1
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Britton D, Katsara O, Mishkit O, Wang A, Pandya N, Liu C, Mao H, Legocki J, Jia S, Xiao Y, Aristizabal O, Paul D, Deng Y, Schneider R, Wadghiri YZ, Montclare JK. Engineered coiled-coil HIF1α protein domain mimic. Biomater Sci 2024; 12:2951-2959. [PMID: 38656316 DOI: 10.1039/d4bm00354c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The development of targeted anti-cancer therapeutics offers the potential for increased efficacy of drugs and diagnostics. Utilizing modalities agnostic to tumor type, such as the hypoxic tumor microenvironment (TME), may assist in the development of universal tumor targeting agents. The hypoxia-inducible factor (HIF), in particular HIF1, plays a key role in tumor adaptation to hypoxia, and inhibiting its interaction with p300 has been shown to provide therapeutic potential. Using a multivalent assembled protein (MAP) approach based on the self-assembly of the cartilage oligomeric matrix protein coiled-coil (COMPcc) domain fused to the critical residues of the C-terminal transactivation domain (C-TAD) of the α subunit of HIF1 (HIF1α), we generate HIF1α-MAP (H-MAP). The resulting H-MAP demonstrates picomolar binding affinity to p300, the ability to downregulate hypoxia-inducible genes, and in vivo tumor targeting capability.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Orin Mishkit
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Andrew Wang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Department of Biomedical Engineering, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
- College of Medicine, State University of New York Downstate Medical Center, Brooklyn, New York, 11203, USA
| | - Neelam Pandya
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Heather Mao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jakub Legocki
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yingxin Xiao
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Orlando Aristizabal
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Deven Paul
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
| | - Yan Deng
- Microscopy Laboratory, New York University Langone Health, New York, NY, 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York, 10016, USA
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, 10016, USA
| | - Youssef Z Wadghiri
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, 10016, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York, 11201, USA.
- Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York, 10016, USA
- Department of Chemistry, New York University, New York, New York, 10012, USA
- Department of Biomaterials, New York University College of Dentistry, New York, New York, 10010, USA
- Department of Biomedical Engineering, New York University, New York, NY, 11201, USA
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2
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Khanppnavar B, Choo JPS, Hagedoorn PL, Smolentsev G, Štefanić S, Kumaran S, Tischler D, Winkler FK, Korkhov VM, Li Z, Kammerer RA, Li X. Structural basis of the Meinwald rearrangement catalysed by styrene oxide isomerase. Nat Chem 2024:10.1038/s41557-024-01523-y. [PMID: 38744914 DOI: 10.1038/s41557-024-01523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
Membrane-bound styrene oxide isomerase (SOI) catalyses the Meinwald rearrangement-a Lewis-acid-catalysed isomerization of an epoxide to a carbonyl compound-and has been used in single and cascade reactions. However, the structural information that explains its reaction mechanism has remained elusive. Here we determine cryo-electron microscopy (cryo-EM) structures of SOI bound to a single-domain antibody with and without the competitive inhibitor benzylamine, and elucidate the catalytic mechanism using electron paramagnetic resonance spectroscopy, functional assays, biophysical methods and docking experiments. We find ferric haem b bound at the subunit interface of the trimeric enzyme through H58, where Fe(III) acts as the Lewis acid by binding to the epoxide oxygen. Y103 and N64 and a hydrophobic pocket binding the oxygen of the epoxide and the aryl group, respectively, position substrates in a manner that explains the high regio-selectivity and stereo-specificity of SOI. Our findings can support extending the range of epoxide substrates and be used to potentially repurpose SOI for the catalysis of new-to-nature Fe-based chemical reactions.
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Affiliation(s)
- Basavraj Khanppnavar
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Joel P S Choo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Saša Štefanić
- Nanobody Service Facility. AgroVet-Strickhof, University of Zurich, Lindau, Switzerland
| | | | - Dirk Tischler
- Microbial Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Volodymyr M Korkhov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore.
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
| | - Xiaodan Li
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
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3
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Britton D, Legocki J, Paul D, Katsara O, Aristizabal O, Pandya N, Mishkit O, Xiao Y, Aristizabal M, Rahman N, Schneider R, Wadghiri YZ, Montclare JK. Coiled-Coil Protein Hydrogels Engineered with Minimized Fiber Diameters for Sustained Release of Doxorubicin in Triple-Negative Breast Cancer. ACS Biomater Sci Eng 2024; 10:3425-3437. [PMID: 38622760 PMCID: PMC11094684 DOI: 10.1021/acsbiomaterials.4c00349] [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: 02/23/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Triple-negative breast cancer (TNBC) lacks expressed protein targets, making therapy development challenging. Hydrogels offer a promising new route in this regard by improving the chemotherapeutic efficacy through increased solubility and sustained release. Moreover, subcutaneous hydrogel administration reduces patient burden by requiring less therapy and shorter treatment times. We recently established the design principles for the supramolecular assembly of single-domain coiled-coils into hydrogels. Using a modified computational design algorithm, we designed Q8, a hydrogel with rapid assembly for faster therapeutic hydrogel preparation. Q8 encapsulates and releases doxorubicin (Dox), enabling localized sustained release via subcutaneous injection. Remarkably, a single subcutaneous injection of Dox-laden Q8 (Q8•Dox) significantly suppresses tumors within just 1 week. This work showcases the bottom-up engineering of a fully protein-based drug delivery vehicle for improved TBNC treatment via noninvasive localized therapy.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Deven Paul
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Olga Katsara
- Department
of Microbiology, New York University Grossman
School of Medicine, New York, New York 10016, United States
| | - Orlando Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Neelam Pandya
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Orin Mishkit
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Matias Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Neha Rahman
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Robert Schneider
- Department
of Microbiology, New York University Grossman
School of Medicine, New York, New York 10016, United States
- Department
of Radiation Oncology, New York University
Grossman School of Medicine, New
York, New York 10016, United States
| | - Youssef Z. Wadghiri
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
- Department
of Biomedical Engineering, New York University
Tandon School of Engineering, Brooklyn ,New York11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
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4
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Nag S, Banerjee C, Goyal M, Siddiqui AA, Saha D, Mazumder S, Debsharma S, Pramanik S, Saha SJ, De R, Bandyopadhyay U. Plasmodium falciparum Alba6 exhibits DNase activity and participates in stress response. iScience 2024; 27:109467. [PMID: 38558939 PMCID: PMC10981135 DOI: 10.1016/j.isci.2024.109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Alba domain proteins, owing to their functional plasticity, play a significant role in organisms. Here, we report an intrinsic DNase activity of PfAlba6 from Plasmodium falciparum, an etiological agent responsible for human malignant malaria. We identified that tyrosine28 plays a critical role in the Mg2+ driven 5'-3' DNase activity of PfAlba6. PfAlba6 cleaves both dsDNA as well as ssDNA. We also characterized PfAlba6-DNA interaction and observed concentration-dependent oligomerization in the presence of DNA, which is evident from size exclusion chromatography and single molecule AFM-imaging. PfAlba6 mRNA expression level is up-regulated several folds following heat stress and treatment with artemisinin, indicating a possible role in stress response. PfAlba6 has no human orthologs and is expressed in all intra-erythrocytic stages; thus, this protein can potentially be a new anti-malarial drug target.
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Affiliation(s)
- Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Manish Goyal
- Department of Molecular & Cell Biology, School of Dental Medicine, Boston University Medical Campus, Boston, MA, USA
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal 712258, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shubhra Jyoti Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal 700135, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal 700091, India
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5
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Yu M, Tang TS, Ghamsari L, Yuen G, Scuoppo C, Rotolo JA, Kappel BJ, Mason JM. Exponential Combination of a and e/g Intracellular Peptide Libraries Identifies a Selective ATF3 Inhibitor. ACS Chem Biol 2024; 19:753-762. [PMID: 38412264 PMCID: PMC10949195 DOI: 10.1021/acschembio.3c00779] [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: 12/18/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/29/2024]
Abstract
Activating transcription factor 3 (ATF3) is an activation transcription factor/cyclic adenosine monophosphate (cAMP) responsive element-binding (CREB) protein family member. It is recognized as an important regulator of cancer progression by repressing expression of key inflammatory factors such as interferon-γ and chemokine (C-C motif) ligand 4 (CCL4). Here, we describe a novel library screening approach that probes individual leucine zipper components before combining them to search exponentially larger sequence spaces not normally accessible to intracellular screening. To do so, we employ two individual semirational library design approaches and screen using a protein-fragment complementation assay (PCA). First, a 248,832-member library explored 12 amino acid positions at all five a positions to identify those that provided improved binding, with all e/g positions fixed as Q, placing selection pressure onto the library options provided. Next, a 59,049-member library probed all ten e/g positions with 3 options. Similarly, during e/g library screening, a positions were locked into a generically bindable sequence pattern (AIAIA), weakly favoring leucine zipper formation, while placing selection pressure onto e/g options provided. The combined a/e/g library represents ∼14.7 billion members, with the resulting peptide, ATF3W_aeg, binding ATF3 with high affinity (Tm = 60 °C; Kd = 151 nM) while strongly disfavoring homodimerization. Moreover, ATF3W_aeg is notably improved over component PCA hits, with target specificity found to be driven predominantly by electrostatic interactions. The combined a/e/g exponential library screening approach provides a robust, accelerated platform for exploring larger peptide libraries, toward derivation of potent yet selective antagonists that avoid homoassociation to provide new insight into rational peptide design.
