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Itagaki T, Ito Y, Ueda M. Peptide flat-rod formation by precise arrangement among enantiomeric hydrophobic helices. J Colloid Interface Sci 2022; 617:129-135. [DOI: 10.1016/j.jcis.2022.02.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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Abosheasha MA, Itagaki T, Ito Y, Ueda M. Tubular Assembly Formation Induced by Leucine Alignment along the Hydrophobic Helix of Amphiphilic Polypeptides. Int J Mol Sci 2021; 22:ijms222112075. [PMID: 34769498 PMCID: PMC8584449 DOI: 10.3390/ijms222112075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023] Open
Abstract
The introduction of α-helical structure with a specific helix-helix interaction into an amphipathic molecule enables the determination of the molecular packing in the assembly and the morphological control of peptide assemblies. We previously reported that the amphiphilic polypeptide SL12 with a polysarcosine (PSar) hydrophilic chain and hydrophobic α-helix (l-Leu-Aib)6 involving the LxxxLxxxL sequence, which induces homo-dimerization due to the concave-convex interaction, formed a nanotube with a uniform 80 nm diameter. In this study, we investigated the importance of the LxxxLxxxL sequence for tube formation by comparing amphiphilic polypeptide SL4A4L4 with hydrophobic α-helix (l-Leu-Aib)2-(l-Ala-Aib)2-(l-Leu-Aib)2 and SL12. SL4A4L4 formed spherical vesicles and micelles. The effect of the LxxxLxxxL sequence elongation on tube formation was demonstrated by studying assemblies of PSar-b-(l-Ala-Aib)-(l-Leu-Aib)6-(l-Ala-Aib) (SA2L12A2) and PSar-b-(l-Leu-Aib)8 (SL16). SA2L12A2 formed nanotubes with a uniform 123 nm diameter, while SL16 assembled into vesicles. These results showed that LxxxLxxxL is a necessary and sufficient sequence for the self-assembly of nanotubes. Furthermore, we fabricated a double-layer nanotube by combining two kinds of nanotubes with 80 and 120 nm diameters-SL12 and SA2L12A2. When SA2L12A2 self-assembled in SL12 nanotube dispersion, SA2L12A2 initially formed a rolled sheet, the sheet then wrapped the SL12 nanotube, and a double-layer nanotube was obtained.
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Affiliation(s)
- Mohammed A. Abosheasha
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
| | - Toru Itagaki
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
| | - Yoshihiro Ito
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
| | - Motoki Ueda
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
- Correspondence:
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Parihar PS, Singh A, Karade SS, Sahasrabuddhe AA, Pratap JV. Structural insights into kinetoplastid coronin oligomerization domain and F-actin interaction. Curr Res Struct Biol 2021; 3:268-276. [PMID: 34746809 PMCID: PMC8554105 DOI: 10.1016/j.crstbi.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/18/2021] [Accepted: 10/11/2021] [Indexed: 12/25/2022] Open
Abstract
The two-domain actin associated protein coronin interacts with filamentous (F-) actin, facilitating diverse biological processes including cell proliferation, motility, phagocytosis, host-parasite interaction and cargo binding. The conserved N-terminal β-propeller domain is involved in protein: protein interactions, while the C-terminal coiled-coil domain mediates oligomerization, transducing conformational changes. The L. donovani coronin coiled-coil (LdCoroCC) domain exhibited a novel topology and oligomer association with an inherent asymmetry, caused primarily by three a residues of successive heptads. In the T.brucei homolog (TbrCoro), two of these 'a' residues are different (Val 493 & 507 replacing LdCoroCC Ile 486 and Met 500 respectively). The elucidated structure possesses a similar topology and assembly while comparative structural analysis shows that the T.brucei coronin coiled-coil domain (TbrCoroCC) too possesses the asymmetry though its magnitude is smaller. Analysis identifies that the asymmetric state is stabilized via cyclic salt bridges formed by Arg 497 and Glu 504. Co-localization studies (LdCoro, TbrCoro and corresponding mutant coiled coil constructs) with actin show that there are subtle differences in their binding patterns, with the double mutant V493I-V507M showing maximal effect. None of the constructs have an effect on F-actin length. Taken together with LdCoroCC, we therefore conclude that the inherent asymmetric structures are essential for kinetoplastids, and are of interest in understanding and exploiting actin dynamics.
