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Cavini IA, Fontes MG, Zeraik AE, Lopes JLS, Araujo APU. Novel lipid-interaction motifs within the C-terminal domain of Septin10 from Schistosoma mansoni. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184371. [PMID: 39025256 DOI: 10.1016/j.bbamem.2024.184371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Septins are cytoskeletal proteins and their interaction with membranes is crucial for their role in various cellular processes. Septins have polybasic regions (PB1 and PB2) which are important for lipid interaction. Earlier, we and others have highlighted the role of the septin C-terminal domain (CTD) to membrane interaction. However, detailed information on residues/group of residues important for such feature is lacking. In this study, we investigate the lipid-binding profile of Schistosoma mansoni Septin10 (SmSEPT10) using PIP strip and Langmuir monolayer adsorption assays. Our findings highlight the CTD as the primary domain responsible for lipid interaction in SmSEPT10, showing binding to phosphatidylinositol phosphates. SmSEPT10 CTD contains a conserved polybasic region (PB3) present in both animals and fungi septins, and a Lys (K367) within its putative amphipathic helix (AH) that we demonstrate as important for lipid binding. PB3 deletion or mutation of this Lys (K367A) strongly impairs lipid interaction. Remarkably, we observe that the AH within a construct lacking the final 43 amino acid residues is insufficient for lipid binding. Furthermore, we investigate the homocomplex formed by SmSEPT10 CTD in solution by cross-linking experiments, CD spectroscopy, SEC-MALS and SEC-SAXS. Taken together, our studies define the lipid-binding region in SmSEPT10 and offer insights into the molecular basis of septin-membrane binding. This information is particularly relevant for less-studied non-human septins, such as SmSEPT10.
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Affiliation(s)
- Italo A Cavini
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil; School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Marina G Fontes
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil; Department of Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Ana Eliza Zeraik
- Laboratory of Chemistry and Function of Proteins and Peptides, Center for Biosciences and Biotechnology, North Fluminense State University Darcy Ribeiro, Campos dos Goytacazes, RJ 28013-602, Brazil
| | - Jose L S Lopes
- Laboratory of Molecular Biophysics, Department of Physics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901, Brazil
| | - Ana Paula U Araujo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil.
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2
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Otzen DE, Pedersen JN, Rasmussen HØ, Pedersen JS. How do surfactants unfold and refold proteins? Adv Colloid Interface Sci 2022; 308:102754. [PMID: 36027673 DOI: 10.1016/j.cis.2022.102754] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/25/2022] [Accepted: 08/10/2022] [Indexed: 11/01/2022]
Abstract
Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein separation and size estimation, there is still controversy about its mode of interaction with proteins. The term "rod-like" structures for the complexes that form between SDS and protein, originally introduced by Tanford, is not sufficiently descriptive and does not distinguish between the two current vying models, namely protein-decorated micelles a.k.a. the core-shell model (in which denatured protein covers the surface of micelles) versus beads-on-a-string model (where unfolded proteins are surrounded by surfactant micelles). Thanks to a combination of structural, kinetic and computational work particularly within the last 5-10 years, it is now possible to rule decisively in favor of the core-shell model. This is supported unambiguously by a combination of calorimetric and small-angle X-ray scattering (SAXS) techniques and confirmed by increasingly sophisticated molecular dynamics simulations. Depending on the SDS:protein ratio and the protein molecular mass, the formed structures can range from multiple partly unfolded protein molecules surrounding a single shared micelle to a single polypeptide chain decorating multiple micelles. We also have much new insight into how this species forms. It is preceded by the binding of small numbers of SDS molecules which subsequently grow by accretion. Time-resolved SAXS analysis reveals an asymmetric attack by SDS micelles followed by distribution of the increasingly unfolded protein around the micelle. The compactness of the protein chain continues to evolve at higher SDS concentrations according to single-molecule studies, though the protein remains completely denatured on the tertiary structural level. SDS denaturation can be reversed by addition of nonionic surfactants that absorb SDS forming mixed micelles, leaving the protein free to refold. Refolding can occur in parallel tracks if only a fraction of the protein is initially stripped of SDS. SDS unfolding is nearly always reversible unless carried out at low pH, where charge neutralization can lead to superclusters of protein-surfactant complexes. With the general mechanism of SDS denaturation now firmly established, it largely remains to explore how other ionic surfactants (including biosurfactants) may diverge from this path.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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3
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Liu Y, Zhao C, Chen C. Chirality-Governed UCST Behavior in Polypeptides. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yali Liu
- Ningbo Key Laboratory of Specialty Polymers, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Chuanzhuang Zhao
- Ningbo Key Laboratory of Specialty Polymers, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Chongyi Chen
- Ningbo Key Laboratory of Specialty Polymers, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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4