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Affiliation(s)
- Miao Yu
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - T.M. Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Lila Ghamsari
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Graham Yuen
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Claudio Scuoppo
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Jim A. Rotolo
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Barry J. Kappel
- Sapience
Therapeutics, Inc. 500
Mamaroneck Ave. Suite 320, Tarrytown, New York 10591, United States
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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6
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Fischer N, Tóth A, Jancsó A, Thulstrup P, Diness F. Inducing α-Helicity in Peptides by Silver Coordination to Cysteine. Chemistry 2024:e202304064. [PMID: 38456607 DOI: 10.1002/chem.202304064] [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: 01/18/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
Short peptide sequences consisting of two cysteine residues separated by three other amino acids display complete change from random coil to α-helical secondary structure in response to addition of Ag+ ions. The folded CXXXC/Ag+ complex involves formation of multinuclear Ag+ species and is stable in a wide pH range from below 3 to above 8. The complex is stable through reversed-phase HPLC separation as well as towards a physiological level of chloride ions, based on far-UV circular dichroism spectroscopy. In electrospray MS under acidic conditions a peptide dimer with four Ag+ ions bound was observed, and modelling based on potentiometric experiments supported this to be the dominating complex at neutral pH together with a peptide dimer with 3 Ag+ and one proton at lower pH. The complex was demonstrated to work as a N-terminal nucleation site for inducing α-helicity into longer peptides. This type of silver-mediated peptide assembly and folding may be of more general use for stabilizing not only peptide folding but also for controlling oligomerization even under acidic conditions.
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Affiliation(s)
- Niklas Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Annamária Tóth
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Attila Jancsó
- Department of Molecular and Analytical Chemistry, University of Szeged, Dómtér 7-8, H-6720, Szeged, Hungary
| | - Peter Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
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7
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Heber S, McClintock MA, Simon B, Mehtab E, Lapouge K, Hennig J, Bullock SL, Ephrussi A. Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport. Nat Struct Mol Biol 2024; 31:476-488. [PMID: 38297086 PMCID: PMC10948360 DOI: 10.1038/s41594-024-01212-x] [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: 03/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In the Drosophila female germline, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliver oskar messenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associated oskar mRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
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Affiliation(s)
- Simone Heber
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Eve Mehtab
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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8
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Deng S, Li Z, Yuan L, Zeng H. An Exceptionally Active and Highly Selective Perchlorate Transporter Containing a Trimesic Amide Scaffold. Molecules 2024; 29:1118. [PMID: 38474632 DOI: 10.3390/molecules29051118] [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: 02/03/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
We report here a series of alkyl group-modified trimesic amide molecules (TAs) with excellent anion transport activities. Among them, TA6, with the highest ion transport activity and excellent selectivity, efficiently transports anions across the membrane in the order of ClO4- > I- > NO3- > Br- > Cl-, with an EC50 value as low as 17.6 nM (0.022 mol% relative to lipid molecules) for ClO4-, which outperforms other anions by 5- to 22-folds and manifests as the best perchlorate transporter ever reported.
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Affiliation(s)
- Shaowen Deng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Zhongyan Li
- College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Lin Yuan
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425100, China
| | - Huaqiang Zeng
- College of Chemistry, Fuzhou University, Fuzhou 350116, China
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9
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Hoyos-Gonzalez N, Ochoa-Leyva A, Benitez-Cardoza CG, Brieba LG, Lukaszewicz G, Trasviña-Arenas CH, Sotelo-Mundo RR. Identification of a cryptic functional apolipophorin-III domain within the Prominin-1 gene of Litopenaeus vannamei. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110928. [PMID: 38043730 DOI: 10.1016/j.cbpb.2023.110928] [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: 10/06/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
The Apolipophorin-III (apoLp-III) is reported as an essential protein element in lipids transport and incorporation in lepidopterans. Structurally, apoLp-III has an α-helix bundle structure composed of five α-helices. Interestingly, classic studies proposed a structural switch triggered by its interaction with lipids, where the α-helix bundle opens. Currently, the study of the apoLp-III has been limited to insects, with no homologs identified in other arthropods. By implementing a structure-based search with the Phyre2 algorithm surveying the shrimp Litopenaeus vannamei's transcriptome, we identified a putative apoLp-III in this farmed penaeid (LvApoLp-III). Unlike canonical apoLp-III, the LvApoLp-III was identified as an internal domain within the transmembrane protein Prominin-1. Structural modeling using the template-based Phyre2 and template-free AlphaFold algorithms rendered two distinct structural topologies: the α-helix bundle and a coiled-coil structure. Notably, the secondary structure composition on both models was alike, with differences in the orientation and distribution of the α-helices and hydrophobic moieties. Both models provide insights into the classical structural switch induced by lipids in apoLp-III. To corroborate structure/function inferences, we cloned the synthetic LvApoLp-III domain, overexpressed, and purified the recombinant protein. Circular dichroism measurements with the recombinant LvApoLp-III agreed with the structural models. In vitro liposome interaction demonstrated that the apoLp-III domain within the PROM1 of L.vannamei associated similarly to exchangeable apolipoproteins. Altogether, this work reports the presence of an apolipophorin-III domain in crustaceans for the first time and opens questions regarding its function and importance in lipid metabolism or the immune system.
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Affiliation(s)
- Nallely Hoyos-Gonzalez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico. https://twitter.com/uga_langebio
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos 62210, Mexico. https://twitter.com/ibt_unam
| | - Claudia G Benitez-Cardoza
- Laboratorio de Bioquímica y Biofísica Computacional, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico. https://twitter.com/IPN_mx
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, Mexico. https://twitter.com/uga_langebio
| | - German Lukaszewicz
- Instituto de Investigaciones Marinas y Costeras, IIMyC, FCEyN, UNMdP, CONICET, Mar del Plata B7608FBY, Argentina. https://twitter.com/fceyn_unmdp
| | - Carlos H Trasviña-Arenas
- Centro de Investigación sobre Envejecimiento, Centro de Investigación y de Estudios Avanzados (CINVESTAV) Unidad Sede Sur, Tlalpan, 14330 Mexico City, Mexico.
| | - Rogerio R Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Ejido La Victoria, Hermosillo, Sonora 83304, Mexico.
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10
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Britton D, Christians LF, Liu C, Legocki J, Xiao Y, Meleties M, Yang L, Cammer M, Jia S, Zhang Z, Mahmoudinobar F, Kowalski Z, Renfrew PD, Bonneau R, Pochan DJ, Pak AJ, Montclare JK. Computational Prediction of Coiled-Coil Protein Gelation Dynamics and Structure. Biomacromolecules 2024; 25:258-271. [PMID: 38110299 PMCID: PMC10777397 DOI: 10.1021/acs.biomac.3c00968] [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: 09/12/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled-coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled-coil hydrogel design. Using Rosetta energy scores and Poisson-Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled-coil proteins while simultaneously exploring five new coiled-coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled-coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled-coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled-coil fiber formation.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Luc F. Christians
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Lin Yang
- National
Synchrotron Light Source-II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Michael Cammer
- Microscopy
Laboratory, New York University Langone
Health, New York, New York 10016, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Zihan Zhang
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Farbod Mahmoudinobar
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center for
Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, United States
| | - Zuzanna Kowalski
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - P. Douglas Renfrew
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Richard Bonneau
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Center
for Genomics and Systems Biology, New York
University, New York, New York 10003, United States
- Courant
Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Darrin J. Pochan
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
| | - Alexander J. Pak
- Department
of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomedical Engineering, New
York University, New York, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department
of Radiology, New York University School
of Medicine, New York, New York 10016, United States
- Department of Biomaterials, New York University
College of Dentistry, New York, New York 10010, United States
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11
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Britton D, Legocki J, Aristizabal O, Mishkit O, Liu C, Jia S, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Protein-Engineered Fibers For Drug Encapsulation Traceable via 19F Magnetic Resonance. ACS APPLIED NANO MATERIALS 2023; 6:21245-21257. [PMID: 38037605 PMCID: PMC10682962 DOI: 10.1021/acsanm.3c04357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization. Herein, we create a protein-engineered fluorinated coiled-coil fiber, Q2TFL, capable of improved sensitivity to 19F magnetic resonance spectroscopy (MRS) detection. Leveraging residue-specific noncanonical amino acid incorporation of trifluoroleucine (TFL) into the coiled-coil, Q2, which self-assembles into nanofibers, we generate Q2TFL. We demonstrate that fluorination results in a greater increase in thermostability and 19F magnetic resonance detection compared to the nonfluorinated parent, Q2. Q2TFL also exhibits linear ratiometric 19F MRS thermoresponsiveness, allowing it to act as a temperature probe. Furthermore, we explore the ability of Q2TFL to encapsulate the anti-inflammatory small molecule, curcumin (CCM), and its impact on the coiled-coil structure. Q2TFL also provides hyposignal contrast in 1H MRI, echogenic signal with high-frequency ultrasound and sensitive detection by 19F MRS in vivo illustrating fluorination of coiled-coils for supramolecular assembly and their use with 1H MRI, 19F MRS and high frequency ultrasound as multimodal theranostic agents.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Orlando Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Orin Mishkit
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Chengliang Liu
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Sihan Jia
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Paul Douglas Renfrew
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
| | - Richard Bonneau
- Center
for Computational Biology, Flatiron Institute,
Simons Foundation, New York, New York 10010, United States
- Center for
Genomics and Systems Biology, New York University, New York, New York 10003, United States
- Courant
Institute
of Mathematical Sciences, Computer Science Department, New York University, New York, New York 10009, United States
| | - Youssef Z. Wadghiri
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
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12
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Flynn AJ, Miller K, Codjoe JM, King MR, Haswell ES. Mechanosensitive ion channels MSL8, MSL9, and MSL10 have environmentally sensitive intrinsically disordered regions with distinct biophysical characteristics in vitro. PLANT DIRECT 2023; 7:e515. [PMID: 37547488 PMCID: PMC10400277 DOI: 10.1002/pld3.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are highly dynamic sequences that rapidly sample a collection of conformations over time. In the past several decades, IDRs have emerged as a major component of many proteomes, comprising ~30% of all eukaryotic protein sequences. Proteins with IDRs function in a wide range of biological pathways and are notably enriched in signaling cascades that respond to environmental stresses. Here, we identify and characterize intrinsic disorder in the soluble cytoplasmic N-terminal domains of MSL8, MSL9, and MSL10, three members of the MscS-like (MSL) family of mechanosensitive ion channels. In plants, MSL channels are proposed to mediate cell and organelle osmotic homeostasis. Bioinformatic tools unanimously predicted that the cytosolic N-termini of MSL channels are intrinsically disordered. We examined the N-terminus of MSL10 (MSL10N) as an exemplar of these IDRs and circular dichroism spectroscopy confirms its disorder. MSL10N adopted a predominately helical structure when exposed to the helix-inducing compound trifluoroethanol (TFE). Furthermore, in the presence of molecular crowding agents, MSL10N underwent structural changes and exhibited alterations to its homotypic interaction favorability. Lastly, interrogations of collective behavior via in vitro imaging of condensates indicated that MSL8N, MSL9N, and MSL10N have sharply differing propensities for self-assembly into condensates, both inherently and in response to salt, temperature, and molecular crowding. Taken together, these data establish the N-termini of MSL channels as intrinsically disordered regions with distinct biophysical properties and the potential to respond uniquely to changes in their physiochemical environment.
