1
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Doerner B, Della Sala F, Wang S, Webb SJ. Reaction, Recognition, Relay: Anhydride Hydrolysis Reported by Conformationally Responsive Fluorinated Foldamers in Micelles. Angew Chem Int Ed Engl 2024:e202405924. [PMID: 38703400 DOI: 10.1002/anie.202405924] [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: 03/27/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural membrane receptors are proteins that can report on changes in the concentration of external chemical messengers. Messenger binding to a receptor produces conformational changes that are relayed through the membrane into the cell; this information allows cells to adapt to changes in their environment. Artificial membrane receptors (R)-1 and (S)-1 are helical α-aminoisobutyric acid (Aib) foldamers that replicate key parts of this information relay. Solution-phase 19F NMR spectroscopy of zinc(II)-capped receptor 1, either in organic solvent or in membrane-mimetic micelles, showed messenger binding produced an enrichment of either left- or right-handed screw-sense; the chirality of the bound messenger was relayed to the other receptor terminus. Furthermore, in situ production of a chemical messenger in the external aqueous environment could be detected in real-time by a racemic mixture of receptor 1 in micelles. The hydrolysis of insoluble anhydrides produced carboxylate in the aqueous phase, which bound to the receptors and gave a distinct 19F NMR output from inside the hydrophobic region of the micelles.
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Affiliation(s)
- Benedicte Doerner
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Flavio Della Sala
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Siyuan Wang
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Simon J Webb
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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2
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Moreland RT, Zhang S, Barreira SN, Ryan JF, Baxevanis AD. An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi. Proteomics 2024:e2300397. [PMID: 38329168 DOI: 10.1002/pmic.202300397] [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: 10/19/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health.
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Affiliation(s)
- R Travis Moreland
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Suiyuan Zhang
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sofia N Barreira
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Andreas D Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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3
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Boulos I, Jabbour J, Khoury S, Mikhael N, Tishkova V, Candoni N, Ghadieh HE, Veesler S, Bassim Y, Azar S, Harb F. Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics. Molecules 2023; 28:7176. [PMID: 37894653 PMCID: PMC10608922 DOI: 10.3390/molecules28207176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.
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Affiliation(s)
- Imad Boulos
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Joy Jabbour
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Serena Khoury
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Nehme Mikhael
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Victoria Tishkova
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Nadine Candoni
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Stéphane Veesler
- CNRS, CINaM (Centre Interdisciplinaire de Nanosciences de Marseille), Campus de Luminy, Case 913, Aix-Marseille University, CEDEX 09, F-13288 Marseille, France; (V.T.); (N.C.); (S.V.)
| | - Youssef Bassim
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
| | - Frédéric Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli P.O. Box 100, Lebanon; (I.B.); (J.J.); (S.K.); (N.M.); (H.E.G.); (Y.B.); (S.A.)
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [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: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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6
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Nhieu J, Miller MC, Lerdall TA, Mayo KH, Wei LN. Molecular basis for cellular retinoic acid-binding protein 1 in modulating CaMKII activation. Front Mol Biosci 2023; 10:1268843. [PMID: 37822422 PMCID: PMC10562560 DOI: 10.3389/fmolb.2023.1268843] [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: 07/28/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction: Cellular retinoic acid (RA)-binding protein 1 (CRABP1) is a highly conserved protein comprised of an anti-parallel, beta-barrel, and a helix-turn-helix segment outside this barrel. Functionally, CRABP1 is thought to bind and sequester cytosolic RA. Recently, CRABP1 has been established as a major mediator of rapid, non-genomic activity of RA in the cytosol, referred to as "non-canonical" activity. Previously, we have reported that CRABP1 interacts with and dampens the activation of calcium-calmodulin (Ca2+-CaM)-dependent kinase 2 (CaMKII), a major effector of Ca2+ signaling. Through biophysical, molecular, and cellular assays, we, herein, elucidate the molecular and structural mechanisms underlying the action of CRABP1 in dampening CaMKII activation. Results: We identify an interaction surface on CRABP1 for CaMKII binding, located on the beta-sheet surface of the barrel, and an allosteric region within the helix segment outside the barrel, where both are important for interacting with CaMKII. Molecular studies reveal that CRABP1 preferentially associates with the inactive form of CaMKII, thereby dampening CaMKII activation. Alanine mutagenesis of residues implicated in the CaMKII interaction results in either a loss of this preference or a shift of CRABP1 from associating with the inactive CaMKII to associating with the active CaMKII, which corresponds to changes in CRABP1's effect in modulating CaMKII activation. Conclusions: This is the first study to elucidate the molecular and structural basis for CRABP1's function in modulating CaMKII activation. These results further shed insights into CRABP1's functional involvement in multiple signaling pathways, as well as its extremely high sequence conservation across species and over evolution.