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Affiliation(s)
- Pankaj Singh Parihar
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Aastha Singh
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Sharanbasappa Shrimant Karade
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Amogh Anant Sahasrabuddhe
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - J Venkatesh Pratap
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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Boruah BM, Kadirvelraj R, Liu L, Ramiah A, Li C, Zong G, Bosman GP, Yang JY, Wang LX, Boons GJ, Wood ZA, Moremen KW. Characterizing human α-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases. J Biol Chem 2020; 295:17027-17045. [PMID: 33004438 PMCID: PMC7863877 DOI: 10.1074/jbc.ra120.014625] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Mammalian Asn-linked glycans are extensively processed as they transit the secretory pathway to generate diverse glycans on cell surface and secreted glycoproteins. Additional modification of the glycan core by α-1,6-fucose addition to the innermost GlcNAc residue (core fucosylation) is catalyzed by an α-1,6-fucosyltransferase (FUT8). The importance of core fucosylation can be seen in the complex pathological phenotypes of FUT8 null mice, which display defects in cellular signaling, development, and subsequent neonatal lethality. Elevated core fucosylation has also been identified in several human cancers. However, the structural basis for FUT8 substrate specificity remains unknown.Here, using various crystal structures of FUT8 in complex with a donor substrate analog, and with four distinct glycan acceptors, we identify the molecular basis for FUT8 specificity and activity. The ordering of three active site loops corresponds to an increased occupancy for bound GDP, suggesting an induced-fit folding of the donor-binding subsite. Structures of the various acceptor complexes were compared with kinetic data on FUT8 active site mutants and with specificity data from a library of glycan acceptors to reveal how binding site complementarity and steric hindrance can tune substrate affinity. The FUT8 structure was also compared with other known fucosyltransferases to identify conserved and divergent structural features for donor and acceptor recognition and catalysis. These data provide insights into the evolution of modular templates for donor and acceptor recognition among GT-B fold glycosyltransferases in the synthesis of diverse glycan structures in biological systems.
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Affiliation(s)
- Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Renuka Kadirvelraj
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Gerlof P Bosman
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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Gorla L, Martí-Centelles V, Altava B, Burguete MI, Luis SV. The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives. CrystEngComm 2019. [DOI: 10.1039/c8ce02088d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Side chain as the main conformational and self-assembly structural factor for C2-pseudopeptides.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | | | - Belén Altava
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
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Kameda T, Nemoto T, Ogawa T, Tosaka M, Kurata H, Schaper AK. Evidence of α-helical coiled coils and β-sheets in hornet silk. J Struct Biol 2014; 185:303-8. [DOI: 10.1016/j.jsb.2013.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
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Elishakoff I. A celebration of mechanics: from nano to macro. The J. Michael T. Thompson Festschrift issue. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20130121. [PMID: 23690647 PMCID: PMC3682718 DOI: 10.1098/rsta.2013.0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This Theme Issue is dedicated to the topic 'Mechanics: from nano to macro' and marks the 75th birthday of Dr J. Michael T. Thompson, Fellow of the Royal Society, whose current affiliations are as follows: (i) Honorary Fellow, Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge; (ii) Emeritus Professor of Nonlinear Dynamics, Department of Civil, Environmental and Geomatic Engineering, University College London; and (iii) Professor of Theoretical and Applied Dynamics (Distinguished Sixth Century Chair, part-time), University of Aberdeen. He also serves as Chairman of the Board of Directors at ES-Consult (consulting engineers) in Copenhagen, Denmark. The pertinent question that arises from the very start is: should we first salute Michael and then describe the Theme Issue, or vice versa? Indeed, according to Blaise Pascal (1623-1662), the last thing one discovers in composing a work is what to put first. I would like to take the liberty of deviating from the tradition of the Philosophical Transactions and start with the tribute to Michael; after all he is the prime cause of this Theme Issue.
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Affiliation(s)
- Isaac Elishakoff
- Department of Ocean and Mechanical Engineering, Florida Atlantic University, Boca Raton, FL 33431-0991, USA.
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