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Affiliation(s)
- Aidan J. Flynn
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of Biochemistry and BiophysicsWashington University in St. LouisSt. LouisMissouriUSA
| | - Kari Miller
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Jennette M. Codjoe
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Matthew R. King
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Elizabeth S. Haswell
- Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- NSF Center for Engineering Mechanobiology, Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
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13
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Tsirigoni AM, Goktas M, Atris Z, Valleriani A, Vila Verde A, Blank KG. Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils. Macromol Biosci 2023; 23:e2200563. [PMID: 36861255 DOI: 10.1002/mabi.202200563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Coiled coils (CCs) are key building blocks of biogenic materials and determine their mechanical response to large deformations. Of particular interest is the observation that CC-based materials display a force-induced transition from α-helices to mechanically stronger β-sheets (αβT). Steered molecular dynamics simulations predict that this αβT requires a minimum, pulling speed-dependent CC length. Here, de novo designed CCs with a length between four to seven heptads are utilized to probe if the transition found in natural CCs can be mimicked with synthetic sequences. Using single-molecule force spectroscopy and molecular dynamics simulations, these CCs are mechanically loaded in shear geometry and their rupture forces and structural responses to the applied load are determined. Simulations at the highest pulling speed (0.01 nm ns-1 ) show the appearance of β-sheet structures for the five- and six-heptad CCs and a concomitant increase in mechanical strength. The αβT is less probable at a lower pulling speed of 0.001 nm ns-1 and is not observed in force spectroscopy experiments. For CCs loaded in shear geometry, the formation of β-sheets competes with interchain sliding. β-sheet formation is only possible in higher-order CC assemblies or in tensile-loading geometries where chain sliding and dissociation are prohibited.
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Affiliation(s)
- Anna-Maria Tsirigoni
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Melis Goktas
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Zeynep Atris
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057, Duisburg, Germany
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Johannes Kepler University Linz, Institute of Experimental Physics, Department of Biomolecular & Selforganizing Matter, Altenberger Strasse 69, Linz, 4040, Austria
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14
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Curti M, Maffeis V, Teixeira Alves Duarte LG, Shareef S, Hallado LX, Curutchet C, Romero E. Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling. Protein Sci 2023; 32:e4579. [PMID: 36715022 PMCID: PMC9951196 DOI: 10.1002/pro.4579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
In photosynthesis, pigment-protein complexes achieve outstanding photoinduced charge separation efficiencies through a set of strategies in which excited states delocalization over multiple pigments ("excitons") and charge-transfer states play key roles. These concepts, and their implementation in bioinspired artificial systems, are attracting increasing attention due to the vast potential that could be tapped by realizing efficient photochemical reactions. In particular, de novo designed proteins provide a diverse structural toolbox that can be used to manipulate the geometric and electronic properties of bound chromophore molecules. However, achieving excitonic and charge-transfer states requires closely spaced chromophores, a non-trivial aspect since a strong binding with the protein matrix needs to be maintained. Here, we show how a general-purpose artificial protein can be optimized via molecular dynamics simulations to improve its binding capacity of a chlorophyll derivative, achieving complexes in which chromophores form two closely spaced and strongly interacting dimers. Based on spectroscopy results and computational modeling, we demonstrate each dimer is excitonically coupled, and propose they display signatures of charge-transfer state mixing. This work could open new avenues for the rational design of chromophore-protein complexes with advanced functionalities.
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Affiliation(s)
- Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Laboratoire de Chimie, UMR 5182, ENS Lyon, CNRSUniversité Lyon 1LyonFrance
| | | | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Luisa Xiomara Hallado
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, Facultat de Farmàcia i Ciències de l'AlimentacióUniversitat de Barcelona (UB)BarcelonaSpain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB)BarcelonaSpain
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
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15
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Berntsson E, Vosough F, Svantesson T, Pansieri J, Iashchishyn IA, Ostojić L, Dong X, Paul S, Jarvet J, Roos PM, Barth A, Morozova-Roche LA, Gräslund A, Wärmländer SKTS. Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides. Sci Rep 2023; 13:3341. [PMID: 36849796 PMCID: PMC9971182 DOI: 10.1038/s41598-023-29901-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-β (Aβ) peptides, and Aβ oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with Aβ peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize Aβ/Ni(II) interactions in vitro, for different Aβ variants: Aβ(1-40), Aβ(1-40)(H6A, H13A, H14A), Aβ(4-40), and Aβ(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length Aβ monomers. Equimolar amounts of Ni(II) ions retard Aβ aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)·Aβ binding affinity is in the low µM range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent Aβ dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in Aβ monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized Aβ oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the Aβ aggregation processes that are involved in AD brain pathology.
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Affiliation(s)
- Elina Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden. .,Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
| | - Faraz Vosough
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Teodor Svantesson
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Jonathan Pansieri
- grid.12650.300000 0001 1034 3451Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Igor A. Iashchishyn
- grid.12650.300000 0001 1034 3451Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Lucija Ostojić
- grid.12650.300000 0001 1034 3451Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Xiaolin Dong
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Suman Paul
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden ,grid.177284.f0000 0004 0410 6208The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Per M. Roos
- grid.4714.60000 0004 1937 0626Institute of Environmental Medicine, Karolinska Institutet, Nobels Väg 13, 171 77 Stockholm, Sweden ,Department of Clinical Physiology, Capio St. Göran Hospital, St. Göransplan 1, 112 19 Stockholm, Sweden
| | - Andreas Barth
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Ludmilla A. Morozova-Roche
- grid.12650.300000 0001 1034 3451Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Astrid Gräslund
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Sebastian K. T. S. Wärmländer
- grid.10548.380000 0004 1936 9377Chemistry Section, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
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16
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Rajkovic A, Kanchugal S, Abdurakhmanov E, Howard R, Wärmländer S, Erwin J, Barrera Saldaña HA, Gräslund A, Danielson H, Flores SC. Amino acid substitutions in human growth hormone affect secondary structure and receptor binding. PLoS One 2023; 18:e0282741. [PMID: 36952491 PMCID: PMC10035860 DOI: 10.1371/journal.pone.0282741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
The interaction between human Growth Hormone (hGH) and hGH Receptor (hGHR) has basic relevance to cancer and growth disorders, and hGH is the scaffold for Pegvisomant, an anti-acromegaly therapeutic. For the latter reason, hGH has been extensively engineered by early workers to improve binding and other properties. We are particularly interested in E174 which belongs to the hGH zinc-binding triad; the substitution E174A is known to significantly increase binding, but to now no explanation has been offered. We generated this and several computationally-selected single-residue substitutions at the hGHR-binding site of hGH. We find that, while many successfully slow down dissociation of the hGH-hGHR complex once bound, they also slow down the association of hGH to hGHR. The E174A substitution induces a change in the Circular Dichroism spectrum that suggests the appearance of coiled-coiling. Here we show that E174A increases affinity of hGH against hGHR because the off-rate is slowed down more than the on-rate. For E174Y (and certain mutations at other sites) the slowdown in on-rate was greater than that of the off-rate, leading to decreased affinity. The results point to a link between structure, zinc binding, and hGHR-binding affinity in hGH.
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Affiliation(s)
- Andrei Rajkovic
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandesh Kanchugal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Rebecca Howard
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | - Sebastian Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | - Joseph Erwin
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | | | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | | | - Samuel Coulbourn Flores
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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17
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Torralba J, de la Arada I, Partida-Hanon A, Rujas E, Arribas M, Insausti S, Valotteau C, Valle J, Andreu D, Caaveiro JMM, Jiménez MA, Apellániz B, Redondo-Morata L, Nieva JL. Molecular recognition of a membrane-anchored HIV-1 pan-neutralizing epitope. Commun Biol 2022; 5:1265. [DOI: 10.1038/s42003-022-04219-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractAntibodies against the carboxy-terminal section of the membrane-proximal external region (C-MPER) of the HIV-1 envelope glycoprotein (Env) are considered as nearly pan-neutralizing. Development of vaccines capable of producing analogous broadly neutralizing antibodies requires deep understanding of the mechanism that underlies C-MPER recognition in membranes. Here, we use the archetypic 10E8 antibody and a variety of biophysical techniques including single-molecule approaches to study the molecular recognition of C-MPER in membrane mimetics. In contrast to the assumption that an interfacial MPER helix embodies the entire C-MPER epitope recognized by 10E8, our data indicate that transmembrane domain (TMD) residues contribute to binding affinity and specificity. Moreover, anchoring to membrane the helical C-MPER epitope through the TMD augments antibody binding affinity and relieves the effects exerted by the interfacial MPER helix on the mechanical stability of the lipid bilayer. These observations support that addition of TMD residues may result in more efficient and stable anti-MPER vaccines.