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Zhang L, Wu Y, Luo X, Jia T, Li K, Zhou L, Mao Z, Huang P. A novel insight into mechanism of derangement of coagulation balance: interactions of quantum dots with coagulation-related proteins. Part Fibre Toxicol 2022; 19:17. [PMID: 35260173 PMCID: PMC8903618 DOI: 10.1186/s12989-022-00458-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Quantum dots (QDs) have gained increased attention for their extensive biomedical and electronic products applications. Due to the high priority of QDs in contacting the circulatory system, understanding the hemocompatibility of QDs is one of the most important aspects for their biosafety evaluation. Thus far, the effect of QDs on coagulation balance haven’t been fully understood, and limited studies also have yet elucidated the potential mechanism from the perspective of interaction of QDs with coagulation-related proteins. Results QDs induced the derangement of coagulation balance by prolonging the activated partial thromboplastin time and prothrombin time as well as changing the expression levels of coagulation and fibrinolytic factors. The contact of QDs with PTM (prothrombin), PLG (plasminogen) and FIB (fibrinogen) which are primary coagulation-related proteins in the coagulation and fibrinolysis systems formed QDs-protein conjugates through hydrogen-bonding and hydrophobic interaction. The affinity of proteins with QDs followed the order of PTM > PLG > FIB, and was larger with CdTe/ZnS QDs than CdTe QDs. Binding with QDs not only induced static fluorescence quenching of PTM, PLG and FIB, but also altered their conformational structures. The binding of QDs to the active sites of PTM, PLG and FIB may promote the activation of proteins, thus interfering the hemostasis and fibrinolysis processes. Conclusions The interactions of QDs with PTM, PLG and FIB may be key contributors for interference of coagulation balance, that is helpful to achieve a reliable and comprehensive evaluation on the potential biological influence of QDs from the molecular level. Supplementary Information The online version contains supplementary material available at 10.1186/s12989-022-00458-x.
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Affiliation(s)
- Lingyan Zhang
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China.,School of Public Health, Baotou Medical College, 31# Jianshe Road, Donghe District, Baotou, 014040, China
| | - Yingting Wu
- Core Facility Center, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Xingling Luo
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Tianjiang Jia
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Kexin Li
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Lihong Zhou
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Zhen Mao
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China
| | - Peili Huang
- School of Public Health, Capital Medical University, No. 10 Xitoutiao You An Men, Beijing, 100069, China.
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5
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Ardalan A, Sowlati-Hashjin S, Oduwoye H, Uwumarenogie SO, Karttunen M, Smith MD, Jelokhani-Niaraki M. Biphasic Proton Transport Mechanism for Uncoupling Proteins. J Phys Chem B 2021; 125:9130-9144. [PMID: 34365794 DOI: 10.1021/acs.jpcb.1c04766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been suggested that uncoupling proteins (UCPs) transport protons via interconversion between two conformational states: one in the "cytoplasmic state" and the other in the "matrix state". Matrix and cytoplasmic salt-bridge networks are key controllers of these states. This study proposes a mechanism for proton transport in tetrameric UCP2, with focus on the role of the matrix network. Eleven mutants were prepared to disrupt (K → Q or D → N mutations) or alter (K → D and D → K mutations) the salt-bridges in the matrix network. Proteins were recombinantly expressed in Escherichia coli membrane, reconstituted in model lipid membranes, and their structures and functions were analyzed by gel electrophoresis, circular dichroism spectroscopy, fluorescence assays, as well as molecular dynamics simulations. It is shown that the UCP2 matrix network contains five salt-bridges (rather than the previously reported three), and the matrix network can regulate the proton transport by holding the protein's transmembrane helices in close proximity, limiting the movement of the activator fatty acid(s). A biphasic two-state molecular model is proposed for proton transport in tetrameric (a dimer of stable dimers) UCP2, in which all the monomers are functional, and monomers in each dimer are in the same transport mode. Purine nucleotide (e.g., ATP) can occlude the internal pore of the monomeric units of UCP tetramers via interacting with positive residues at or in the proximity of the matrix network (K38, K141, K239, R88, R185, and R279) and prevent switching between cytoplasmic and matrix states, thus inhibiting the proton transport. This study provides new insights into the mechanism of proton transport and regulation in UCPs.
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Affiliation(s)
- Afshan Ardalan
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada.,The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario N6K 3K7, Canada
| | - Habib Oduwoye
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Stephanie O Uwumarenogie
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada.,The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario N6K 3K7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
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6
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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7
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Structural Analysis of the cl-Par-4 Tumor Suppressor as a Function of Ionic Environment. Biomolecules 2021; 11:biom11030386. [PMID: 33807852 PMCID: PMC7998163 DOI: 10.3390/biom11030386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/09/2023] Open
Abstract
Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate the 25 kDa functionally active cleaved Par-4 protein (cl-Par-4) that inhibits NF-κB-mediated cell survival pathways and causes selective apoptosis in tumor cells. Here, we have employed circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) to assess the effects of various monovalent and divalent salts upon the conformation of cl-Par-4 in vitro. We have previously shown that high levels of sodium can induce the cl-Par-4 fragment to form highly compact, highly helical tetramers in vitro. Spectral characteristics suggest that most or at least much of the helical content in these tetramers are non-coiled coils. Here, we have shown that potassium produces a similar effect as was previously reported for sodium and that magnesium salts also produce a similar conformation effect, but at an approximately five times lower ionic concentration. We have also shown that anion identity has far less influence than does cation identity. The degree of helicity induced by each of these salts suggests that the "Selective for Apoptosis in Cancer cells" (SAC) domain-the region of Par-4 that is most indispensable for its apoptotic function-is likely to be helical in cl-Par-4 under the studied high salt conditions. Furthermore, we have shown that under medium-strength ionic conditions, a combination of high molecular weight aggregates and smaller particles form and that the smaller particles are also highly helical, resembling at least in secondary structure, the tetramers found at high salt.
