird MD, Dixon IR, Toth J, Boebinger GS, Cross TA. NMR spectroscopy up to 35.2T using a series-connected hybrid magnet. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 284:125-136. [PMID: 28890288 PMCID: PMC5675800 DOI: 10.1016/j.jmr.2017.08.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 05/05/2023]
Abstract
The National High Magnetic Field Laboratory has brought to field a Series-Connected Hybrid magnet for NMR spectroscopy. As a DC powered magnet it can be operated at fields up to 36.1T. The series connection between a superconducting outsert and a resistive insert dramatically minimizes the high frequency fluctuations of the magnetic field typically observed in purely resistive magnets. Current-density-grading among various resistive coils was used for improved field homogeneity. The 48mm magnet bore and 42mm outer diameter of the probes leaves limited space for conventional shims and consequently a combination of resistive and ferromagnetic shims are used. Field maps corrected for field instabilities were obtained and shimming achieved better than 1ppm homogeneity over a cylindrical volume of 1cm diameter and height. The magnetic field is regulated within 0.2ppm using an external 7Li lock sample doped with paramagnetic MnCl2. The improved field homogeneity and field regulation using a modified AVANCE NEO console enables NMR spectroscopy at 1H frequencies of 1.0, 1.2 and 1.5GHz. NMR at 1.5GHz reflects a 50% increase in field strength above the highest superconducting magnets currently available. Three NMR probes have been constructed each equipped with an external lock rf coil for field regulation. Initial NMR results obtained from the SCH magnet using these probes illustrate the very exciting potential of ultra-high magnetic fields.
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Affiliation(s)
- Zhehong Gan
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Ivan Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Joana Paulino
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Ilya M Litvak
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - William W Brey
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Pietro Lendi
- Bruker BioSpin AG, 26, Industriestrasse Fällanden, 8117, Switzerland
| | - Jeffrey L Schiano
- School of Electrical Engineering and Computer Science, Penn State University, University Park, PA 16802, United States
| | - Mark D Bird
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Iain R Dixon
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Jack Toth
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Gregory S Boebinger
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States; Department of Physics, Florida State University, Tallahassee, FL 32306, United States
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States.
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40
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Tzitzoglaki C, Wright A, Freudenberger K, Hoffmann A, Tietjen I, Stylianakis I, Kolarov F, Fedida D, Schmidtke M, Gauglitz G, Cross TA, Kolocouris A. Binding and Proton Blockage by Amantadine Variants of the Influenza M2WT and M2S31N Explained. J Med Chem 2017; 60:1716-1733. [DOI: 10.1021/acs.jmedchem.6b01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christina Tzitzoglaki
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Anna Wright
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Anja Hoffmann
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Ian Tietjen
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ioannis Stylianakis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - David Fedida
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michaela Schmidtke
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Timothy A. Cross
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
- Department
of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
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41
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Koroloff SN, Nevzorov AA. Selective excitation for spectral editing and assignment in separated local field experiments of oriented membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 274:7-12. [PMID: 27835748 DOI: 10.1016/j.jmr.2016.10.013] [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: 08/27/2016] [Revised: 10/18/2016] [Accepted: 10/23/2016] [Indexed: 06/06/2023]
Abstract
Spectroscopic assignment of NMR spectra for oriented uniformly labeled membrane proteins embedded in their native-like bilayer environment is essential for their structure determination. However, sequence-specific assignment in oriented-sample (OS) NMR is often complicated by insufficient resolution and spectral crowding. Therefore, the assignment process is usually done by a laborious and expensive "shotgun" method involving multiple selective labeling of amino acid residues. Presented here is a strategy to overcome poor spectral resolution in crowded regions of 2D spectra by selecting resolved "seed" residues via soft Gaussian pulses inserted into spin-exchange separated local-field experiments. The Gaussian pulse places the selected polarization along the z-axis while dephasing the other signals before the evolution of the 1H-15N dipolar couplings. The transfer of magnetization is accomplished via mismatched Hartmann-Hahn conditions to the nearest-neighbor peaks via the proton bath. By optimizing the length and amplitude of the Gaussian pulse, one can also achieve a phase inversion of the closest peaks, thus providing an additional phase contrast. From the superposition of the selective spin-exchanged SAMPI4 onto the fully excited SAMPI4 spectrum, the 15N sites that are directly adjacent to the selectively excited residues can be easily identified, thereby providing a straightforward method for initiating the assignment process in oriented membrane proteins.