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18
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Britton D, Monkovic J, Jia S, Liu C, Mahmoudinobar F, Meleties M, Renfrew PD, Bonneau R, Montclare JK. Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers. Biomacromolecules 2022; 23:4851-4859. [PMID: 36227640 DOI: 10.1021/acs.biomac.2c01031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to engineer a solvent-exposed surface of self-assembling coiled coils allows one to achieve a higher-order hierarchical assembly such as nano- or microfibers. Currently, these materials are being developed for a range of biomedical applications, including drug delivery systems; however, ways to mechanistically optimize the coiled-coil structure for drug binding are yet to be explored. Our laboratory has previously leveraged the functional properties of the naturally occurring cartilage oligomeric matrix protein coiled coil (C), not only for its favorable motif but also for the presence of a hydrophobic pore to allow for small-molecule binding. This includes the development of Q, a rationally designed pentameric coiled coil derived from C. Here, we present a small library of protein microfibers derived from the parent sequences of C and Q bearing various electrostatic potentials with the aim to investigate the influence of higher-order assembly and encapsulation of candidate small molecule, curcumin. The supramolecular fiber size appears to be well-controlled by sequence-imbued electrostatic surface potential, and protein stability upon curcumin binding is well correlated to relative structure loss, which can be predicted by in silico docking.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Julia Monkovic
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York10016, United States.,Department of Chemistry, New York University, New York, New York10012, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York10010, United States
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19
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Klug YA, Schwarzer R, Ravula T, Rotem E, Ramamoorthy A, Shai Y. Structural and Mechanistic Evidence for Calcium Interacting Sites in the HIV Transmembrane Protein gp41 Involved in Membrane Fusion. Biochemistry 2022; 61:1915-1922. [PMID: 35994087 PMCID: PMC9454089 DOI: 10.1021/acs.biochem.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The HIV envelope protein gp160 comprises two subunits, gp120 and gp41, responsible for receptor binding and membrane fusion during viral entry, respectively. In the course of the membrane fusion process, gp41 undergoes a conformational change, leading to the formation of a six-helix bundle (SHB), which ultimately drives membrane fusion. The gp41 C-terminal and N-terminal heptad repeats (CHR and NHR) interact with one another to form the SHB, and this step can be targeted by peptide inhibitors, which are used in the clinic to mitigate HIV infection. Here, we discover the calcium interaction motifs (CIMs) in the gp41 CHR and NHR regions via NMR spectroscopy. We find that the assembly of the CHR-NHR SHB is facilitated in Ca2+-containing media and impaired in CIM mutants. Of note, the clinically approved, gp41-derived fusion inhibitor T20, which does not contain the CIM motif, exhibits reduced inhibitory efficiency when challenged with calcium. This finding could have important implications for the development of better fusion inhibitors for HIV.
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Affiliation(s)
- Yoel A. Klug
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
| | - Roland Schwarzer
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
- Institute
for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Thirupathi Ravula
- Biophysics
Program, Department of Chemistry, Macromolecular Science and Engineering,
Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Etai Rotem
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
| | - Ayyalusamy Ramamoorthy
- Biophysics
Program, Department of Chemistry, Macromolecular Science and Engineering,
Biomedical Engineering, Michigan Neuroscience Institute, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Yechiel Shai
- Department
of Biomolecular Sciences, The Weizmann Institute
of Science, Rehovot 7632701, Israel
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20
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Berntsson E, Sardis M, Noormägi A, Jarvet J, Roos PM, Tõugu V, Gräslund A, Palumaa P, Wärmländer SKTS. Mercury Ion Binding to Apolipoprotein E Variants ApoE2, ApoE3, and ApoE4: Similar Binding Affinities but Different Structure Induction Effects. ACS OMEGA 2022; 7:28924-28931. [PMID: 36033665 PMCID: PMC9404194 DOI: 10.1021/acsomega.2c02254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Mercury intoxication typically produces more severe outcomes in people with the APOE-ε4 gene, which codes for the ApoE4 variant of apolipoprotein E, compared to individuals with the APOE-ε2 and APOE-ε3 genes. Why the APOE-ε4 allele is a risk factor in mercury exposure remains unknown. One proposed possibility is that the ApoE protein could be involved in clearing of heavy metals, where the ApoE4 protein might perform this task worse than the ApoE2 and ApoE3 variants. Here, we used fluorescence and circular dichroism spectroscopies to characterize the in vitro interactions of the three different ApoE variants with Hg(I) and Hg(II) ions. Hg(I) ions displayed weak binding to all ApoE variants and induced virtually no structural changes. Thus, Hg(I) ions appear to have no biologically relevant interactions with the ApoE protein. Hg(II) ions displayed stronger and very similar binding affinities for all three ApoE isoforms, with K D values of 4.6 μM for ApoE2, 4.9 μM for ApoE3, and 4.3 μM for ApoE4. Binding of Hg(II) ions also induced changes in ApoE superhelicity, that is, altered coil-coil interactions, which might modify the protein function. As these structural changes were most pronounced in the ApoE4 protein, they could be related to the APOE-ε4 gene being a risk factor in mercury toxicity.
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Affiliation(s)
- Elina Berntsson
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 12618 Tallinn, Estonia
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Merlin Sardis
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 12618 Tallinn, Estonia
| | - Andra Noormägi
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 12618 Tallinn, Estonia
| | - Jüri Jarvet
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
- The
National Institute of Chemical Physics and Biophysics, 12618 Tallinn, Estonia
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
| | - Per M. Roos
- Institute
of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department
of Clinical Physiology, Capio Saint Göran
Hospital, 112 19 Stockholm, Sweden
| | - Vello Tõugu
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 12618 Tallinn, Estonia
| | - Astrid Gräslund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
| | - Peep Palumaa
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 12618 Tallinn, Estonia
| | - Sebastian K. T. S. Wärmländer
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
- CellPept
Sweden AB, Kvarngatan
10B, 118 47 Stockholm, Sweden
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21
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Rončević T, Gerdol M, Mardirossian M, Maleš M, Cvjetan S, Benincasa M, Maravić A, Gajski G, Krce L, Aviani I, Hrabar J, Trumbić Ž, Derks M, Pallavicini A, Weingarth M, Zoranić L, Tossi A, Mladineo I. Anisaxins, helical antimicrobial peptides from marine parasites, kill resistant bacteria by lipid extraction and membrane disruption. Acta Biomater 2022; 146:131-144. [PMID: 35470073 DOI: 10.1016/j.actbio.2022.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022]
Abstract
An infecting and propagating parasite relies on its innate defense system to evade the host's immune response and to survive challenges from commensal bacteria. More so for the nematode Anisakis, a marine parasite that during its life cycle encounters both vertebrate and invertebrate hosts and their highly diverse microbiotas. Although much is still unknown about how the nematode mitigates the effects of these microbiota, its antimicrobial peptides likely play an important role in its survival. We identified anisaxins, the first cecropin-like helical antimicrobial peptides originating from a marine parasite, by mining available genomic and transcriptomic data for Anisakis spp. These peptides are potent bactericidal agents in vitro, selectively active against Gram-negative bacteria, including multi-drug resistant strains, at sub-micromolar concentrations. Their interaction with bacterial membranes was confirmed by solid state NMR (ssNMR) and is highly dependent on the peptide concentration as well as peptide to lipid ratio, as evidenced by molecular dynamics (MD) simulations. MD results indicated that an initial step in the membranolytic mode of action involves membrane bulging and lipid extraction; a novel mechanism which may underline the peptides' potency. Subsequent steps include membrane permeabilization leading to leakage of molecules and eventually cell death, but without visible macroscopic damage, as shown by atomic force microscopy and flow cytometry. This membranolytic antibacterial activity does not translate to cytotoxicity towards human peripheral blood mononuclear cells (HPBMCs), which was minimal at well above bactericidal concentrations, making anisaxins promising candidates for further drug development. STATEMENT OF SIGNIFICANCE: Witnessing the rapid spread of antibiotic resistance resulting in millions of infected and dozens of thousands dying worldwide every year, we identified anisaxins, antimicrobial peptides (AMPs) from marine parasites, Anisakis spp., with potent bactericidal activity and selectivity towards multi-drug resistant Gram-negative bacteria. Anisaxins are membrane-active peptides, whose activity, very sensitive to local peptide concentrations, involves membrane bulging and lipid extraction, leading to membrane permeabilization and bacterial cell death. At the same time, their toxicity towards host cells is negligible, which is often not the case for membrane-active AMPs, therefore making them suitable drug candidates. Membrane bulging and lipid extraction are novel concepts that broaden our understanding of peptide interactions with bacterial functional structures, essential for future design of such biomaterials.
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Affiliation(s)
- Tomislav Rončević
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, Split 21000, Croatia.
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, Trieste 34125, Italy
| | - Matko Maleš
- Faculty of Maritime Studies, University of Split, Split 21000, Croatia
| | - Svjetlana Cvjetan
- Laboratory for Aquaculture, Institute of Oceanography and Fisheries, Split 21000, Croatia
| | - Monica Benincasa
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, Split 21000, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb 10000, Croatia
| | - Lucija Krce
- Department of Physics, Faculty of Science, University of Split, Split 21000, Croatia
| | - Ivica Aviani
- Department of Physics, Faculty of Science, University of Split, Split 21000, Croatia
| | - Jerko Hrabar
- Laboratory for Aquaculture, Institute of Oceanography and Fisheries, Split 21000, Croatia
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, Split 21000, Croatia
| | - Maik Derks
- NMR spectroscopy, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht 3584CH, The Netherlands; Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy; Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Markus Weingarth
- NMR spectroscopy, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht 3584CH, The Netherlands
| | - Larisa Zoranić
- Department of Physics, Faculty of Science, University of Split, Split 21000, Croatia
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Ivona Mladineo
- Laboratory of Functional Helminthology, Biology Centre Czech Academy of Sciences, Institute of Parasitology BC CAS, Branisovska 31, Ceske Budejovice 37005, Czech Republic.