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Affiliation(s)
- Jennifer Nhieu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Michelle C. Miller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Thomas A. Lerdall
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Kevin H. Mayo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Li-Na Wei
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
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Cho Y, Ryu H, Lim G, Nam S, Lee J. Improving Geometric Validation Metrics and Ensuring Consistency with Experimental Data through TrioSA: An NMR Refinement Protocol. Int J Mol Sci 2023; 24:13337. [PMID: 37686144 PMCID: PMC10487420 DOI: 10.3390/ijms241713337] [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: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Protein model refinement a the crucial step in improving the quality of a predicted protein model. This study presents an NMR refinement protocol called TrioSA (torsion-angle and implicit-solvation-optimized simulated annealing) that improves the accuracy of backbone/side-chain conformations and the overall structural quality of proteins. TrioSA was applied to a subset of 3752 solution NMR protein structures accompanied by experimental NMR data: distance and dihedral angle restraints. We compared the initial NMR structures with the TrioSA-refined structures and found significant improvements in structural quality. In particular, we observed a reduction in both the maximum and number of NOE (nuclear Overhauser effect) violations, indicating better agreement with experimental NMR data. TrioSA improved geometric validation metrics of NMR protein structure, including backbone accuracy and the secondary structure ratio. We evaluated the contribution of each refinement element and found that the torsional angle potential played a significant role in improving the geometric validation metrics. In addition, we investigated protein-ligand docking to determine if TrioSA can improve biological outcomes. TrioSA structures exhibited better binding prediction compared to the initial NMR structures. This study suggests that further development and research in computational refinement methods could improve biomolecular NMR structural determination.
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Affiliation(s)
- Youngbeom Cho
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea;
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (H.R.); (G.L.)
| | - Hyojung Ryu
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (H.R.); (G.L.)
| | - Gyutae Lim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (H.R.); (G.L.)
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Republic of Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea
| | - Jinhyuk Lee
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea;
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (H.R.); (G.L.)
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8
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Osetrina DA, Kusova AM, Bikmullin AG, Klochkova EA, Yulmetov AR, Semenova EA, Mukhametzyanov TA, Usachev KS, Klochkov VV, Blokhin DS. Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation. Int J Mol Sci 2023; 24:ijms24108949. [PMID: 37240295 DOI: 10.3390/ijms24108949] [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: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.
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Affiliation(s)
- Daria A Osetrina
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Aleksandra M Kusova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan 420111, Russia
| | - Aydar G Bikmullin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Evelina A Klochkova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Aydar R Yulmetov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Evgenia A Semenova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Timur A Mukhametzyanov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Konstantin S Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan 420111, Russia
| | - Vladimir V Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Dmitriy S Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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10
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Krishnarjuna B, Marte J, Ravula T, Ramamoorthy A. Enhancing the stability and homogeneity of non-ionic polymer nanodiscs by tuning electrostatic interactions. J Colloid Interface Sci 2023; 634:887-896. [PMID: 36566634 PMCID: PMC10838601 DOI: 10.1016/j.jcis.2022.12.112] [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: 08/26/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The nanodisc technology is increasingly used for structural studies on membrane proteins and drug delivery. The development of synthetic polymer nanodiscs and the recent discovery of non-ionic inulin-based polymers have significantly broadened the scope of nanodiscs. While the lipid exchange and size flexibility properties of the self-assembled polymer-based nanodiscs are valuable for various applications, the non-ionic polymer nanodiscs are remarkably unique in that they enable the reconstitution of any protein, protein-protein complexes, or drugs irrespective of their charge. However, the non-ionic nature of the belt could influence the stability and size homogeneity of inulin-based polymer nanodiscs. In this study, we investigate the size stability and homogeneity of nanodiscs formed by non-ionic lipid-solubilizing polymers using different biophysical methods. Polymer nanodiscs containing zwitterionic DMPC and different ratios of DMPC:DMPG lipids were made using anionic SMA-EA or non-ionic pentyl-inulin polymers. Non-ionic polymer nanodiscs made using zwitterionic DMPC lipids produced a very broad elution profile on SEC due to their instability in the column, thus affecting sample monodispersity which was confirmed by DLS experiments that showed multiple peaks. However, the inclusion of anionic DMPG lipids improved the stability as observed from SEC and DLS profiles, which was further confirmed by TEM images. Whereas, anionic SMA-EA-based DMPC-nanodiscs showed excellent stability and size homogeneity when solubilizing zwitterionic lipids. The stability of DMPC:DMPG non-ionic polymer nanodiscs is attributed to the inter-nanodisc repulsion by the anionic-DMPG that prevents the uncontrolled collision and fusion of nanodiscs. Thus, the reported results demonstrate the use of electrostatic interactions to tune the solubility, stability, and size homogeneity of non-ionic polymer nanodiscs which are important features for enabling functional and atomic-resolution structural studies of membrane proteins, other lipid-binding molecules, and water-soluble biomolecules including cytosolic proteins, nucleic acids and metabolites.
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Affiliation(s)
- Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Joseph Marte
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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11
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Liu H, Gong Z, Zhao Y. Methods and Applications in Proteins and RNAs. Life (Basel) 2023; 13:life13030672. [PMID: 36983828 PMCID: PMC10059988 DOI: 10.3390/life13030672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Proteins and RNAs are primary biomolecules that are involved in most biological processes [...]