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8
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Ardalan A, Sowlati-Hashjin S, Uwumarenogie SO, Fish M, Mitchell J, Karttunen M, Smith MD, Jelokhani-Niaraki M. Functional Oligomeric Forms of Uncoupling Protein 2: Strong Evidence for Asymmetry in Protein and Lipid Bilayer Systems. J Phys Chem B 2020; 125:169-183. [PMID: 33373220 DOI: 10.1021/acs.jpcb.0c09422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Stoichiometry of uncoupling proteins (UCPs) and their coexistence as functional monomeric and associated forms in lipid membranes remain intriguing open questions. In this study, tertiary and quaternary structures of UCP2 were analyzed experimentally and through molecular dynamics (MD) simulations. UCP2 was overexpressed in the inner membrane of Escherichia coli, then purified and reconstituted in lipid vesicles. Structure and proton transport function of UCP2 were characterized by circular dichroism (CD) spectroscopy and fluorescence methods. Findings suggest a tetrameric functional form for UCP2. MD simulations conclude that tetrameric UCP2 is a dimer of dimers, is more stable than its monomeric and dimeric forms, is asymmetrical and induces asymmetry in the membrane's lipid structure, and a biphasic on-off switch between the dimeric units is its possible mode of transport. MD simulations also show that the water density inside the UCP2 monomer is asymmetric, with the cytoplasmic side having a higher water density and a wider radius. In contrast, the structurally comparable adenosine 5'-diphosphate (ADP)/adenosine 5'-triphosphate (ATP) carrier (AAC1) did not form tetramers, implying that tetramerization cannot be generalized to all mitochondrial carriers.
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Affiliation(s)
- Afshan Ardalan
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 3K7.,Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario, Canada N6K 3K7
| | - Stephanie O Uwumarenogie
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Michael Fish
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5.,Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Joel Mitchell
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 3K7.,Center for Advanced Materials and Biomaterials Research, The University of Western Ontario, London, Ontario, Canada N6K 3K7.,Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada N2L 3C5
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9
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Li J, Zhao Y, Zhou P, Hu X, Wang D, King SM, Rogers SE, Wang J, Lu JR, Xu H. Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003945. [PMID: 33015967 DOI: 10.1002/smll.202003945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Sarah E Rogers
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
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10
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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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11
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Fujii S, Kuroyanagi S, Shimada N, Matsuno J, Lee JH, Takahashi R, Maruyama A, Sakurai K. Bundling Process of Citrulline Polypeptides upon UCST-Type Phase Separation. J Phys Chem B 2020; 124:4036-4043. [PMID: 32311261 DOI: 10.1021/acs.jpcb.0c00934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ureido-modified poly(l-citrulline) (l-ornithine-co-l-citrulline denoted by PlOC) shows UCST-type phase separation behavior even under physiologically relevant conditions, which forms an α-helix structure above its phase separation temperature (Tp) but transforms into a solid-like aggregation composed of regular hexagonal packed cylinders below the Tp. This morphological transformation is characteristic of the phase separation behavior, but the mechanism behind it has remained incompletely understood. Here, we studied the phase separation behavior using small-angle X-ray scattering (SAXS) measurements. To analyze the SAXS data, we employed the modified unified model proposed previously, which decomposes the scattering profile into each structural element, such as the α-helices and their aggregation formed via hydrogen-bonding interactions between the ureido groups. The aggregation level is dependent on the temperature (T) and grouped into three classes: (1) mass-fractal aggregation composed of the α-helix (T > Tp), (2) spherical aggregation composed of the hexagonal packed cylinder (T < Tp), and (3) micro-order agglomeration formed by mutual fusion of the spherical aggregation, which appears as a solid-like aggregation. The SAXS analysis suggested that the transformation from the dispersed state as the α-helix to the agglomeration containing hierarchical structures occurs in a stepwise manner when the temperature falls below the Tp, which might also be transition behavior similar to the process of protein folding through folding intermediates.