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22
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Jorgensen M, Chmielewski J. Co-assembled Coiled-Coil Peptide Nanotubes with Enhanced Stability and Metal-Dependent Cargo Loading. ACS OMEGA 2022; 7:20945-20951. [PMID: 35755377 PMCID: PMC9219066 DOI: 10.1021/acsomega.2c01669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 05/07/2023]
Abstract
Peptide nanotube biomaterials are attractive for their range of applications. Herein, we disclose the co-assembly of coiled-coil peptides, one with ligands for metal ions that demonstrate hierarchical assembly into nanotubes, with spatial control of the metal-binding ligands. Enhanced stability of the nanotubes to phosphate-buffered saline was successfully accomplished in a metal-dependent fashion, depending on the levels and placement of the ligand-containing coiled-coil peptide. This spatial control also allowed for site-specific labeling of the nanotubes with His-tagged fluorophores through the length of the tubes or at the termini, in a metal-dependent manner.
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23
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Insight into binding behavior, structure, and foam properties of α-lactalbumin/glycyrrhizic acid complex in an acidic environment. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107411] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Bellavita R, Maione A, Merlino F, Siciliano A, Dardano P, De Stefano L, Galdiero S, Galdiero E, Grieco P, Falanga A. Antifungal and Antibiofilm Activity of Cyclic Temporin L Peptide Analogues against Albicans and Non-Albicans Candida Species. Pharmaceutics 2022; 14:pharmaceutics14020454. [PMID: 35214187 PMCID: PMC8877061 DOI: 10.3390/pharmaceutics14020454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 12/13/2022] Open
Abstract
Temporins are one of the largest families of antimicrobial peptides with both anti-inflammatory and antimicrobial activity. Herein, for a panel of cyclic temporin L isoform analogues, the antifungal and antibiofilm activities were determined against representative Candida strains, including C. albicans, C. glabrata, C. auris, C. parapsilosis and C. tropicalis. The outcomes indicated a significant anti-candida activity against planktonic and biofilm growth for four peptides (3, 7, 15 and 16). The absence of toxicity up to high concentrations and survival after infection were assessed in vivo by using Galleria mellonella larvae, and the correlation between conformation and cytotoxicity was investigated by fluorescence assays and circular dichroism (CD). By combining fluorescence spectroscopy, CD, dynamic light scattering, confocal and atomic force microscopy, the mode of action of four analogues was hypothesized. The results pinpointed that peptide 3 emerged as a non-toxic compound showing a potent antibiofilm activity and represents a promising compound for biomedical applications.
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Affiliation(s)
- Rosa Bellavita
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy; (R.B.); (F.M.); (S.G.)
| | - Angela Maione
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (A.M.); (A.S.)
| | - Francesco Merlino
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy; (R.B.); (F.M.); (S.G.)
| | - Antonietta Siciliano
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (A.M.); (A.S.)
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy; (P.D.); (L.D.S.)
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy; (P.D.); (L.D.S.)
| | - Stefania Galdiero
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy; (R.B.); (F.M.); (S.G.)
| | - Emilia Galdiero
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (A.M.); (A.S.)
- Correspondence: (E.G.); (P.G.); (A.F.); Tel.: +39-081-679182 (E.G.); +39-081-678620 (P.G.); +39-081-2534503 (A.F.)
| | - Paolo Grieco
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy; (R.B.); (F.M.); (S.G.)
- Correspondence: (E.G.); (P.G.); (A.F.); Tel.: +39-081-679182 (E.G.); +39-081-678620 (P.G.); +39-081-2534503 (A.F.)
| | - Annarita Falanga
- Department of Agricultural Science, University of Naples ‘Federico II’, Via Università 100, 80055 Portici, Italy
- Correspondence: (E.G.); (P.G.); (A.F.); Tel.: +39-081-679182 (E.G.); +39-081-678620 (P.G.); +39-081-2534503 (A.F.)
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25
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ALBA MARYILORENASEGURA, DURÁN-RODRIGUEZ ANDREATATIANA, PULIDO LUZMARYSALAZAR, ESCOBAR-PÉREZ JAVIER, GUTIÉRREZ SERGIOALEJANDRO, OSPINA JEANNETTENAVARRETE, BERMÚDEZ GLADYSPINILLA, MOLINA LILIANACONSTANZAMUÑOZ. Peptides DLL37-1 and LL37-1, an alternative to inhibit biofilm formation in clinical isolates of Staphylococcus aureus and Staphylococcus epidermidis. AN ACAD BRAS CIENC 2022; 94:e20210848. [DOI: 10.1590/0001-3765202220210848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022] Open
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26
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Maddur AA, Voehler M, Panizzi P, Meiler J, Bock PE, Verhamme IM. Mapping of the fibrinogen-binding site on the staphylocoagulase C-terminal repeat region. J Biol Chem 2021; 298:101493. [PMID: 34915025 PMCID: PMC8761706 DOI: 10.1016/j.jbc.2021.101493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 01/12/2023] Open
Abstract
Fibrin (Fbn) deposits are a hallmark of staphylocoagulase (SC)-positive endocarditis. Binding of the N terminus of Staphylococcus aureus SC to host prothrombin triggers formation of an active SC·prothrombin∗ complex that cleaves host fibrinogen to Fbn. In addition, the C-terminal domain of the prototypical SC contains one pseudorepeat (PR) and seven repeats (R1 → R7) that bind fibrinogen/Fbn fragment D (frag D) by a mechanism that is unclear. Here, we define affinities and stoichiometries of frag D binding to C-terminal SC constructs, using fluorescence equilibrium binding, NMR titration, alanine scanning, and native PAGE. We found that constructs containing the PR and single repeats bound frag D with KD ∼50 to 130 nM and a 1:1 stoichiometry, indicating a conserved binding site bridging the PR and each repeat. NMR titration of PR-R7 with frag D revealed that residues 22 to 49, bridging PR and R7, constituted the minimal peptide (MP) for binding, corroborated by alanine scanning, and binding of labeled MP to frag D. MP alignment with the PR-R and inter-repeat junctions identified critical conserved residues. Full-length PR-(R1 → R7) bound frag D with KD ∼20 nM and a stoichiometry of 1:5, whereas constructs containing the PR and various three repeats competed with PR-(R1 → R7) for frag D binding, with a 1:3 stoichiometry. These findings are consistent with binding at PR-R and R-R junctions with modest inter-repeat sequence variability. CD of PR-R7 and PR-(R1 → R7) suggested a disordered flexible structure, allowing binding of multiple fibrin(ogen) molecules. Taken together, these results provide insights into pathogen localization on host fibrin networks.
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Affiliation(s)
- Ashoka A. Maddur
- FUJIFILM Diosynth Biotechnologies, College Station, Texas, USA,For correspondence: Ingrid M. Verhamme; Ashoka A. Maddur
| | - Markus Voehler
- Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Peter Panizzi
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, Alabama, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA,Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Paul E. Bock
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ingrid M. Verhamme
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,For correspondence: Ingrid M. Verhamme; Ashoka A. Maddur
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27
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Masquelier E, Liang SP, Sepunaru L, Morse DE, Gordon MJ. Reversible electrochemical triggering and optical interrogation of polylysine α-helix formation. Bioelectrochemistry 2021; 144:108007. [PMID: 34871847 DOI: 10.1016/j.bioelechem.2021.108007] [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: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Reversible electrochemical triggering of the random coil to α-helix conformational transition of polylysine (Lys10, Lys20, Lys50) was accomplished at a Pt electrode at potentials < |1| V vs. Ag/AgCl. Direct electroreduction of the N-terminus vs ε-amino groups in Lys sidechains, as well as hydronium reduction and electrolysis, could be easily distinguished and deconvolved using differential pulse voltammetry. Electrochemistry was coupled with in situ UV absorbance and circular dichroism spectroscopies to dynamically follow the evolution of α-helix formation at different potentials. Isotope experiments in H2O vs. D2O unequivocally confirm that direct electroreduction of ε-NH3+/ND3+ groups in Lys sidechains, rather than electrochemically generated pH gradient-induced deprotonation, leads to subsequent α-helix formation. The site-selective electrochemistry and optical methodologies presented herein can be generalized and extended to interrogate other protonation-sensitive biomolecular systems, and potentially provide access to early intermediates and control over the dynamic structural evolution of peptides and proteins.
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Affiliation(s)
- Eloise Masquelier
- Materials Department, University of California, Santa Barbara, CA, United States
| | - Sheng-Ping Liang
- Dept. Of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Lior Sepunaru
- Dept. Of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Daniel E Morse
- Dept. Of Molecular, Cellular and Development Biology, University of California, Santa Barbara, CA, United States; Institue for Collaborative Biotechnologies, University of California, Santa Barbara, CA, United States
| | - Michael J Gordon
- Dept. Of Chemical Engineering, University of California, Santa Barbara, CA, United States; Institue for Collaborative Biotechnologies, University of California, Santa Barbara, CA, United States.