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Affiliation(s)
- Haoquan Liu
- Department of Physics, Institute of Biophysics, Central China Normal University, Wuhan 430079, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- Correspondence: (Z.G.); (Y.Z.)
| | - Yunjie Zhao
- Department of Physics, Institute of Biophysics, Central China Normal University, Wuhan 430079, China
- Correspondence: (Z.G.); (Y.Z.)
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Skeens E, Lisi GP. Analysis of coordinated NMR chemical shifts to map allosteric regulatory networks in proteins. Methods 2023; 209:40-47. [PMID: 36535575 PMCID: PMC10173519 DOI: 10.1016/j.ymeth.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The exquisite sensitivity of the NMR chemical shift to local environment makes it an ideal probe to assess atomic level perturbations in proteins of all sizes and structural compositions. Recent advances in solution and solid-state NMR spectroscopy of biomolecules have leveraged the chemical shift to report on short- and long-range couplings between individual amino acids to establish "networks" of residues that form the basis of allosteric pathways that transmit chemical signals through the protein matrix to induce functional responses. The simple premise that thermodynamically and functionally coupled regions of a protein (i.e. active and allosteric sites) should be reciprocally sensitive to structural or dynamic perturbations has enabled NMR spectroscopy, the premier method for molecular resolution of protein structural fluctuations, to occupy a place at the forefront of investigations into protein allostery. Here, we detail several key methods of NMR chemical shift analysis to extract mechanistic information about long-range chemical signaling in a protein, focusing on practical methodological aspects and the circumstances under which a given approach would be relevant. We also detail some of the experimental considerations that should be made when applying these methods to specific protein systems.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, United States
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, United States.
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Ma J, Pathirana C, Liu DQ, Miller SA. NMR spectroscopy as a characterization tool enabling biologics formulation development. J Pharm Biomed Anal 2023; 223:115110. [DOI: 10.1016/j.jpba.2022.115110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
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Deciphering Structure-Function Relationship Unveils Salt-Resistant Mode of Action of a Potent MRSA-Inhibiting Antimicrobial Peptide, RR14. J Bacteriol 2022; 204:e0031222. [PMID: 36377870 PMCID: PMC9765028 DOI: 10.1128/jb.00312-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant (MDR) bacteria lead to considerable morbidity and mortality, threatening public health worldwide. In particular, infections of methicillin-resistant Staphylococcus aureus (MRSA) in hospital and community settings are becoming a serious health problem. Antimicrobial peptides (AMPs) are considered novel therapeutic targets against MDR bacteria. However, salt sensitivity reduces the bactericidal potency of AMPs, posing a major obstacle for their development as antibiotics. Thus, the design and development of salt-insensitive peptides with potent antibacterial activity is imperative. Here, we employed biochemical and biophysical examinations coupled with molecular modeling to systematically investigate the structure-function relationship of a novel salt-insensitive AMP, RR14. The secondary structure of RR14 was characterized as an apparent α-helix, a structure that confers strong membrane-permeabilizing ability targeting bacterial-mimetic membranes. Additionally, the bioactive structure of RR14 was determined in complex with dodecylphosphocholine (DPC) micelles, where it possesses a central α-helical segment comprising residues R4 to K13 (R4-K13). RR14 was observed to orient itself into the DPC micelle with its N terminus and the α-helical segment (I5-R10) buried inside the micelles, which is essential for membrane permeabilization and bactericidal activity. Moreover, the specific and featured arrangement of positively charged residues of RR14 on its amphipathic helical conformation has great potential to render its strong salt resistance ability. Our study explored the structure-function relationship of RR14, explaining its possible mode of action against MRSA and other microbes. The insights obtained are of great applicability for the development of new antibacterial agents. IMPORTANCE Many antimicrobial peptides have been observed to become inactive in the presence of high salt concentrations. To further develop new and novel AMPs with potent bactericidal activity and salt insensitivity, understanding the structural basis for salt resistance is important. Here, we employed biochemical and biophysical examinations to systematically investigate the structure-function relationship of a novel salt-insensitive AMP, RR14. RR14 was observed to orient itself into DPC micelles with the N terminus and the α-helical segment (I5-R10) buried inside the micelles, which is essential for membrane permeabilization and bactericidal activity. Moreover, the specific and featured arrangement of cationic residues of RR14 on its amphipathic helical conformation renders its strong salt resistance ability. The insights obtained are of great applicability for developing new antibacterial agents.
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Keating PM, Pennington HN, Collins SD, Lee J. Purification and characterization of the Lassa virus transmembrane domain. Biochem Biophys Rep 2022; 33:101409. [PMID: 36583076 PMCID: PMC9792740 DOI: 10.1016/j.bbrep.2022.101409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Lassa virus (LASV) is the most prevalent arenavirus afflicting humans and has high potential to become a threat to global public health. The transmembrane domain (TM) of the LASV glycoprotein complex forms critical interactions with the LASV stable signal peptide that are important for the maturation and fusion activity of the virus. A further study of the structure-based molecular mechanisms is required to understand the role of the TM in the lifecycle of LASV in greater detail. However, it is challenging to obtain the TM in high quantity and purity due to its hydrophobic nature which results in solubility issues that makes it prone to aggregation in typical buffer systems. Here, we designed a purification and detergent screen protocol for the highly insoluble TM to enhance the yield and purity for structural studies. Based on the detergents tested, the TM had the highest incorporation in LMPG. Circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy were utilized to confirm the best detergent system for structural studies. Through CD spectroscopy, we were able to characterize the secondary structure of the TM as largely alpha-helical, while NMR spectroscopy showed a well-structured and stable TM in LMPG. From these results, LMPG was determined to be the optimal detergent for further structural studies.
