1
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Pasquadibisceglie A, Quadrotta V, Polticelli F. In Silico Analysis of the Structural Dynamics and Substrate Recognition Determinants of the Human Mitochondrial Carnitine/Acylcarnitine SLC25A20 Transporter. Int J Mol Sci 2023; 24:ijms24043946. [PMID: 36835358 PMCID: PMC9961348 DOI: 10.3390/ijms24043946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The Carnitine-Acylcarnitine Carrier is a member of the mitochondrial Solute Carrier Family 25 (SLC25), known as SLC25A20, involved in the electroneutral exchange of acylcarnitine and carnitine across the inner mitochondrial membrane. It acts as a master regulator of fatty acids β-oxidation and is known to be involved in neonatal pathologies and cancer. The transport mechanism, also known as "alternating access", involves a conformational transition in which the binding site is accessible from one side of the membrane or the other. In this study, through a combination of state-of-the-art modelling techniques, molecular dynamics, and molecular docking, the structural dynamics of SLC25A20 and the early substrates recognition step have been analyzed. The results obtained demonstrated a significant asymmetry in the conformational changes leading to the transition from the c- to the m-state, confirming previous observations on other homologous transporters. Moreover, analysis of the MD simulations' trajectories of the apo-protein in the two conformational states allowed for a better understanding of the role of SLC25A20 Asp231His and Ala281Val pathogenic mutations, which are at the basis of Carnitine-Acylcarnitine Translocase Deficiency. Finally, molecular docking coupled to molecular dynamics simulations lend support to the multi-step substrates recognition and translocation mechanism already hypothesized for the ADP/ATP carrier.
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Affiliation(s)
| | | | - Fabio Polticelli
- Department of Sciences, University of Roma Tre, 00146 Rome, Italy
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
- Correspondence:
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2
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The effects of cardiolipin on the structural dynamics of the mitochondrial ADP/ATP carrier in its cytosol-open state. J Lipid Res 2022; 63:100227. [PMID: 35569528 PMCID: PMC9189224 DOI: 10.1016/j.jlr.2022.100227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
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3
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Mao X, Yao S, Yi Q, Xu ZM, Cang X. Function-related asymmetry of the specific cardiolipin binding sites on the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183466. [PMID: 32871114 DOI: 10.1016/j.bbamem.2020.183466] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/16/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023]
Abstract
The ADP/ATP carrier (AAC) transports matrix ATP and cytosolic ADP across the inner mitochondrial membrane (IMM). It is well known that cardiolipin (CL) plays an important role in regulating the function of AAC, yet the underlying mechanism still remains elusive. AAC is composed of three homologous domains, and three specific CL binding sites are located at the domain-domain interfaces near the matrix side. Here we report an in-depth investigation on the dynamic properties of the bound CL within the three specific sites through all-atom molecular dynamics simulations of up to 13 μs in total. Our results highlight the importance of the basic and polar residues in CL binding. The basic residues from the linker helix and/or the [Y/W/F][K/R]G motif enable the bound CL to form an intra-domain binding mode, and the canonical inter-domain binding mode only forms when these basic residues are occupied by an additional phospholipid. Of special significance, differences in the basic and polar residues lead to remarkable asymmetry among the three specific CL binding sites. We found that the bound CL at the interface of domains 2 and 3 predominantly adopts inter-domain binding mode, while CLs at the other two sites have much more intra-domain populations. This is consistent with the asymmetric crystal structure of the matrix state (m-state) AAC which implies an asymmetric transport mechanism. The dynamic equilibrium between the inter-domain and intra-domain binding modes observed in our simulations could be highly important for the bound CLs to adapt to the movements during state transitions.
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Affiliation(s)
- Xiaoting Mao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Shihao Yao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zhe-Ming Xu
- Department of Urology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health and National Children's Regional Medical Center, Hangzhou, Zhejiang 310052, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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4
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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5
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Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine. J Phys Chem Lett 2018; 9:933-938. [PMID: 29397729 PMCID: PMC5834942 DOI: 10.1021/acs.jpclett.8b00269] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 05/30/2023]
Abstract
Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent-membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states.