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28
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Basso LGM, Zeraik AE, Felizatti AP, Costa-Filho AJ. Membranotropic and biological activities of the membrane fusion peptides from SARS-CoV spike glycoprotein: The importance of the complete internal fusion peptide domain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183697. [PMID: 34274319 PMCID: PMC8280623 DOI: 10.1016/j.bbamem.2021.183697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022]
Abstract
Fusion peptides (FP) are prominent hydrophobic segments of viral fusion proteins that play critical roles in viral entry. FPs interact with and insert into the host lipid membranes, triggering conformational changes in the viral protein that leads to the viral-cell fusion. Multiple membrane-active domains from the severe acute respiratory syndrome (SARS) coronavirus (CoV) spike protein have been reported to act as the functional fusion peptide such as the peptide sequence located between the S1/S2 and S2' cleavage sites (FP1), the S2'-adjacent fusion peptide domain (FP2), and the internal FP sequence (cIFP). Using a combined biophysical approach, we demonstrated that the α-helical coiled-coil-forming internal cIFP displayed the highest membrane fusion and permeabilizing activities along with membrane ordering effect in phosphatidylcholine (PC)/phosphatidylglycerol (PG) unilamellar vesicles compared to the other two N-proximal fusion peptide counterparts. While the FP1 sequence displayed intermediate membranotropic activities, the well-conserved FP2 peptide was substantially less effective in promoting fusion, leakage, and membrane ordering in PC/PG model membranes. Furthermore, Ca2+ did not enhance the FP2-induced lipid mixing activity in PC/phosphatidylserine/cholesterol lipid membranes, despite its strong erythrocyte membrane perturbation. Nonetheless, we found that the three putative SARS-CoV membrane-active fusion peptide sequences here studied altered the physical properties of model and erythrocyte membranes to different extents. The importance of the distinct membranotropic and biological activities of all SARS-CoV fusion peptide domains and the pronounced effect of the internal fusion peptide sequence to the whole spike-mediated membrane fusion process are discussed.
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Affiliation(s)
- Luis Guilherme Mansor Basso
- Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
| | - Ana Eliza Zeraik
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Ana Paula Felizatti
- Laboratório de Produtos Naturais, Departamento de Química, Centro de Ciências Exatas e de Tecnologia, Universidade Federal de São Carlos, Rod. Washington Luiz, Km 235, Monjolinho, 13565905, São Carlos, SP, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Antonio José Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
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29
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Bellavita R, Casciaro B, Di Maro S, Brancaccio D, Carotenuto A, Falanga A, Cappiello F, Buommino E, Galdiero S, Novellino E, Grossmann TN, Mangoni ML, Merlino F, Grieco P. First-in-Class Cyclic Temporin L Analogue: Design, Synthesis, and Antimicrobial Assessment. J Med Chem 2021; 64:11675-11694. [PMID: 34296619 PMCID: PMC8389922 DOI: 10.1021/acs.jmedchem.1c01033] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 02/08/2023]
Abstract
The pharmacodynamic and pharmacokinetic properties of bioactive peptides can be modulated by introducing conformational constraints such as intramolecular macrocyclizations, which can involve either the backbone and/or side chains. Herein, we aimed at increasing the α-helicity content of temporin L, an isoform of an intriguing class of linear antimicrobial peptides (AMPs), endowed with a wide antimicrobial spectrum, by the employment of diverse side-chain tethering strategies, including lactam, 1,4-substituted [1,2,3]-triazole, hydrocarbon, and disulfide linkers. Our approach resulted in a library of cyclic temporin L analogues that were biologically assessed for their antimicrobial, cytotoxic, and antibiofilm activities, leading to the development of the first-in-class cyclic peptide related to this AMP family. Our results allowed us to expand the knowledge regarding the relationship between the α-helical character of temporin derivatives and their biological activity, paving the way for the development of improved antibiotic cyclic AMP analogues.
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Affiliation(s)
- Rosa Bellavita
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Bruno Casciaro
- Center
for Life Nano- & Neuro-Science, Fondazione
Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi
Vanvitelli”, Caserta 81100, Italy
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Annarita Falanga
- Department
of Agricultural Sciences, University of
Naples “Federico II”, Portici 80055, Italy
| | - Floriana Cappiello
- Department
of Biochemical Sciences, Laboratory affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | - Elisabetta Buommino
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Stefania Galdiero
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Tom N. Grossmann
- Department
of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Maria Luisa Mangoni
- Department
of Biochemical Sciences, Laboratory affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | - Francesco Merlino
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
| | - Paolo Grieco
- Department
of Pharmacy, University of Naples “Federico
II”, Naples 80131, Italy
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30
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Bellavita R, Falanga A, Buommino E, Merlino F, Casciaro B, Cappiello F, Mangoni ML, Novellino E, Catania MR, Paolillo R, Grieco P, Galdieroa S. Novel temporin L antimicrobial peptides: promoting self-assembling by lipidic tags to tackle superbugs. J Enzyme Inhib Med Chem 2021; 35:1751-1764. [PMID: 32957844 PMCID: PMC7534258 DOI: 10.1080/14756366.2020.1819258] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rapid development of antimicrobial resistance is pushing the search in the discovering of novel antimicrobial molecules to prevent and treat bacterial infections. Self-assembling antimicrobial peptides, as the lipidated peptides, are a novel and promising class of molecules capable of meeting this need. Based on previous work on Temporin L analogs, several new molecules lipidated at the N- or and the C-terminus were synthesised. Our goal is to improve membrane interactions through finely tuning self-assembly to reduce oligomerisation in aqueous solution and enhance self-assembly in bacterial membranes while reducing toxicity against human cells. The results here reported show that the length of the aliphatic moiety is a key factor to control target cell specificity and the oligomeric state of peptides either in aqueous solution or in a membrane-mimicking environment. The results of this study pave the way for the design of novel molecules with enhanced activities.
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Affiliation(s)
- Rosa Bellavita
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Annarita Falanga
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | | | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Bruno Casciaro
- Center for Life Nano Science@Sapienza, Italian Institute of Technology, Rome, Italy
| | - Floriana Cappiello
- Department of Biochemical Sciences, Laboratory affiliated to Pasteur Institute Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences, Laboratory affiliated to Pasteur Institute Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Maria Rosaria Catania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Rossella Paolillo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Stefania Galdieroa
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
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31
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Martins IBS, Viegas TG, Dos Santos Alvares D, de Souza BM, Palma MS, Ruggiero Neto J, de Araujo AS. The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy. Amino Acids 2021; 53:753-767. [PMID: 33890127 DOI: 10.1007/s00726-021-02982-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/12/2021] [Indexed: 01/09/2023]
Abstract
Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.
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Affiliation(s)
- Ingrid Bernardes Santana Martins
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Taisa Giordano Viegas
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Dayane Dos Santos Alvares
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil
| | - Bibiana Monson de Souza
- Department of Basic and Applied Biology, Institute of Biosciences, UNESP-São Paulo State University, Rio Claro, SP, Brazil
| | - Mário Sérgio Palma
- Department of Basic and Applied Biology, Institute of Biosciences, UNESP-São Paulo State University, Rio Claro, SP, Brazil
| | - João Ruggiero Neto
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil.
| | - Alexandre Suman de Araujo
- Department of Physics, IBILCE, UNESP-São Paulo State University, Cristóvão Colombo, 2265-Jardim Nazareth, São José do Rio Preto, SP, 15054-000, Brazil.
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32
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Huynh L, Velásquez J, Rabara R, Basu S, Nguyen HB, Gupta G. Rational design of antimicrobial peptides targeting Gram-negative bacteria. Comput Biol Chem 2021; 92:107475. [PMID: 33813188 DOI: 10.1016/j.compbiolchem.2021.107475] [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: 12/31/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 01/16/2023]
Abstract
Membrane-targeting host antimicrobial peptides (AMPs) can kill or inhibit the growth of Gram-negative bacteria. However, the evolution of resistance among microbes poses a substantial barrier to the long-term utility of the host AMPs. Combining experiment and molecular dynamics simulations, we show that terminal carboxyl capping enhances both membrane insertion and antibacterial activity of an AMP called P1. Furthermore, we show that a bacterial strain with evolved resistance to this peptide becomes susceptible to P1 variants with either backbone capping or lysine-to-arginine substitutions. Our results suggest that cocktails of closely related AMPs may be useful in overcoming evolved resistance.
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Affiliation(s)
- Loan Huynh
- New Mexico Consortium, Los Alamos, NM, 87544, USA
| | | | - Roel Rabara
- New Mexico Consortium, Los Alamos, NM, 87544, USA
| | | | - Hau B Nguyen
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Goutam Gupta
- New Mexico Consortium, Los Alamos, NM, 87544, USA.
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33
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Yu M, Ghamsari L, Rotolo JA, Kappel BJ, Mason JM. Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor. RSC Chem Biol 2021; 2:656-668. [PMID: 34458807 PMCID: PMC8341738 DOI: 10.1039/d1cb00012h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022] Open
Abstract
To date, most research into the inhibition of oncogenic transcriptional regulator, Activator Protein 1 (AP-1), has focused on heterodimers of cJun and cFos. However, the Fra1 homologue remains an important cancer target. Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts. To do so the isCAN computational tool was used to rapidly screen >75 million peptide library members, narrowing the library size by >99.8% to one accessible to intracellular PCA selection. The resulting 131 072-member library was predicted to contain high quality binders with both a high likelihood of target engagement, while simultaneously avoiding homodimerization and off-target interaction with Jun homologues. PCA screening was next performed to enrich those members that meet these criteria. In particular, optimization was achieved via inclusion of options designed to generate the potential for compromised intermolecular contacts in both desired and non-desired species. This is an often-overlooked prerequisite in the conflicting design requirement of libraries that must be selective for their target in the context of a range of alternative potential interactions. Here we demonstrate that specificity is achieved via a combination of both hydrophobic and electrostatic contacts as exhibited by the selected peptide (Fra1W). In vitro analysis of the desired Fra1-Fra1W interaction further validates high Fra1 affinity (917 nM) yet selective binding relative to Fra1W homodimers or affinity for cJun. The isCAN → PCA based multidisciplinary approach provides a robust screening pipeline in generating target-specific hits, as well as new insight into rational peptide design in the search for novel bZIP family inhibitors.