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Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods. Antibodies (Basel) 2022; 11:antib11040071. [PMID: 36412837 PMCID: PMC9680451 DOI: 10.3390/antib11040071] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody-antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.
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17
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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Zhai G, Zhang Z, Dong C. Mutagenesis and functional analysis of SotB: A multidrug transporter of the major facilitator superfamily from Escherichia coli. Front Microbiol 2022; 13:1024639. [PMID: 36386622 PMCID: PMC9650428 DOI: 10.3389/fmicb.2022.1024639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 10/28/2023] Open
Abstract
Dysfunction of the major facilitator superfamily multidrug (MFS Mdr) transporters can lead to a variety of serious diseases in human. In bacteria, such membrane proteins are often associated with bacterial resistance. However, as one of the MFS Mdr transporters, the physiological function of SotB from Escherichia coli is poorly understood to date. To better understand the function and mechanism of SotB, a systematic study on this MFS Mdr transporter was carried out. In this study, SotB was found to directly efflux L-arabinose in E. coli by overexpressing sotB gene combined with cell based radiotracer uptake assay. Besides, the surface plasmon resonance (SPR) studies, the L-arabinose inhibition assays, together with precise molecular docking analysis, reveal the following: (i) the functional importance of E29 (protonation), H115/N343 (substrate recognition), and W119/S339 (substrate efflux) in the SotB mediated export of L-arabinose, and (ii) for the first time find that D-xylose, an isomer of L-arabinose, likely hinders the binding of L-arabinose with SotB as a competitive inhibitor. Finally, by analyzing the structure of SotB2 (shares 62.8% sequence similarity with SotB) predicted by AlphaFold 2, the different molecular mechanism of substrate recognition between SotB and SotB2 is explained. To our knowledge, this is the first systematic study of MFS Mdr transporter SotB. The structural information, together with the biochemical inspections in this study, provide a valuable framework for further deciphering the functional mechanisms of the physiologically important L-arabinose transporter SotB and its family.
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Affiliation(s)
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changjiang Dong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 2022; 12:1425. [PMID: 36291635 PMCID: PMC9599165 DOI: 10.3390/biom12101425] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dennis W. Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196448. [PMID: 36234985 PMCID: PMC9573641 DOI: 10.3390/molecules27196448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.
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21
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Advanced Research on Structure–Function Relationships of Membrane Proteins. MEMBRANES 2022; 12:membranes12070672. [PMID: 35877875 PMCID: PMC9320922 DOI: 10.3390/membranes12070672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
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22
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Kusova A, Abramova M, Skvortsova P, Yulmetov A, Mukhametzyanov T, Klochkov V, Blokhin D. Structure of amyloidogenic PAP(85-120) peptide by high-resolution NMR spectroscopy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [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: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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Zhang C, Wu J, Chen Q, Tan H, Huang F, Guo J, Zhang X, Yu H, Shi W. Allosteric binding on nuclear receptors: Insights on screening of non-competitive endocrine-disrupting chemicals. ENVIRONMENT INTERNATIONAL 2022; 159:107009. [PMID: 34883459 DOI: 10.1016/j.envint.2021.107009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) can compete with endogenous hormones and bind to the orthosteric site of nuclear receptors (NRs), affecting normal endocrine system function and causing severe symptoms. Recently, a series of pharmaceuticals and personal care products (PPCPs) have been discovered to bind to the allosteric sites of NRs and induce similar effects. However, it remains unclear how diverse EDCs work in this new way. Therefore, we have systematically summarized the allosteric sites and underlying mechanisms based on existing studies, mainly regarding drugs belonging to the PPCP class. Advanced methods, classified as structural biology, biochemistry and computational simulation, together with their advantages and hurdles for allosteric site recognition and mechanism insight have also been described. Furthermore, we have highlighted two available strategies for virtual screening of numerous EDCs, relying on the structural features of allosteric sites and lead compounds, respectively. We aim to provide reliable theoretical and technical support for a broader view of various allosteric interactions between EDCs and NRs, and to drive high-throughput and accurate screening of potential EDCs with non-competitive effects.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jinqiu Wu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Qinchang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Haoyue Tan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Fuyan Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jing Guo
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China.