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Affiliation(s)
- Shota Fujii
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu-City, Fukuoka 808-0135, Japan
| | - Sotaro Kuroyanagi
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Jun Matsuno
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu-City, Fukuoka 808-0135, Japan
| | - Ji Ha Lee
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu-City, Fukuoka 808-0135, Japan
| | - Rintaro Takahashi
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu-City, Fukuoka 808-0135, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu-City, Fukuoka 808-0135, Japan
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12
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Cosert KM, Castro-Forero A, Steidl RJ, Worden RM, Reguera G. Bottom-Up Fabrication of Protein Nanowires via Controlled Self-Assembly of Recombinant Geobacter Pilins. mBio 2019; 10:e02721-19. [PMID: 31822587 PMCID: PMC6904877 DOI: 10.1128/mbio.02721-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Metal-reducing bacteria in the genus Geobacter use a complex protein apparatus to guide the self-assembly of a divergent type IVa pilin peptide and synthesize conductive pilus appendages that show promise for the sustainable manufacturing of protein nanowires. The preferential helical conformation of the Geobacter pilin, its high hydrophobicity, and precise distribution of charged and aromatic amino acids are critical for biological self-assembly and conductivity. We applied this knowledge to synthesize via recombinant methods truncated pilin peptides for the bottom-up fabrication of protein nanowires and identified rate-limiting steps of pilin nucleation and fiber elongation that control assembly efficiency and nanowire length, respectively. The synthetic fibers retained the biochemical and electronic properties of the native pili even under chemical fixation, a critical consideration for integration of the nanowires into electronic devices. The implications of these results for the design and mass production of customized protein nanowires for diverse applications are discussed.IMPORTANCE The discovery in 2005 of conductive protein appendages (pili) in the metal-reducing bacterium Geobacter sulfurreducens challenged our understanding of biological electron transfer and pioneered studies in electromicrobiology that revealed the electronic basis of many microbial metabolisms and interactions. The protein nature of the pili afforded opportunities for engineering novel conductive peptides for the synthesis of nanowires via cost-effective and scalable manufacturing approaches. However, methods did not exist for efficient production, purification, and in vitro assembly of pilins into nanowires. Here we describe platforms for high-yield recombinant synthesis of Geobacter pilin derivatives and their assembly as protein nanowires with biochemical and electronic properties rivaling those of the native pili. The bottom-up fabrication of protein nanowires exclusively from pilin building blocks confirms unequivocally the charge transport capacity of the peptide assembly and establishes the intellectual foundation needed to manufacture pilin-based nanowires in bioelectronics and other applications.
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Affiliation(s)
- K M Cosert
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | | | - Rebecca J Steidl
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Robert M Worden
- Department of Chemical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - G Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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13
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Kuroyanagi S, Shimada N, Fujii S, Furuta T, Harada A, Sakurai K, Maruyama A. Highly Ordered Polypeptide with UCST Phase Separation Behavior. J Am Chem Soc 2018; 141:1261-1268. [DOI: 10.1021/jacs.8b10168] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sotaro Kuroyanagi
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Shota Fujii
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu City, Fukuoka 808-0135, Japan
| | - Tadaomi Furuta
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
| | - Atsushi Harada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu City, Fukuoka 808-0135, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Yokohama 226-8501, Japan
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14
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Clark AM, Ponniah K, Warden MS, Raitt EM, Yawn AC, Pascal SM. pH-Induced Folding of the Caspase-Cleaved Par-4 Tumor Suppressor: Evidence of Structure Outside of the Coiled Coil Domain. Biomolecules 2018; 8:biom8040162. [PMID: 30518159 PMCID: PMC6316887 DOI: 10.3390/biom8040162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022] Open
Abstract
Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, with high disorder and aggregation at neutral pH, but a largely folded, non-aggregated conformation at acidic pH.
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Affiliation(s)
- Andrea M Clark
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Emily M Raitt
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Andrea C Yawn
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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15
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Potential in vitro and ex vivo targeting of bZIP53 involved in stress response and seed maturation in Arabidopsis thaliana by five designed peptide inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1249-1259. [DOI: 10.1016/j.bbapap.2018.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/31/2018] [Accepted: 09/25/2018] [Indexed: 11/19/2022]
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16
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Figueira TN, Mendonça DA, Gaspar D, Melo MN, Moscona A, Porotto M, Castanho MARB, Veiga AS. Structure-Stability-Function Mechanistic Links in the Anti-Measles Virus Action of Tocopherol-Derivatized Peptide Nanoparticles. ACS NANO 2018; 12:9855-9865. [PMID: 30230818 PMCID: PMC6399014 DOI: 10.1021/acsnano.8b01422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Measles remains one of the leading causes of child mortality worldwide and is re-emerging in some countries due to poor vaccine coverage, concomitant with importation of measles virus (MV) from endemic areas. The lack of specific chemotherapy contributes to negative outcomes, especially in infants or immunodeficient individuals. Fusion inhibitor peptides derived from the MV Fusion protein C-terminal Heptad Repeat (HRC) targeting MV envelope fusion glycoproteins block infection at the stage of entry into host cells, thus preventing viral multiplication. To improve efficacy of such entry inhibitors, we have modified a HRC peptide inhibitor by introducing properties of self-assembly into nanoparticles (NP) and higher affinity for both viral and cell membranes. Modification of the peptide consisted of covalent grafting with tocopherol to increase amphipathicity and lipophilicity (HRC5). One additional peptide inhibitor consisting of a peptide dimer grafted to tocopherol was also used (HRC6). Spectroscopic, imaging, and simulation techniques were used to characterize the NP and explore the molecular basis for their antiviral efficacy. HRC5 forms micellar stable NP while HRC6 aggregates into amorphous, loose, unstable NP. Interpeptide cluster bridging governs NP assembly into dynamic metastable states. The results are consistent with the conclusion that the improved efficacy of HRC6 relative to HRC5 can be attributed to NP instability, which leads to more extensive partition to target membranes and binding to viral target proteins.