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Affiliation(s)
- Sophie N Koroloff
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, USA
| | - Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, USA.
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42
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Mote KR, Agarwal V, Madhu PK. Five decades of homonuclear dipolar decoupling in solid-state NMR: Status and outlook. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:1-39. [PMID: 27888838 DOI: 10.1016/j.pnmrs.2016.08.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/11/2016] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
It has been slightly more than fifty years since the first homonuclear spin decoupling scheme, Lee-Goldburg decoupling, was proposed for removing homonuclear dipolar interactions in solid-state nuclear magnetic resonance. A family of such schemes has made observation of high-resolution NMR spectra of abundant spins possible in various applications in solid state. This review outlines the strategies used in this field and the future prospects of homonuclear spin decoupling in solid-state NMR.
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Affiliation(s)
- Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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43
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Nishiyama Y. Fast magic-angle sample spinning solid-state NMR at 60-100kHz for natural abundance samples. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 78:24-36. [PMID: 27400153 DOI: 10.1016/j.ssnmr.2016.06.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
In spite of tremendous progress made in pulse sequence designs and sophisticated hardware developments, methods to improve sensitivity and resolution in solid-state NMR (ssNMR) are still emerging. The rate at which sample is spun at magic angle determines the extent to which sensitivity and resolution of NMR spectra are improved. To this end, the prime objective of this article is to give a comprehensive theoretical and experimental framework of fast magic angle spinning (MAS) technique. The engineering design of fast MAS rotors based on spinning rate, sample volume, and sensitivity is presented in detail. Besides, the benefits of fast MAS citing the recent progress in methodology, especially for natural abundance samples are also highlighted. The effect of the MAS rate on (1)H resolution, which is a key to the success of the (1)H inverse detection methods, is described by a simple mathematical factor named as the homogeneity factor k. A comparison between various (1)H inverse detection methods is also presented. Moreover, methods to reduce the number of spinning sidebands (SSBs) for the systems with huge anisotropies in combination with (1)H inverse detection at fast MAS are discussed.
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Affiliation(s)
- Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 186-8558, Japan.
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44
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Reddy KR, Lobo NP, Narasimhaswamy T. Molecular Order and Mesophase Investigation of Thiophene-Based Forked Mesogens. J Phys Chem B 2016; 120:6897-909. [PMID: 27294350 DOI: 10.1021/acs.jpcb.6b05827] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiophene-based rodlike molecules constructed from a three phenyl ring core and terminal dialkoxy chains recognized as forked mesogens are synthesized, and their mesophase properties as well as the molecular order are investigated. The synthesized forked mesogens would serve as model compounds for tetracatenar or biforked mesogens. On the basis of the position of the thiophene link with the rest of the core, 2-substituted and 3-substituted mesogens are realized in which the length of the terminal alkoxy chains is varied. The mesophase properties are evaluated using a hot-stage polarizing microscope and differential scanning calorimetry. For both homologues, the appearance of either nematic phase alone or in conjunction with smectic C phase is noticed depending on the length of the terminal alkoxy chains. The existence of layer ordering characteristic of the smectic C phase is confirmed for a representative mesogen using variable-temperature powder X-ray diffraction. High-resolution solid-state (13)C NMR measurements of C12 homologues of the two series reveal orientational order parameters of all rings of the core as well as terminal chains in the liquid crystalline phase. For both homologues, because of the asymmetry of ring I, the order parameter value is higher in contrast to ring II, ring III, and the thiophene ring. The chemical shifts and (13)C-(1)H dipolar couplings of OCH2 carbons of the terminal dodecyloxy chains provide contrasting conformations, reflecting the orientational constraints. Furthermore, the investigations also reveal that the mesophase range and the tendency for layer ordering are higher for 3-substituted mesogens compared to 2-substituted homologues.