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NMR spectroscopy of lipidic cubic phases. Biophys Rev 2021; 14:67-74. [DOI: 10.1007/s12551-021-00900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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29
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Shepherd DC, Dalvi S, Ghosal D. From cells to atoms: Cryo-EM as an essential tool to investigate pathogen biology, host-pathogen interaction, and drug discovery. Mol Microbiol 2021; 117:610-617. [PMID: 34592048 DOI: 10.1111/mmi.14820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/18/2023]
Abstract
Electron cryo-microscopy (cryo-EM) has lately emerged as a powerful method in structural biology and cell biology. While cryo-EM single-particle analysis (SPA) is now routinely delivering structures of purified proteins and protein complexes at near-atomic resolution, the use of electron cryo-tomography (cryo-ET), together with subtomogram averaging, is allowing visualization of macromolecular complexes in their native cellular environment, at unprecedented resolution. The unique ability of cryo-EM to provide information at many spatial resolution scales from ångströms to microns makes it an invaluable tool that bridges the classic "resolution-gap" between structural biology and cell biology domains. Like in many other fields of biology, in recent years, cryo-EM has revolutionized our understanding of pathogen biology, host-pathogen interaction and has made significant strides toward structure-based drug discovery. In a very recent example, during the ongoing coronavirus disease (COVID-19) pandemic, the structure of the stabilized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein was deciphered by SPA. This led to the development of multiple vaccines. Alongside, cryo-ET provided key insights into the structure of the native virion, mechanism of its entry, replication, and budding; demonstrating the unrivaled power of cryo-EM in investigating pathogen biology, host-pathogen interaction, and drug discovery. In this review, we showcase a few examples of how different imaging modalities within cryo-EM have enabled the study of microbiology and host-pathogen interaction.
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Affiliation(s)
- Doulin C Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Somavally Dalvi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
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30
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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31
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Bialas F, Becker CFW. Biomimetic Silica Encapsulation of Lipid Nanodiscs and β-Sheet-Stabilized Diacylglycerol Kinase. Bioconjug Chem 2021; 32:1742-1752. [PMID: 34288667 PMCID: PMC8382255 DOI: 10.1021/acs.bioconjchem.1c00260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/08/2021] [Indexed: 12/21/2022]
Abstract
Integral membrane proteins (IMPs) comprise highly important classes of proteins such as transporters, sensors, and channels, but their investigation and biotechnological application are complicated by the difficulty to stabilize them in solution. We set out to develop a biomimetic procedure to encapsulate functional integral membrane proteins in silica to facilitate their handling under otherwise detrimental conditions and thereby extend their applicability. To this end, we designed and expressed new fusion constructs of the membrane scaffold protein MSP with silica-precipitating peptides based on the R5 sequence from the diatom Cylindrotheca fusiformis. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) revealed that membrane lipid nanodiscs surrounded by our MSP variants fused to an R5 peptide, so-called nanodiscs, were formed. Exposing them to silicic acid led to silica-encapsulated nanodiscs, a new material for stabilizing membrane structures and a first step toward incorporating membrane proteins in such structures. In an alternative approach, four fusion constructs based on the amphiphilic β-sheet peptide BP-1 and the R5 peptide were generated and successfully employed toward silica encapsulation of functional diacylglycerol kinase (DGK). Silica-encapsulated DGK was significantly more stable against protease exposure and incubation with simulated gastric fluid (SGF) and intestinal fluid (SIF).
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Affiliation(s)
- Friedrich Bialas
- Institute of Biological Chemistry,
Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Christian F. W. Becker
- Institute of Biological Chemistry,
Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
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32
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Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021; 22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Affiliation(s)
- Amita R. Sahoo
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
- Department of Neurosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence:
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33
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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34
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Aneskievich BJ, Shamilov R, Vinogradova O. Intrinsic disorder in integral membrane proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:101-134. [PMID: 34656327 DOI: 10.1016/bs.pmbts.2021.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The well-defined roles and specific protein-protein interactions of many integral membrane proteins (IMPs), such as those functioning as receptors for extracellular matrix proteins and soluble growth factors, easily align with considering IMP structure as a classical "lock-and-key" concept. Nevertheless, continued advances in understanding protein conformation, such as those which established the widespread existence of intrinsically disordered proteins (IDPs) and especially intrinsically disordered regions (IDRs) in otherwise three-dimensionally organized proteins, call for ongoing reevaluation of transmembrane proteins. Here, we present basic traits of IDPs and IDRs, and, for some select single-span IMPs, consider the potential functional advantages intrinsic disorder might provide and the possible conformational impact of disease-associated mutations. For transmembrane proteins in general, we highlight several investigational approaches, such as biophysical and computational methods, stressing the importance of integrating them to produce a more-complete mechanistic model of disorder-containing IMPs. These procedures, when synergized with in-cell assessments, will likely be key in translating in silico and in vitro results to improved understanding of IMP conformational flexibility in normal cell physiology as well as disease, and will help to extend their potential as therapeutic targets.
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Affiliation(s)
- Brian J Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Rambon Shamilov
- Graduate Program in Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Olga Vinogradova
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States.
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35
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Wang Z, Zhang Q, Mim C. Coming of Age: Cryo-Electron Tomography as a Versatile Tool to Generate High-Resolution Structures at Cellular/Biological Interfaces. Int J Mol Sci 2021; 22:6177. [PMID: 34201105 PMCID: PMC8228724 DOI: 10.3390/ijms22126177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has matured as a method, delivering structures between 2 and 5 Å from complexes in cells as well as in vitro complexes. While this resolution range is not standard, novel developments point toward a promising future. Here, we provide a guide for the workflow from sample to structure to gain insight into this emerging field.