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Affiliation(s)
- Tiago N. Figueira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Diogo A. Mendonça
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Diana Gaspar
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2775-412 Oeiras, Portugal
| | - Anne Moscona
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, United States
- Center for Host−Pathogen Interaction, Columbia University Medical Center, New York, New York 10032, United States
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York 10032, United States
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, United States
- Center for Host−Pathogen Interaction, Columbia University Medical Center, New York, New York 10032, United States
- Department of Experimental Medicine, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy
| | - Miguel A. R. B. Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Ana Salomé Veiga
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
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17
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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18
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Joseph A, Nagaraja V, Natesh R. MSMEG_6292, a Mycobacterium smegmatis RNA polymerase secondary channel-binding protein: purification, crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:543-548. [PMID: 30198886 PMCID: PMC6130422 DOI: 10.1107/s2053230x18009755] [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: 06/08/2018] [Accepted: 07/09/2018] [Indexed: 11/10/2022] Open
Abstract
The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals. The crystals belonged to the trigonal space group P3121 (or its enantiomorph P3221), with unit-cell parameters a = b = 83.15, c = 107.07 Å, α = β = 90, γ = 120°. The crystals diffracted to better than 3.0 Å resolution. Molecular-replacement attempts did not yield any phasing models; hence, platinum derivatization was carried out with K2PtCl4 and derivative data were collected to 3.4 Å resolution.
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Affiliation(s)
- Abyson Joseph
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, Kerala 695 016, India
| | - Valakunja Nagaraja
- Microbiology and Cell Biology Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ramanathan Natesh
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, Kerala 695 016, India
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19
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Österlund N, Kulkarni YS, Misiaszek AD, Wallin C, Krüger DM, Liao Q, Mashayekhy Rad F, Jarvet J, Strodel B, Wärmländer SKTS, Ilag LL, Kamerlin SCL, Gräslund A. Amyloid-β Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects. ACS Chem Neurosci 2018; 9:1680-1692. [PMID: 29683649 DOI: 10.1021/acschemneuro.8b00065] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The amphiphilic nature of the amyloid-β (Aβ) peptide associated with Alzheimer's disease facilitates various interactions with biomolecules such as lipids and proteins, with effects on both structure and toxicity of the peptide. Here, we investigate these peptide-amphiphile interactions by experimental and computational studies of Aβ(1-40) in the presence of surfactants with varying physicochemical properties. Our findings indicate that electrostatic peptide-surfactant interactions are required for coclustering and structure induction in the peptide and that the strength of the interaction depends on the surfactant net charge. Both aggregation-prone peptide-rich coclusters and stable surfactant-rich coclusters can form. Only Aβ(1-40) monomers, but not oligomers, are inserted into surfactant micelles in this surfactant-rich state. Surfactant headgroup charge is suggested to be important as electrostatic peptide-surfactant interactions on the micellar surface seems to be an initiating step toward insertion. Thus, no peptide insertion or change in peptide secondary structure is observed using a nonionic surfactant. The hydrophobic peptide-surfactant interactions instead stabilize the Aβ monomer, possibly by preventing self-interaction between the peptide core and C-terminus, thereby effectively inhibiting the peptide aggregation process. These findings give increased understanding regarding the molecular driving forces for Aβ aggregation and the peptide interaction with amphiphilic biomolecules.