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Affiliation(s)
- Vilius Kurauskas
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Audrey Hessel
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Peixiang Ma
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Paola Lunetti
- Department
of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | | | - Lionel Imbert
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Martin S. King
- MRC-MBU, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Rémy Sounier
- CNRS,
INSERM, Université de Montpellier, 34094 Montpellier, France
| | - Vincenza Dolce
- Dept
of Pharmacy, University of Calabria, 87036 Arcavacata
di Rende, Italy
| | | | - Loredana Capobianco
- Department
of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Christophe Chipot
- LPCT, UMR
7019 Université de Lorraine, CNRS and Laboratoire International
Associé & University of Illinois at Urbana−Champaign, F-54500 Vandoeuvre-lès-Nancy, France
| | - François Dehez
- LPCT, UMR
7019 Université de Lorraine, CNRS and Laboratoire International
Associé & University of Illinois at Urbana−Champaign, F-54500 Vandoeuvre-lès-Nancy, France
| | - Beate Bersch
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Paul Schanda
- Université
Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
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6
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Agrahari AK, Kumar A, R S, Zayed H, C GPD. Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-tooth disease: A computational study. J Theor Biol 2018; 437:305-317. [PMID: 29111421 DOI: 10.1016/j.jtbi.2017.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
Abstract
X-linked Charcot-Marie-Tooth type 1 X (CMTX1) disease is a subtype of Charcot-Marie-Tooth (CMT), which is mainly caused by mutations in the GJB1 gene. It is also known as connexin 32 (Cx32) that leads to Schwann cell abnormalities and peripheral neuropathy. CMTX1 is considered as the second most common form of CMT disease. The aim of this study is to computationally predict the potential impact of different single amino acid substitutions at position 75 of Cx32, from arginine (R) to proline (P), glutamine (Q) and tryptophan (W). This position is known to be highly conserved among the family of connexin. To understand the structural and functional changes due to these single amino acid substitutions, we employed a homology-modeling technique to build the three-dimensional structure models for the native and mutant proteins. The protein structures were further embedded into a POPC lipid bilayer, inserted into a water box, and subjected to molecular dynamics simulation for 50 ns. Our results show that the mutants R75P, R75Q and R75W display variable structural conformation and dynamic behavior compared to the native protein. Our data proves useful in predicting the potential pathogenicity of the mutant proteins and is expected to serve as a platform for drug discovery for patients with CMT.
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Affiliation(s)
| | - Amit Kumar
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy; Biosciences Sector, Center for advanced study research and development in Sardinia (CRS4), Loc. Piscina Manna, 09010 Pula, Italy
| | - Siva R
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
| | - George Priya Doss C
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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7
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Christenson ET, Gallegos AS, Banerjee A. In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1. J Biol Chem 2018; 293:3819-3828. [PMID: 29305420 DOI: 10.1074/jbc.m117.817478] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/21/2017] [Indexed: 01/01/2023] Open
Abstract
Iron is universally important to cellular metabolism, and mitoferrin-1 and -2 have been proposed to be the iron importers of mitochondria, the cell's assembly plant of heme and iron-sulfur clusters. These iron-containing prosthetic groups are critical for a host of physiological processes ranging from oxygen transport and energy consumption to maintaining protein structural integrity. Mitoferrin-1 (Mfrn1) belongs to the mitochondrial carrier (MC) family and is atypical given its putative metallic cargo; most MCs transport nucleotides, amino acids, or other small- to medium-size metabolites. Despite the clear importance of Mfrn1 in iron utilization, its transport activity has not been demonstrated unambiguously. To bridge this knowledge gap, we have purified recombinant Mfrn1 under non-denaturing conditions and probed its metal ion-binding and transport functions. Isothermal titration calorimetry indicates that Mfrn1 has micromolar affinity for Fe(II), Mn(II), Co(II), and Ni(II). Mfrn1 was incorporated into defined liposomes, and iron transport was reconstituted in vitro, demonstrating that Mfrn1 can transport iron. Mfrn1 can also transport manganese, cobalt, copper, and zinc but discriminates against nickel. Experiments with candidate ligands for cellular labile iron reveal that Mfrn1 transports free iron and not a chelated iron complex and selects against alkali divalent ions. Extensive mutagenesis identified multiple residues that are crucial for metal binding, transport activity, or both. There is a clear abundance of residues with side chains that can coordinate first-row transition metal ions, suggesting that these could form primary or auxiliary metal-binding sites during the transport process.