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Affiliation(s)
| | | | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute (KTH), Hälsovägen 11C, 141 27 Huddinge, Sweden; (Z.W.); (Q.Z.)
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36
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Barnes CA, Starich MR, Tjandra N, Mishra P. Simultaneous measurement of 1H C/N-R 2's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:109-118. [PMID: 33625630 PMCID: PMC8096723 DOI: 10.1007/s10858-021-00359-9] [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: 10/12/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand-protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous 1H-15 N, 1H-13C SESAME based pulse scheme for the rapid acquisition of 1HC/N-R2 relaxation rates for the determination of backbone and sidechain PREs of proteins. The 1HN-R2 rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R2 = 0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.
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Affiliation(s)
- C Ashley Barnes
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mary R Starich
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pushpa Mishra
- Department of Biophysics, University of Mumbai, Maharashtra, Mumbai, 400098, India.
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37
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Pochapsky TC. A dynamic understanding of cytochrome P450 structure and function through solution NMR. Curr Opin Biotechnol 2020; 69:35-42. [PMID: 33360373 DOI: 10.1016/j.copbio.2020.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
Many economically important biosyntheses incorporate regiospecific and stereospecific oxidations at unactivated carbons. Such oxidations are commonly catalyzed by cytochrome P450 monooxygenases, heme-containing enzymes that activate molecular oxygen while selectively binding and orienting the substrate for reaction. Despite the plethora of P450-catalyzed reactions, the P450 fold is highly conserved, and static structures are often insufficient for characterizing conformational states that contribute to specificity. High-resolution solution nuclear magnetic resonance (NMR) offers insights into dynamic processes and conformational changes that are required of a P450 in order to attain the combination of specificity and efficiency required for these reactions.
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Affiliation(s)
- Thomas C Pochapsky
- Departments of Chemistry, Biochemistry and The Rosenstiel Institute for Basic Medical Research, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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38
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The Potential of 19F NMR Application in GPCR Biased Drug Discovery. Trends Pharmacol Sci 2020; 42:19-30. [PMID: 33250272 DOI: 10.1016/j.tips.2020.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/14/2023]
Abstract
Although structure-based virtual drug discovery is revolutionizing the conventional high-throughput cell-based screening system, its limitation is obvious, together with other critical challenges. In particular, the resolved static snapshots fail to represent a full free-energy landscape due to homogenization in structural determination processing. The loss of conformational heterogeneity and related functional diversity emphasize the necessity of developing an approach that can fill this space. In this regard, NMR holds undeniable potential. However, outstanding questions regarding the NMR application remain. This review summarizes the limitations of current drug discovery and explores the potential of 19F NMR in establishing a conformation-guided drug screening system, advancing the cell- and structure-based discovery strategy for G protein-coupled receptor (GPCR) biased drug screening.
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39
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Yeh V, Goode A, Bonev BB. Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR. BIOLOGY 2020; 9:E396. [PMID: 33198410 PMCID: PMC7697852 DOI: 10.3390/biology9110396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022]
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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Affiliation(s)
| | | | - Boyan B. Bonev
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (V.Y.); (A.G.)
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40
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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41
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Dufourc EJ. Bicelles and nanodiscs for biophysical chemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183478. [PMID: 32971065 DOI: 10.1016/j.bbamem.2020.183478] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/14/2023]
Abstract
Membrane nanoobjects are very important tools to study biomembrane properties. Two types are described herein: Bicelles and Nanodiscs. Bicelles are obtained by thorough water mixing of long chain and short chain lipids and may take the form of membranous discs of 10-50 nm. Temperature-composition-hydration diagrams have been established for Phosphatidylcholines and show limited domains of existence. Bicelles can be doped with charged lipids, surfactants or with cholesterol and offer a wide variety of membranous platforms for structural biology. Internal dynamics as measured by solid-state NMR is very similar to that of liposomes in their fluid phase. Because of the magnetic susceptibility anisotropy of the lipid chains, discs may be aligned along or perpendicular to the magnetic field. They may serve as weak orienting media to provide distance information in determining the 3D structure of soluble proteins. In different conditions they show strong orienting properties which may be used to study the 3D structure, topology and dynamics of membrane proteins. Lipid Bicelles with biphenyl chains or doped with lanthanides show long lasting remnant orientation after removing the magnetic field due to smectic-like properties. An alternative to pure lipid Bicelles is provided by nanodiscs where the half torus composed by short chain lipids is replaced by proteins. This renders the nano-objects less fragile as they can be used to stabilize membrane protein assemblies to be studied by electron microscopy. Internal dynamics is again similar to liposomes except that the phase transition is abolished, possibly due to lateral constrain imposed by the toroidal proteins limiting the disc size. Advantages and drawbacks of both nanoplatforms are discussed.
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Affiliation(s)
- Erick J Dufourc
- Institute of Chemistry and Biology of membranes and Nanoobjects, UMR5248, CNRS, University of Bordeaux, Bordeaux Polytechnic Institute, Allée Geoffroy Saint Hilaire, 33600 Pessac, France.