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Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Yashraj S. Kulkarni
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Agata D. Misiaszek
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Cecilia Wallin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Dennis M. Krüger
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Qinghua Liao
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Farshid Mashayekhy Rad
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, 12618 Tallinn, Estonia
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | | | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
| | - Shina C. L. Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
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20
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Haider MJ, Zhang HV, Sinha N, Fagan JA, Kiick KL, Saven JG, Pochan DJ. Self-assembly and soluble aggregate behavior of computationally designed coiled-coil peptide bundles. SOFT MATTER 2018; 14:5488-5496. [PMID: 29923575 PMCID: PMC6355460 DOI: 10.1039/c8sm00435h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coiled-coil peptides have proven useful in a range of materials applications ranging from the formation of well-defined fibrils to responsive hydrogels. The ability to design from first principles their oligomerization and subsequent higher order assembly offers their expanded use in producing new materials. Toward these ends, homo-tetrameric, antiparallel, coiled-coil, peptide bundles have been designed computationally, synthesized via solid-phase methods, and their solution behavior characterized. Two different bundle-forming peptides were designed and examined. Within the targeted coiled coil structure, both bundles contained the same hydrophobic core residues. However, different exterior residues on the two different designs yielded sequences with different distributions of charged residues and two different expected isoelectric points of pI 4.4 and pI 10.5. Both coiled-coil bundles were extremely stable with respect to temperature (Tm > 80 C) and remained soluble in solution even at high (millimolar) peptide concentrations. The coiled-coil tetramer was confirmed to be the dominant species in solution by analytical sedimentation studies and by small-angle neutron scattering, where the scattering form factor is well represented by a cylinder model with the dimensions of the targeted coiled coil. At high concentrations (5-15 mM), evidence of interbundle structure was observed via neutron scattering. At these concentrations, the synthetic bundles form soluble aggregates, and interbundle distances can be determined via a structure factor fit to scattering data. The data support the successful design of robust coiled-coil bundles. Despite their different sequences, each sequence forms loosely associated but soluble aggregates of the bundles, suggesting similar dissociated states for each. The behavior of the dispersed bundles is similar to that observed for natural proteins.
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Affiliation(s)
- Michael J. Haider
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA. ,
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21
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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22
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Tartas A, Zarkadas C, Palaiomylitou M, Gounalaki N, Tzamarias D, Vlassi M. Ssn6-Tup1 global transcriptional co-repressor: Role of the N-terminal glutamine-rich region of Ssn6. PLoS One 2017; 12:e0186363. [PMID: 29053708 PMCID: PMC5650148 DOI: 10.1371/journal.pone.0186363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/29/2017] [Indexed: 11/19/2022] Open
Abstract
The Ssn6-Tup1 complex is a general transcriptional co-repressor formed by the interaction of Ssn6, a tetratricopeptide repeat (TPR) protein, with the Tup1 repressor. We have previously shown that the N-terminal domain of Ssn6 comprising TPRs 1 to 3 is necessary and sufficient for this interaction and that TPR1 plays critical role. In a subsequent study, we provided evidence that in the absence of Tup1, TPR1 is susceptible to proteolysis and that conformational change(s) accompany the Ssn6-Tup1 complex formation. In this study, we address the question whether the N-terminal non-TPR, glutamine-rich tail of Ssn6 (NTpolyQ), plays any role in the Ssn6/Tup1 association. Our biochemical and yeast-two-hybrid data show that truncation/deletion of the NTpolyQ domain of Ssn6 results in its self association and prevents Tup1 interaction. These results combined with in silico modeling data imply a major role of the NTpolyQ tail of Ssn6 in regulating its interaction with Tup1.
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Affiliation(s)
- Athanassios Tartas
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Christoforos Zarkadas
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Maria Palaiomylitou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
| | - Niki Gounalaki
- Institute of Molecular Biology & Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Dimitris Tzamarias
- Biology Department, University of Crete, Heraklion, Crete, Greece
- * E-mail: (MV); (DT)
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi Attikis, Athens, Greece
- * E-mail: (MV); (DT)
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23
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Tian Y, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Transition from disordered aggregates to ordered lattices: kinetic control of the assembly of a computationally designed peptide. Org Biomol Chem 2017; 15:6109-6118. [PMID: 28639674 PMCID: PMC8783983 DOI: 10.1039/c7ob01197k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly. The computationally designed peptide forms a homotetrameric coiled-coil bundle that further self-assembles into 2-D plate structures with well-defined inter-bundle symmetry. Herein, we present how modulation of solution conditions, such as pH and temperature, can be used to control the kinetics of the inter-bundle assembly and manipulate the final morphology. Changes in solution pH primarily influence the inter-bundle assembly by affecting the charged state of ionizable residues on the bundle exterior while leaving the homotetrameric coiled-coil structure intact. At low pH, repulsive interactions prevent 2-D lattice nanostructure formation. Near the estimated isoelectric point of the peptide, bundle aggregation is rapid and yields disordered products, which subsequently transform into ordered nanostructures over days to weeks. At elevated temperatures (T = 40 °C or 50 °C), the formation of disordered, kinetically-trapped products largely can be eliminated, allowing the system to quickly assemble into plate-like nanostructured lattices. Moreover, subtle changes in pH and in the peptide charge state have a significant influence on the thickness of formed plates and on the hierarchical manner in which plates fuse into larger material structures with observable grain boundaries. These findings confirm the ability to finely tune the peptide assembly process to achieve a range of engineered structures with one simple 29-residue peptide building block.