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Affiliation(s)
- Eric T Christenson
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Austin S Gallegos
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Anirban Banerjee
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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8
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Crichton PG, Lee Y, Kunji ERS. The molecular features of uncoupling protein 1 support a conventional mitochondrial carrier-like mechanism. Biochimie 2017; 134:35-50. [PMID: 28057583 PMCID: PMC5395090 DOI: 10.1016/j.biochi.2016.12.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/24/2016] [Indexed: 12/14/2022]
Abstract
Uncoupling protein 1 (UCP1) is an integral membrane protein found in the mitochondrial inner membrane of brown adipose tissue, and facilitates the process of non-shivering thermogenesis in mammals. Its activation by fatty acids, which overcomes its inhibition by purine nucleotides, leads to an increase in the proton conductance of the inner mitochondrial membrane, short-circuiting the mitochondrion to produce heat rather than ATP. Despite 40 years of intense research, the underlying molecular mechanism of UCP1 is still under debate. The protein belongs to the mitochondrial carrier family of transporters, which have recently been shown to utilise a domain-based alternating-access mechanism, cycling between a cytoplasmic and matrix state to transport metabolites across the inner membrane. Here, we review the protein properties of UCP1 and compare them to those of mitochondrial carriers. UCP1 has the same structural fold as other mitochondrial carriers and, in contrast to past claims, is a monomer, binding one purine nucleotide and three cardiolipin molecules tightly. The protein has a single substrate binding site, which is similar to those of the dicarboxylate and oxoglutarate carriers, but also contains a proton binding site and several hydrophobic residues. As found in other mitochondrial carriers, UCP1 has two conserved salt bridge networks on either side of the central cavity, which regulate access to the substrate binding site in an alternating way. The conserved domain structures and mobile inter-domain interfaces are consistent with an alternating access mechanism too. In conclusion, UCP1 has retained all of the key features of mitochondrial carriers, indicating that it operates by a conventional carrier-like mechanism.
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Affiliation(s)
- Paul G Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.
| | - Yang Lee
- Laboratory of Molecular Biology, Medical Research Council, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Edmund R S Kunji
- Mitochondrial Biology Unit, Medical Research Council, Cambridge Biomedical Campus, Wellcome Trust, MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom.
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9
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Min J, Shih WM, Bellot G. Designing DNA Nanotube Liquid Crystals as a Weak-Alignment Medium for NMR Structure Determination of Membrane Proteins. Methods Mol Biol 2017; 1500:203-215. [PMID: 27813010 DOI: 10.1007/978-1-4939-6454-3_14] [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] [Indexed: 06/06/2023]
Abstract
Thirty percent of the human proteome is composed of membrane proteins that can perform a wide range of cellular functions and communications. They represent the core of modern medicine as the targets of about 50 % of all prescription pharmaceuticals. However, elucidating the structure of membrane proteins has represented a constant challenge, even in the modern era. To date, only a few hundred high-resolution structural models of membrane proteins are available. This chapter describes the emergence of DNA nanotechnology as a powerful tool for the structural characterization of membrane protein using solution-state nuclear magnetic resonance (NMR) spectroscopy. Here, we detail the large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into a dilute liquid crystal to be used as a weak-alignment media in solution NMR structure determination of membrane proteins.
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Affiliation(s)
- John Min
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Sculpting Evolution Group, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gaëtan Bellot
- Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique, CNRS Unité Mixte de Recherche UMR 5203, Institut National de la Santé et de la Recherche Médicale, INSERM U1191, Montpellier, 34000, France.
- Université de Montpellier, Montpellier, 34000, France.
- Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex 5, 34094, France.
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10
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Abstract
Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC.