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42
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Zhou G, Chu S, Kohli A, Szoka FC, Gochin M. Biophysical studies of HIV-1 glycoprotein-41 interactions with peptides and small molecules - Effect of lipids and detergents. Biochim Biophys Acta Gen Subj 2020; 1864:129724. [PMID: 32889078 DOI: 10.1016/j.bbagen.2020.129724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND The hydrophobic pocket (HP) of HIV-1 glycoprotein-41 ectodomain is defined by two chains of the N-heptad repeat trimer, within the protein-protein interface that mediates 6HB formation. It is a potential target for inhibitors of viral fusion, but its hydrophobic nature and proximity to membrane in situ has precluded ready analysis of inhibitor interactions. METHODS We evaluated the sensitivity of 19F NMR and fluorescence for detecting peptide and small molecule binding to the HP and explored the effect of non-denaturing detergent or phospholipid as cosolvents and potential mimics of the membrane environment surrounding gp41. RESULTS Chemical shifts of aromatic fluorines were found to be sensitive to changes in the hydrogen bonding network that occurred when inhibitors transitioned from solvent into the HP or into ordered detergent micelles. Fluorescence intensities and emission maxima of autofluorescent compounds responded to changes in the local environment. CONCLUSIONS Gp41 - ligand binding occurred under all conditions, but was diminished in the presence of detergents. NMR and fluorescence studies revealed that dodecylphosphocholine (DPC) was a poor substitute for membrane in this system, while liposomes could mimic the membrane surroundings. GENERAL SIGNIFICANCE Our findings suggest that development of high potency small molecule binders to the HP may be frustrated by competition between binding to the HP and binding to the bilayer membrane.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Shidong Chu
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America
| | - Aditya Kohli
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Francis C Szoka
- Department of Bioengineering and Therapeutic Sciences, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America
| | - Miriam Gochin
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, United States of America; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, United States of America.
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43
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Evans LS, Hussain R, Siligardi G, Williamson PT. Magnetically aligned membrane mimetics enabling comparable chiroptical and magnetic resonance spectroscopy studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183343. [DOI: 10.1016/j.bbamem.2020.183343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
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44
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Chiang WC, Lee MH, Chen TC, Huang JR. Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43's Conformational Transition. Int J Mol Sci 2020; 21:ijms21165930. [PMID: 32824743 PMCID: PMC7460674 DOI: 10.3390/ijms21165930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 12/28/2022] Open
Abstract
Most biological functions involve protein-protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43's IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2's IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other's functions through their IDRs.
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Affiliation(s)
- Wan-Chin Chiang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Ming-Hsuan Lee
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Tsai-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
| | - Jie-rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan; (W.-C.C.); (M.-H.L.); (T.-C.C.)
- Institute of Biomedical Informatics, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-Nong Street, Taipei 11221, Taiwan
- Correspondence:
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Sinha S, Ng WJ, Bhattacharjya S. NMR structure and localization of the host defense antimicrobial peptide thanatin in zwitterionic dodecylphosphocholine micelle: Implications in antimicrobial activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183432. [PMID: 32781154 DOI: 10.1016/j.bbamem.2020.183432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/11/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Antimicrobial peptides (AMPs) are potentially vital as the next generation of antibiotics against multidrug resistant bacterial pathogens. Thanatin, an insect derived pathogen inducible 21-residue long antimicrobial peptide, demonstrates antimicrobial activity toward broad range of pathogens. Thanatin is an excellent candidate for antibiotics development due to potent in vivo activity in animal model and low toxicity to human cells. Recent studies indicated mode of action of thanatin could be intriguing and may comprise bacterial membrane permeabilization and interactions with periplasmic proteins. In order to better understand selectivity and membrane disruption, here, we determined 3-D structure of the thanatin in zwitterionic DPC-d38 micelle by NMR spectroscopy. The depth of insertion of thanatin into micelle structure was investigated by spin labelled doxyl lipids, 5-DSA and 16-DSA. DPC-bound structure of thanatin is defined by a β-hairpin structure and an extended and turn conformations, for residues G1-I8, at the N-terminus. The β-hairpin structure is delineated by two antiparallel β-strands, residues I9-C11 and residues K17-R20, which is connected by loop consisted of residues N12-G16. There are cross β-strands sidechain-sidechain packing interactions among hydrophobic and aromatic residues. Spin labelled lipid studies revealed a set of spatially proximal residues V6, I8, Q19, R20 and M21 may be deeply inserted into the hydrophobic core of the DPC micelle. While, residues including those at the turn/loop are merely surface localized. The atomic resolution structure and orientation of thanatin in zwitterionic DPC micelle may be utilized for understating mode of action in lipid membrane and further development of non-toxic analogs.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Wun Jern Ng
- Environmental Bio-Innovation Group (EBiG), School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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46
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Meikle TG, Keizer DW, Babon JJ, Drummond CJ, Separovic F, Conn CE, Yao S. Physiochemical Characterization and Stability of Lipidic Cubic Phases by Solution NMR. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6254-6260. [PMID: 32418433 DOI: 10.1021/acs.langmuir.0c00949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Lipidic inverse bicontinuous cubic phases (LCPs), formed via the spontaneous self-assembly of lipids such as monoolein, have found increasing applications in the stabilization and crystallization of integral membrane proteins for structural characterization using X-ray crystallography. Their use as effective drug release matrices has also been demonstrated. Nuclear magnetic resonance (NMR) spectroscopy, both solution and solid state, has previously been employed for the characterization of LCPs and related systems. Herein, we report a number of novel features of solution NMR for probing the fundamental composition and structural properties of monoolein-based LCPs. These include (1) more complete assignments of both 1H and 13C chemical shifts, (2) direct quantification of hydration level in LCPs using one-dimensional (1D) 1H NMR, and (3) monitoring longer-term stability of LCPs and evaluating alterations introduced into standard LCPs at the submolecular level.