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Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Kristi L Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
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24
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Heterotypic Coiled-Coil Formation is Essential for the Correct Assembly of the Septin Heterofilament. Biophys J 2017; 111:2608-2619. [PMID: 28002737 DOI: 10.1016/j.bpj.2016.10.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 11/20/2022] Open
Abstract
Protein-protein interactions play a critical role in promoting the stability of protein quaternary structure and in the assembly of large macromolecular complexes. What drives the stabilization of such assemblies is a central question in biology. A limiting factor in fully understanding such systems is the transient nature of many complexes, making structural studies difficult. Septins comprise a conserved family of guanine nucleotide binding proteins that polymerize in the form of heterofilaments. In structural terms, they have a common organization: a central GTPase domain, an N-terminal domain, and a C-terminal domain; the latter is predicted to form a coiled coil. Currently, even for the best characterized human septin heterocomplex (SEPT2/SEPT6/SEPT7), the role of C-terminal domain is not fully established, and this is partly due to the absence of electron density for the C-terminal domains in the x-ray structure. Here we present results on the homo/heterotypical affinity for the C-terminal domains of human septins belonging to the SEPT6 and SEPT7 groups (SEPT6C/8C/10C/11C and SEPT7C, respectively) and provide clear evidence that this domain determines the preference for heterotypic interactions at one specific interface during the assembly of the heterofilament. This observation has wider implications where macromolecular assemblies are defined by coiled-coil protein interactions.
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25
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Kaplan AR, Brady MR, Maciejewski MW, Kammerer RA, Alexandrescu AT. Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix. Biochemistry 2017; 56:1604-1619. [PMID: 28230348 DOI: 10.1021/acs.biochem.6b00634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1H-15N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13C rotating frame T1 relaxation (T1ρ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
| | - Megan R Brady
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
| | - Mark W Maciejewski
- Department of Molecular Biology and Biophysics, UConn Health , Farmington, Connecticut 06030-3305, United States
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut , 5232 Villigen-PSI, Switzerland
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269-3125, United States
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26
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Santis ED, Castelletto V, Ryadnov MG. Interfacial zippering-up of coiled-coil protein filaments. Phys Chem Chem Phys 2016; 17:31055-60. [PMID: 26534782 DOI: 10.1039/c5cp05938k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein self-assembled materials find increasing use in medicine and nanotechnology. A challenge remains in our ability to tailor such materials at a given length scale. Here we report a de novo self-assembly topology which enables the engineering of filamentous protein nanostructures under morphological control. The rationale is exemplified by a ubiquitous self-assembly motif - an α-helical coiled-coil stagger. The stagger incorporates regularly spaced interfacial tryptophan residues, which allows it to zipper up into discrete filaments that bundle together without thickening by maturation. Using a combination of spectroscopy, microscopy, X-ray small-angle scattering and fibre diffraction methods we show that the precise positioning of tryptophan residues at the primary and secondary structure levels defines the extent of coiled-coil packing in resultant filaments. Applicable to other self-assembling systems, the rationale holds promise for the construction of advanced protein-based architectures and materials.
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Affiliation(s)
- Emiliana De Santis
- National Physical Laboratory, Hampton Rd, Teddington, Middlesex, TW11 0LW, UK.
| | - Valeria Castelletto
- National Physical Laboratory, Hampton Rd, Teddington, Middlesex, TW11 0LW, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Rd, Teddington, Middlesex, TW11 0LW, UK.
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27
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Madsen JLH, Hjørringgaard CU, Vad BS, Otzen D, Skrydstrup T. Incorporation of β-Silicon-β3-Amino Acids in the Antimicrobial Peptide Alamethicin Provides a 20-Fold Increase in Membrane Permeabilization. Chemistry 2016; 22:8358-67. [DOI: 10.1002/chem.201600445] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Julie L. H. Madsen
- Department of Chemistry and; Interdisciplinary Nanoscience Center; Center for Insoluble Protein Structures; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Claudia U. Hjørringgaard
- Department of Chemistry and; Interdisciplinary Nanoscience Center; Center for Insoluble Protein Structures; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Brian S. Vad
- Department of Molecular Biology and Genetics and; Interdisciplinary Nanoscience Center; Center for Insoluble Protein Structures; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Daniel Otzen
- Department of Molecular Biology and Genetics and; Interdisciplinary Nanoscience Center; Center for Insoluble Protein Structures; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Troels Skrydstrup
- Department of Chemistry and; Interdisciplinary Nanoscience Center; Center for Insoluble Protein Structures; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
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28
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Frislev HS, Jessen CM, Oliveira CLP, Pedersen JS, Otzen DE. Liprotides made of α-lactalbumin and cis fatty acids form core-shell and multi-layer structures with a common membrane-targeting mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:847-59. [PMID: 27068540 DOI: 10.1016/j.bbapap.2016.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 10/22/2022]
Abstract
α-Lactalbumin (aLA) has been shown to form complexes with oleic acid (OA), which may target cancer cells. We recently showed that aLA and several other proteins all form protein-OA complexes called liprotides with a generic structure consisting of a micellar OA core surrounded by a shell of partially denatured protein. Here we report that a heat treatment and an alkaline treatment method both allow us to prepare liprotide complexes composed of aLA and a range of unsaturated fatty acids (FA), provided the FAs contain cis (but not trans) double bonds. All liprotides containing cis-FA form both small and large species, which all consist of partially denatured aLA, though the overall shape of the species differs. Small liprotides have a simple core-shell structure while the larger liprotides are multi-layered, i.e. they have an additional layer of both FA and aLA surrounding the outside of the core-shell structure. All liprotides can transfer their entire FA content to vesicles, releasing aLA as monomers and softening the lipid membrane. The more similar to OA, the more efficiently the different FAs induce hemolysis. We conclude that aLA can take up and transfer a wide variety of FA to membranes, provided they contain a cis-bond. This highlights liprotides as a general class of complexes where both protein and cis-FA component can be varied without departing from a generic (though sometimes multi-layered) core-shell structure.