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Affiliation(s)
- Miao Yu
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
| | - Lila Ghamsari
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jim A Rotolo
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Barry J Kappel
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
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34
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Hervás R, Del Carmen Fernández-Ramírez M, Galera-Prat A, Suzuki M, Nagai Y, Bruix M, Menéndez M, Laurents DV, Carrión-Vázquez M. Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. BMC Biol 2021; 19:43. [PMID: 33706787 PMCID: PMC7953810 DOI: 10.1186/s12915-021-00967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Amyloids are ordered, insoluble protein aggregates, characterized by a cross-β sheet quaternary structure in which molecules in a β-strand conformation are stacked along the filament axis via intermolecular interactions. While amyloids are typically associated with pathological conditions, functional amyloids have also been identified and are present in a wide variety of organisms ranging from bacteria to humans. The cytoplasmic polyadenylation element-binding (CPEB) prion-like protein is an mRNA-binding translation regulator, whose neuronal isoforms undergo activity-dependent aggregation, a process that has emerged as a plausible biochemical substrate for memory maintenance. CPEB aggregation is driven by prion-like domains (PLD) that are divergent in sequence across species, and it remains unknown whether such divergent PLDs follow a similar aggregating assembly pathway. Here, we describe the amyloid-like features of the neuronal Aplysia CPEB (ApCPEB) PLD and compare them to those of the Drosophila ortholog, Orb2 PLD. RESULTS Using in vitro single-molecule and bulk biophysical methods, we find transient oligomers and mature amyloid-like filaments that suggest similarities in the late stages of the assembly pathway for both ApCPEB and Orb2 PLDs. However, while prior to aggregation the Orb2 PLD monomer remains mainly as a random coil in solution, ApCPEB PLD adopts a diversity of conformations comprising α-helical structures that evolve to coiled-coil species, indicating structural differences at the beginning of their amyloid assembly pathways. CONCLUSION Our results indicate that divergent PLDs of CPEB proteins from different species retain the ability to form a generic amyloid-like fold through different assembly mechanisms.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, E-28002, Madrid, Spain. .,Present address: School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | | | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Department of Neurology, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), C/ Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
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35
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Draganova EB, Heldwein EE. Virus-derived peptide inhibitors of the herpes simplex virus type 1 nuclear egress complex. Sci Rep 2021; 11:4206. [PMID: 33603021 PMCID: PMC7893173 DOI: 10.1038/s41598-021-83402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/01/2021] [Indexed: 11/12/2022] Open
Abstract
Herpesviruses infect a majority of the human population, establishing lifelong latent infections for which there is no cure. Periodic viral reactivation spreads infection to new hosts while causing various disease states particularly detrimental in the immunocompromised. Efficient viral replication, and ultimately the spread of infection, is dependent on the nuclear egress complex (NEC), a conserved viral heterodimer that helps translocate viral capsids from the nucleus to the cytoplasm where they mature into infectious virions. Here, we have identified peptides, derived from the capsid protein UL25, that are capable of inhibiting the membrane-budding activity of the NEC from herpes simplex virus type 1 in vitro. We show that the inhibitory ability of the peptides depends on their length and the propensity to form an α-helix but not on the exact amino acid sequence. Current therapeutics that target viral DNA replication machinery are rendered ineffective by drug resistance due to viral mutations. Our results establish a basis for the development of an alternative class of inhibitors against nuclear egress, an essential step in herpesvirus replication, potentially expanding the current repertoire of available therapeutics.
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Affiliation(s)
- Elizabeth B Draganova
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Ekaterina E Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA.
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36
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Jorgensen MD, Chmielewski J. Reversible crosslinked assembly of a trimeric coiled-coil peptide into a three-dimensional matrix for cell encapsulation and release. J Pept Sci 2021; 28:e3302. [PMID: 33506586 DOI: 10.1002/psc.3302] [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: 09/29/2020] [Revised: 12/16/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
Mimicking the extracellular matrix (ECM) continues to be a goal in the field of regenerative medicine. Herein, we report a modified trimeric GCN4 coiled-coil sequence containing three ligands for metal ions specifically positioned for crosslinked assembly (TriCross). In the presence of metal ions, TriCross assembles into a three-dimensional (3D) matrix with significant cavities to accommodate cells. The matrix was found to be stable in media with serum, and mild removal of the metal leads to disassembly. By assembling TriCross with a suspension of cells in media, the matrix encapsulates cells during the assembly process leading to high cell viability. Further disassembly under mild conditions allows for the release of cells from the scaffold. As such, this peptide-based material displays many of the characteristics necessary for successful 3D cell culture.
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Affiliation(s)
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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37
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Shigedomi K, Osada S, Jelokhani-Niaraki M, Kodama H. Systematic Design and Validation of Ion Channel Stabilization of Amphipathic α-Helical Peptides Incorporating Tryptophan Residues. ACS OMEGA 2021; 6:723-732. [PMID: 33553860 PMCID: PMC7853622 DOI: 10.1021/acsomega.0c05254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/17/2020] [Indexed: 05/27/2023]
Abstract
Aromatic interactions such as π-π interaction and cation-π interaction are present in membrane proteins and play important roles in both structure and function. To systematically investigate the effect of aromatic residues on the structural stability and ion permeability of peptide-formed ion channels, we designed several peptides with one or two tryptophan (Trp) residues incorporated at different positions in amphipathic α-helical peptides. Circular dichroism (CD) studies revealed the preferable position of Trp residues for self-association in these designed peptides. Systematically designed di-substituted peptides with two Trps at each helix termini demonstrated intermolecular Trp-Trp interactions caused by aggregation. In the presence of liposomes, Trp on the hydrophilic face of the peptide enhanced interaction with the lipid membrane to increase the amphipathic α-helical contents. Appropriate incorporation and positioning of Trp enabled peptides to form more stable channels and had notable effects with Trp di-substituted peptides. The ion channel forming capability of a series of these peptides showed that the cation-π interactions between Trp and Lys residues in adjacent transmembrane helices contribute to remarkable stabilization of the channel structure.
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Affiliation(s)
- Keita Shigedomi
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Satoshi Osada
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masoud Jelokhani-Niaraki
- Department
of Chemistry and Biochemistry, Wilfrid Laurier
University, Waterloo, Ontario N2L3C5, Canada
| | - Hiroaki Kodama
- Department
of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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López‐García P, de Araujo AD, Bergues‐Pupo AE, Tunn I, Fairlie DP, Blank KG. Fortified Coiled Coils: Enhancing Mechanical Stability with Lactam or Metal Staples. Angew Chem Int Ed Engl 2021; 60:232-236. [PMID: 32940968 PMCID: PMC7821110 DOI: 10.1002/anie.202006971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 12/19/2022]
Abstract
Coiled coils (CCs) are powerful supramolecular building blocks for biomimetic materials, increasingly used for their mechanical properties. Here, we introduce helix-inducing macrocyclic constraints, so-called staples, to tune thermodynamic and mechanical stability of CCs. We show that thermodynamic stabilization of CCs against helix uncoiling primarily depends on the number of staples, whereas staple positioning controls CC mechanical stability. Inserting a covalent lactam staple at one key force application point significantly increases the barrier to force-induced CC dissociation and reduces structural deformity. A reversible His-Ni2+ -His metal staple also increases CC stability, but ruptures upon mechanical loading to allow helix uncoiling. Staple type, position and number are key design parameters in using helical macrocyclic templates for fine-tuning CC properties in emerging biomaterials.
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Affiliation(s)
- Patricia López‐García
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Aline D. de Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Ana E. Bergues‐Pupo
- Department of Theory and Bio-SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Present address: Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine10115BerlinGermany
| | - Isabell Tunn
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - David P. Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Kerstin G. Blank
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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Hurd CA, Brear P, Revell J, Ross S, Mott HR, Owen D. Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases. J Biol Chem 2021; 296:100101. [PMID: 33214225 PMCID: PMC7949049 DOI: 10.1074/jbc.ra120.015735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Ral GTPases have been implicated as critical drivers of cell growth and metastasis in numerous Ras-driven cancers. We have previously reported stapled peptides, based on the Ral effector RLIP76, that can disrupt Ral signaling. Stapled peptides are short peptides that are locked into their bioactive form using a synthetic brace. Here, using an affinity maturation of the RLIP76 Ral-binding domain, we identified several sequence substitutions that together improve binding to Ral proteins by more than 20-fold. Hits from the selection were rigorously analyzed to determine the contributions of individual residues and two 1.5 Å cocrystal structures of the tightest-binding mutants in complex with RalB revealed key interactions. Insights gained from this maturation were used to design second-generation stapled peptides based on RLIP76 that exhibited vastly improved selectivity for Ral GTPases when compared with the first-generation lead peptide. The binding of second-generation peptides to Ral proteins was quantified and the binding site of the lead peptide on RalB was determined by NMR. Stapled peptides successfully competed with multiple Ral-effector interactions in cellular lysates. Our findings demonstrate how manipulation of a native binding partner can assist in the rational design of stapled peptide inhibitors targeting a protein-protein interaction.
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Affiliation(s)
- Catherine A Hurd
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jefferson Revell
- AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge, UK
| | - Sarah Ross
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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40
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Drab E, Sugihara K. Cooperative Function of LL-37 and HNP1 Protects Mammalian Cell Membranes from Lysis. Biophys J 2020; 119:2440-2450. [PMID: 33157121 DOI: 10.1016/j.bpj.2020.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/08/2020] [Indexed: 01/10/2023] Open
Abstract
LL-37, cleaved from human cathelicidin, and human neutrophil peptide-1 (HNP1) from the defensin family are antimicrobial peptides that are occasionally co-released from neutrophils, which synergistically kill bacteria. We report that this couple presents another type of cooperativity against host eukaryotic cells, in which they antagonistically minimize cytotoxicity by protecting membranes from lysis. Our results describe the potential of the LL-37/HNP1 cooperativity that switches from membrane-destructive to membrane-protective functions, depending on whether the target is an enemy or a host.