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11
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Kalita MM, Fischer WB. Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1462-70. [PMID: 27079148 DOI: 10.1016/j.bbamem.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/01/2023]
Abstract
Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
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12
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Li Y, Liew LSY, Li Q, Kang C. Structure of the transmembrane domain of human nicastrin-a component of γ-secretase. Sci Rep 2016; 6:19522. [PMID: 26776682 PMCID: PMC4726005 DOI: 10.1038/srep19522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
Nicastrin is the largest component of γ-secretase that is an intramembrane protease important in the development of Alzheimer's disease. Nicastrin contains a large extracellular domain, a single transmembrane (TM) domain, and a short C-terminus. Its TM domain is important for the γ-secretase complex formation. Here we report nuclear magnetic resonance (NMR) studies of the TM and C-terminal regions of human nicastrin in both sodium dodecyl sulfate (SDS) and dodecylphosphocholine (DPC) micelles. Structural study and dynamic analysis reveal that the TM domain is largely helical and stable under both SDS and DPC micelles with its N-terminal region undergoing intermediate time scale motion. The TM helix contains a hydrophilic patch that is important for TM-TM interactions. The short C-terminus is not structured in solution and a region formed by residues V697-A702 interacts with the membrane, suggesting that these residues may play a role in the γ-secretase complex formation. Our study provides structural insight into the function of the nicastrin TM domain and the C-terminus in γ-secretase complex.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Lynette Sin Yee Liew
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - Qingxin Li
- Institute of Chemical &Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore, 138669 Singapore
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13
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Ahmad K, Waris M, Hayat M. Prediction of Protein Submitochondrial Locations by Incorporating Dipeptide Composition into Chou's General Pseudo Amino Acid Composition. J Membr Biol 2016; 249:293-304. [PMID: 26746980 DOI: 10.1007/s00232-015-9868-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/30/2015] [Indexed: 12/15/2022]
Abstract
Mitochondrion is the key organelle of eukaryotic cell, which provides energy for cellular activities. Submitochondrial locations of proteins play crucial role in understanding different biological processes such as energy metabolism, program cell death, and ionic homeostasis. Prediction of submitochondrial locations through conventional methods are expensive and time consuming because of the large number of protein sequences generated in the last few decades. Therefore, it is intensively desired to establish an automated model for identification of submitochondrial locations of proteins. In this regard, the current study is initiated to develop a fast, reliable, and accurate computational model. Various feature extraction methods such as dipeptide composition (DPC), Split Amino Acid Composition, and Composition and Translation were utilized. In order to overcome the issue of biasness, oversampling technique SMOTE was applied to balance the datasets. Several classification learners including K-Nearest Neighbor, Probabilistic Neural Network, and support vector machine (SVM) are used. Jackknife test is applied to assess the performance of classification algorithms using two benchmark datasets. Among various classification algorithms, SVM achieved the highest success rates in conjunction with the condensed feature space of DPC, which are 95.20 % accuracy on dataset SML3-317 and 95.11 % on dataset SML3-983. The empirical results revealed that our proposed model obtained the highest results so far in the literatures. It is anticipated that our proposed model might be useful for future studies.
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Affiliation(s)
- Khurshid Ahmad
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Waris
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan.
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14
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Agrahari A, George Priya Doss C. Impact of I30T and I30M substitution in MPZ gene associated with Dejerine–Sottas syndrome type B (DSSB): A molecular modeling and dynamics. J Theor Biol 2015; 382:23-33. [DOI: 10.1016/j.jtbi.2015.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 06/10/2015] [Indexed: 11/28/2022]
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15
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Run C, Yang Q, Liu Z, OuYang B, Chou JJ. Molecular Basis of MgATP Selectivity of the Mitochondrial SCaMC Carrier. Structure 2015; 23:1394-1403. [PMID: 26165595 DOI: 10.1016/j.str.2015.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/28/2015] [Accepted: 06/04/2015] [Indexed: 01/21/2023]
Abstract
The mitochondrial matrix is the supplier of cellular ATP. The short Ca(2+)-binding mitochondrial carrier (SCaMC) is one of the two mitochondrial carriers responsible for transporting ATP across the mitochondrial inner membrane. While the ADP/ATP carrier (AAC) accounts for the bulk ADP/ATP recycling in the matrix, the function of SCaMC is important for mitochondrial activities that depend on adenine nucleotides, such as gluconeogenesis and mitochondrial biogenesis. A key difference between SCaMC and AAC is that SCaMC selectively transports MgATP whereas AAC only transports free nucleotides. Here, we use a combination of nuclear magnetic resonance experiments and functional mutagenesis to investigate the structural basis of the MgATP selectivity in SCaMC. Our data revealed an MgATP binding site inside the transporter cavity, while identifying an aspartic acid residue that plays an important role in the higher selectivity for MgATP over free ATP.
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Affiliation(s)
- Changqing Run
- National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qin Yang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhijun Liu
- National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo OuYang
- National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - James J Chou
- National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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