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Affiliation(s)
- Thomas G Meikle
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia
| | - David W Keizer
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, VIC 3010, Australia
| | - Calum J Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia
| | - Frances Separovic
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
- School of Chemistry, The University of Melbourne, VIC 3010, Australia
| | - Charlotte E Conn
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
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Richardson RJ, Fink JK, Glynn P, Hufnagel RB, Makhaeva GF, Wijeyesakere SJ. Neuropathy target esterase (NTE/PNPLA6) and organophosphorus compound-induced delayed neurotoxicity (OPIDN). ADVANCES IN NEUROTOXICOLOGY 2020; 4:1-78. [PMID: 32518884 PMCID: PMC7271139 DOI: 10.1016/bs.ant.2020.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Systemic inhibition of neuropathy target esterase (NTE) with certain organophosphorus (OP) compounds produces OP compound-induced delayed neurotoxicity (OPIDN), a distal degeneration of axons in the central nervous system (CNS) and peripheral nervous system (PNS), thereby providing a powerful model for studying a spectrum of neurodegenerative diseases. Axonopathies are important medical entities in their own right, but in addition, illnesses once considered primary neuronopathies are now thought to begin with axonal degeneration. These disorders include Alzheimer's disease, Parkinson's disease, and motor neuron diseases such as amyotrophic lateral sclerosis (ALS). Moreover, conditional knockout of NTE in the mouse CNS produces vacuolation and other degenerative changes in large neurons in the hippocampus, thalamus, and cerebellum, along with degeneration and swelling of axons in ascending and descending spinal cord tracts. In humans, NTE mutations cause a variety of neurodegenerative conditions resulting in a range of deficits including spastic paraplegia and blindness. Mutations in the Drosophila NTE orthologue SwissCheese (SWS) produce neurodegeneration characterized by vacuolization that can be partially rescued by expression of wild-type human NTE, suggesting a potential therapeutic approach for certain human neurological disorders. This chapter defines NTE and OPIDN, presents an overview of OP compounds, provides a rationale for NTE research, and traces the history of discovery of NTE and its relationship to OPIDN. It then briefly describes subsequent studies of NTE, including practical applications of the assay; aspects of its domain structure, subcellular localization, and tissue expression; abnormalities associated with NTE mutations, knockdown, and conventional or conditional knockout; and hypothetical models to help guide future research on elucidating the role of NTE in OPIDN.
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Affiliation(s)
- Rudy J. Richardson
- Molecular Simulations Laboratory, Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States,Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States,Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, United States,Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI, United States,Corresponding author:
| | - John K. Fink
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, United States,Ann Arbor Veterans Affairs Medical Center, Ann Arbor, MI, United States
| | - Paul Glynn
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Galina F. Makhaeva
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka, Russia
| | - Sanjeeva J. Wijeyesakere
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
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Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: An enduring enigma. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49904-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: An enduring enigma. J Biol Chem 2019; 295:914-925. [PMID: 31848223 DOI: 10.1074/jbc.rev119.009411] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
T cells are critical for protective immune responses to pathogens and tumors. The T-cell receptor (TCR)-CD3 complex is composed of a diverse αβ TCR heterodimer noncovalently associated with the invariant CD3 dimers CD3ϵγ, CD3ϵδ, and CD3ζζ. The TCR mediates recognition of antigenic peptides bound to MHC molecules (pMHC), whereas the CD3 molecules transduce activation signals to the T cell. Whereas much is known about downstream T-cell signaling pathways, the mechanism whereby TCR engagement by pMHC is first communicated to the CD3 signaling apparatus, a process termed early T-cell activation, remains largely a mystery. In this review, we examine the molecular basis for TCR activation in light of the recently determined cryoEM structure of a complete TCR-CD3 complex. This structure provides an unprecedented opportunity to assess various signaling models that have been proposed for the TCR. We review evidence from single-molecule and structural studies for force-induced conformational changes in the TCR-CD3 complex, for dynamically-driven TCR allostery, and for pMHC-induced structural changes in the transmembrane and cytoplasmic regions of CD3 subunits. We identify major knowledge gaps that must be filled in order to arrive at a comprehensive model of TCR activation that explains, at the molecular level, how pMHC-specific information is transmitted across the T-cell membrane to initiate intracellular signaling. An in-depth understanding of this process will accelerate the rational design of immunotherapeutic agents targeting the TCR-CD3 complex.
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Affiliation(s)
- Roy A Mariuzza
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850 .,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Pragati Agnihotri
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - John Orban
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850 .,Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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