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Affiliation(s)
- Ewa Drab
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
| | - Kaori Sugihara
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan; Department of Physical Chemistry, University of Geneva, Geneva, Switzerland.
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41
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López‐García P, Araujo AD, Bergues‐Pupo AE, Tunn I, Fairlie DP, Blank KG. Mechanische Verstärkung von Coiled Coils mit Lactam und Histidin‐Metall‐Klammern. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patricia López‐García
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
| | - Aline D. Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australien
| | - Ana E. Bergues‐Pupo
- Abteilung für Theorie und Bio-Systeme Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
- Aktuelle Adresse: Berlin Institute for Medical Systems Biology Max-Delbrück-Centrum für Molekulare Medizin 10115 Berlin Deutschland
| | - Isabell Tunn
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
| | - David P. Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australien
| | - Kerstin G. Blank
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
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42
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McKay MJ, Greathouse DV, Koeppe RE. Flanking aromatic residue competition influences transmembrane peptide helix dynamics. FEBS Lett 2020; 594:4280-4291. [DOI: 10.1002/1873-3468.13926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew J. McKay
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Denise V. Greathouse
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville AR USA
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43
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Armiento V, Hille K, Naltsas D, Lin JS, Barron AE, Kapurniotu A. Das humane Wirtsabwehrpeptid Cathelicidin LL‐37 ist ein nanomolarer Inhibitor der amyloiden Selbstassoziation von Inselamyloid‐Polypeptid (IAPP). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Valentina Armiento
- Division of Peptide Biochemistry TUM School of Life Sciences Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
| | - Kathleen Hille
- Division of Peptide Biochemistry TUM School of Life Sciences Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
| | - Denise Naltsas
- Division of Peptide Biochemistry TUM School of Life Sciences Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
| | - Jennifer S. Lin
- Department of Bioengineering Stanford University 443 Via Ortega, Shriram Center for Bioengineering Stanford CA 94305 USA
| | - Annelise E. Barron
- Department of Bioengineering Stanford University 443 Via Ortega, Shriram Center for Bioengineering Stanford CA 94305 USA
| | - Aphrodite Kapurniotu
- Division of Peptide Biochemistry TUM School of Life Sciences Emil-Erlenmeyer-Forum 5 85354 Freising Deutschland
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44
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Armiento V, Hille K, Naltsas D, Lin JS, Barron AE, Kapurniotu A. The Human Host-Defense Peptide Cathelicidin LL-37 is a Nanomolar Inhibitor of Amyloid Self-Assembly of Islet Amyloid Polypeptide (IAPP). Angew Chem Int Ed Engl 2020; 59:12837-12841. [PMID: 31999880 PMCID: PMC7497016 DOI: 10.1002/anie.202000148] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Indexed: 01/18/2023]
Abstract
Amyloid self-assembly of islet amyloid polypeptide (IAPP) is linked to pancreatic inflammation, β-cell degeneration, and the pathogenesis of type 2 diabetes (T2D). The multifunctional host-defence peptides (HDPs) cathelicidins play crucial roles in inflammation. Here, we show that the antimicrobial and immunomodulatory polypeptide human cathelicidin LL-37 binds IAPP with nanomolar affinity and effectively suppresses its amyloid self-assembly and related pancreatic β-cell damage in vitro. In addition, we identify key LL-37 segments that mediate its interaction with IAPP. Our results suggest a possible protective role for LL-37 in T2D pathogenesis and offer a molecular basis for the design of LL-37-derived peptides that combine antimicrobial, immunomodulatory, and T2D-related anti-amyloid functions as promising candidates for multifunctional drugs.
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Affiliation(s)
- Valentina Armiento
- Division of Peptide BiochemistryTUM School of Life SciencesEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Kathleen Hille
- Division of Peptide BiochemistryTUM School of Life SciencesEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Denise Naltsas
- Division of Peptide BiochemistryTUM School of Life SciencesEmil-Erlenmeyer-Forum 585354FreisingGermany
| | - Jennifer S. Lin
- Department of BioengineeringStanford University443 Via Ortega, Shriram Center for BioengineeringStanfordCA94305USA
| | - Annelise E. Barron
- Department of BioengineeringStanford University443 Via Ortega, Shriram Center for BioengineeringStanfordCA94305USA
| | - Aphrodite Kapurniotu
- Division of Peptide BiochemistryTUM School of Life SciencesEmil-Erlenmeyer-Forum 585354FreisingGermany
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45
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Marichal L, Degrouard J, Gatin A, Raffray N, Aude JC, Boulard Y, Combet S, Cousin F, Hourdez S, Mary J, Renault JP, Pin S. From Protein Corona to Colloidal Self-Assembly: The Importance of Protein Size in Protein-Nanoparticle Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8218-8230. [PMID: 32585107 DOI: 10.1021/acs.langmuir.0c01334] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein adsorption on nanoparticles is an important field of study, particularly with regard to nanomedicine and nanotoxicology. Many factors can influence the composition and structure of the layer(s) of adsorbed proteins, the so-called protein corona. However, the role of protein size has not been specifically investigated, although some evidence has indicated its potential important role in corona composition and structure. To assess the role of protein size, we studied the interactions of hemoproteins (spanning a large size range) with monodisperse silica nanoparticles. We combined various techniques-adsorption isotherms, isothermal titration calorimetry, circular dichroism, and transmission electron cryomicroscopy-to address this issue. Overall, the results show that small proteins behaved as typical model proteins, forming homogeneous monolayers on the nanoparticle surface (protein corona). Their adsorption is purely enthalpy-driven, with subtle structural changes. In contrast, large proteins interact with nanoparticles via entropy-driven mechanisms. Their structure is completely preserved during adsorption, and any given protein can directly bind to several nanoparticles, forming bridges in these newly formed protein-nanoparticle assemblies. Protein size is clearly an overlooked factor that should be integrated into proteomics and toxicological studies.
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Affiliation(s)
- Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Anouchka Gatin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | - Nolwenn Raffray
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
| | | | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, 91190 Gif-sur-Yvette, France
| | - Sophie Combet
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Fabrice Cousin
- Université Paris-Saclay, Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Jean Mary
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Team DYDIV, Station Biologique de Roscoff, 29680 Roscoff, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91190 Gif-sur-Yvette, France
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46
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Sano KI, Yuki T, Nomata Y, Nakayama N, Iida R, Mitomo H, Ijiro K, Osada Y. Intrahelical Interactions in an α-Helical Coiled Coil Determine the Structural Stability of Tropomyosin. Biochemistry 2020; 59:2194-2202. [DOI: 10.1021/acs.biochem.0c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ken-Ichi Sano
- Department of Applied Chemistry, Faculty of Fundamental Engineering, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Tsubasa Yuki
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Yuta Nomata
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major, Nippon Institute of Technology, Miyashiro, Saitama 345-8501, Japan
| | - Ryo Iida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hideyuki Mitomo
- Research Institute for Electronic Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0021, Japan
| | - Kuniharu Ijiro
- Research Institute for Electronic Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 001-0021, Japan
| | - Yoshihito Osada
- Nano Medical Engineering Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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47
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Knox-Brown P, Rindfleisch T, Günther A, Balow K, Bremer A, Walther D, Miettinen MS, Hincha DK, Thalhammer A. Similar Yet Different-Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins. Int J Mol Sci 2020; 21:E2794. [PMID: 32316452 PMCID: PMC7215670 DOI: 10.3390/ijms21082794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.
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Affiliation(s)
- Patrick Knox-Brown
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Tobias Rindfleisch
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Anne Günther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Kim Balow
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anne Bremer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
- Department for Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dirk Walther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Markus S. Miettinen
- Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476 Potsdam, Germany;
| | - Dirk K. Hincha
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
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48
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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49
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Comparison of the structural dynamic and mitochondrial electron-transfer properties of the proapoptotic human cytochrome c variants, G41S, Y48H and A51V. J Inorg Biochem 2020; 203:110924. [DOI: 10.1016/j.jinorgbio.2019.110924] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023]
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50
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Chen X, Ji S, Li A, Liu H, Fei H. Toggling Preassembly with Single-Site Mutation Switches the Cytotoxic Mechanism of Cationic Amphipathic Peptides. J Med Chem 2020; 63:1132-1141. [PMID: 31927997 DOI: 10.1021/acs.jmedchem.9b01458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Precise regulation of membrane-active peptide activity is a frontier of research to facilitate its applicational translation. A clear understanding of how a peptide's physicochemical properties determine its mode of action (MOA) will aid the process. Herein, anionic glutamate residue-based scanning was applied to the hydrophobic surface of a self-assembling lysine-rich cationic amphipathic peptide (CAP) KL1. Single-site mutations from leucine to glutamate dramatically changed the MOA of all mutants from membranolytic to nonlytic. An apoptosis-inducing mutant L2E unable to self-assemble under extracellular anions exhibited a different conformational transformation process in the amphiphilic environment than KL1. Further adjustment of the overall positive charge allowed regulation of cytotoxic potency without affecting the MOA determined by the lack of preassembly formation. Compared with KL1, hemolytic toxicities of nonmembranolytic peptides were greatly reduced, with safety indices increased. This work thus provided novel insights into and integrated rationales on the improvement of CAPs for both anticancer activity and safety profile.
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Affiliation(s)
- Xiaolong Chen
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , P R China.,CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P R China
| | - Shuangshuang Ji
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , P R China.,CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P R China
| | - Ang Li
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , P R China.,CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P R China
| | - Hanjie Liu
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , P R China.,CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P R China
| | - Hao Fei
- School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , P R China.,CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine , Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123 , P R China
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