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Affiliation(s)
- K Rajasekhar Reddy
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - Nitin P Lobo
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - T Narasimhaswamy
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
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45
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Windisch D, Ziegler C, Grage SL, Bürck J, Zeitler M, Gor'kov PL, Ulrich AS. Hydrophobic Mismatch Drives the Interaction of E5 with the Transmembrane Segment of PDGF Receptor. Biophys J 2016; 109:737-49. [PMID: 26287626 PMCID: PMC4547410 DOI: 10.1016/j.bpj.2015.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/05/2023] Open
Abstract
The oncogenic E5 protein from bovine papillomavirus is a short (44 amino acids long) integral membrane protein that forms homodimers. It activates platelet-derived growth factor receptor (PDGFR) β in a ligand-independent manner by transmembrane helix-helix interactions. The nature of this recognition event remains elusive, as numerous mutations are tolerated in the E5 transmembrane segment, with the exception of one hydrogen-bonding residue. Here, we examined the conformation, stability, and alignment of the E5 protein in fluid lipid membranes of substantially varying bilayer thickness, in both the absence and presence of the PDGFR transmembrane segment. Quantitative synchrotron radiation circular dichroism analysis revealed a very long transmembrane helix for E5 of ∼26 amino acids. Oriented circular dichroism and solid-state 15N-NMR showed that the alignment and stability of this unusually long segment depend critically on the membrane thickness. When reconstituted alone in exceptionally thick DNPC lipid bilayers, the E5 helix was found to be inserted almost upright. In moderately thick bilayers (DErPC and DEiPC), it started to tilt and became slightly deformed, and finally it became aggregated in conventional DOPC, POPC, and DMPC membranes due to hydrophobic mismatch. On the other hand, when E5 was co-reconstituted with the transmembrane segment of PDGFR, it was able to tolerate even the most pronounced mismatch and was stabilized by binding to the receptor, which has the same hydrophobic length. As E5 is known to activate PDGFR within the thin membranes of the Golgi compartment, we suggest that the intrinsic hydrophobic mismatch of these two interaction partners drives them together. They seem to recognize each other by forming a closely packed bundle of mutually aligned transmembrane helices, which is further stabilized by a specific pair of hydrogen-bonding residues.
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Affiliation(s)
- Dirk Windisch
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Colin Ziegler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcel Zeitler
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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46
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47
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Kharkov BB, Chizhik VI, Dvinskikh SV. Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids. J Chem Phys 2016; 144:034201. [DOI: 10.1063/1.4939798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Jeong JH, Kim JS, Choi SS, Kim Y. NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs. Biophys J 2016; 110:423-430. [PMID: 26789765 PMCID: PMC4724650 DOI: 10.1016/j.bpj.2015.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023] Open
Abstract
Lactophoricin (LPcin), a component of proteose peptone (113-135) isolated from bovine milk, is a cationic amphipathic antimicrobial peptide consisting of 23 amino acids. We designed a series of N- or C-terminal truncated variants, mutated analogs, and truncated mutated analogs using peptide-engineering techniques. Then, we selected three LPcin analogs of LPcin-C8 (LPcin-YK1), LPcin-T2WT6W (LPcin-YK2), and LPcin-T2WT6W-C8 (LPcin-YK3), which may have better antimicrobial activities than LPcin, and successfully expressed them in E. coli with high yield. We elucidated the 3D structures and topologies of the three LPcin analogs in membrane environments by conducting NMR structural studies. We investigated the purity of the LPcin analogs and the α-helical secondary structures by performing (1)H-(15)N 2D HSQC and HMQC-NOESY liquid-state NMR spectroscopy using protein-containing micelle samples. We measured the 3D structures and tilt angles in membranes by conducting (15)N 1D and 2D (1)H-(15)N SAMMY type solid-state NMR spectroscopy with an 800 MHz in-house-built (1)H-(15)N double-resonance solid-state NMR probe with a strip-shield coil, using protein-containing large bicelle samples aligned and confirmed by molecular-dynamics simulations. The three LPcin analogs were found to be curved α-helical structures, with tilt angles of 55-75° for normal membrane bilayers, and their enhanced activities may be correlated with these topologies.
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Affiliation(s)
- Ji-Ho Jeong
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Ji-Sun Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Sung-Sub Choi
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Yongae Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yong-In, Korea; Protein Research Center for Bio-Industry, Hankuk University of Foreign Studies, Yong-In, Korea.
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49
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Veeraprakash B, Lobo NP, Narasimhaswamy T. (13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens. J Phys Chem B 2015; 119:15063-74. [PMID: 26551439 DOI: 10.1021/acs.jpcb.5b09859] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate.
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Affiliation(s)
- B Veeraprakash
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - Nitin P Lobo
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
| | - T Narasimhaswamy
- Polymer Laboratory and ‡Chemical Physics Laboratory, CSIR-Central Leather Research Institute , Adyar, Chennai 600020, India
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50
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Hirschinger J, Raya J. Analytical descriptions of cross-polarisation dynamics: relaxing the secular approximations. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1008596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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