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Affiliation(s)
- Henriette S Frislev
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Christian M Jessen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Cristiano L P Oliveira
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; Institute of Physics, University of São Paulo, Rua do Matão, 187, São Paulo, São Paulo, 05314-970, Brazil
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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29
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Sharma AK, Friedman DJ, Pollak MR, Alper SL. Structural characterization of the C-terminal coiled-coil domains of wild-type and kidney disease-associated mutants of apolipoprotein L1. FEBS J 2016; 283:1846-62. [PMID: 26945671 DOI: 10.1111/febs.13706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 01/25/2016] [Accepted: 03/02/2016] [Indexed: 01/08/2023]
Abstract
Trypanosomes that cause sleeping sickness endocytose apolipoprotein L1 (APOL1)-containing trypanolytic factors from human serum, leading to trypanolytic death through generation of APOL1-associated lytic pores in trypanosomal membranes. The trypanosome Trypanosoma brucei rhodesiense counteracts trypanolysis by expressing the surface protein serum response-associated (SRA), which can bind APOL1 common variant G0 to block its trypanolytic activity. However, two missense variants in the C terminal predicted coiled-coil (CC) domains of human APOL1 G1 (S342G/I384M) and G2 (ΔN388Y389) decrease or abrogate APOL1 binding to T. brucei rhodesiense SRA, thus preserving APOL1 trypanolytic activity. These evolutionarily selected APOL1 missense variants, found at a high frequency in some populations of African descent, also confer elevated risk of kidney disease. Understanding the SRA-APOL1 interaction and the role of APOL1 G1 and G2 variants in kidney disease demands structural characterization of the APOL1 CC domain. Using CD, heteronuclear NMR, and molecular dynamics (MD) simulation on structural homology models, we report here unique and dynamic solution conformations of nephropathy variants G1 and G2 as compared with the common variant G0. Conformational plasticity in G1 and G2 CC domains led to interhelical α1-α2 approximation coupled with secondary structural changes and delimited motional properties absent in the G0 CC domain. The G1 substitutions conferred local structural changes principally along helix α1, whereas the G2 deletion altered the structure of both helix α2 and helix α1. These dynamic features of APOL1 CC variants likely reflect their intrinsic structural properties, and should help interpret future APOL1 structural studies and define the contribution of APOL1 risk variants to kidney disease.
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Affiliation(s)
- Alok K Sharma
- Nephrology Division, Harvard Medical School, Boston, MA, USA.,Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David J Friedman
- Nephrology Division, Harvard Medical School, Boston, MA, USA.,Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Martin R Pollak
- Nephrology Division, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Seth L Alper
- Nephrology Division, Harvard Medical School, Boston, MA, USA.,Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
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30
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Appadu A, Jelokhani-Niaraki M, DeBruin L. Conformational Changes and Association of Membrane-Interacting Peptides in Myelin Membrane Models: A Case of the C-Terminal Peptide of Proteolipid Protein and the Antimicrobial Peptide Melittin. J Phys Chem B 2015; 119:14821-30. [DOI: 10.1021/acs.jpcb.5b07375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashtina Appadu
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
| | - Masoud Jelokhani-Niaraki
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
| | - Lillian DeBruin
- Department
of Chemistry and
Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario, Canada N2L 3C5
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31
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Cabral KMS, Raymundo DP, Silva VS, Sampaio LAG, Johanson L, Hill LF, Almeida FCL, Cordeiro Y, Almeida MS. Biophysical Studies on BEX3, the p75NTR-Associated Cell Death Executor, Reveal a High-Order Oligomer with Partially Folded Regions. PLoS One 2015; 10:e0137916. [PMID: 26383250 PMCID: PMC4575080 DOI: 10.1371/journal.pone.0137916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/23/2015] [Indexed: 12/27/2022] Open
Abstract
BEX3 (Brain Expressed X-linked protein 3) is a member of a mammal-specific placental protein family. Several studies have found the BEX proteins to be associated with neurodegeneration, the cell cycle and cancer. BEX3 has been predicted to be intrinsically disordered and also to represent an intracellular hub for cell signaling. The pro-apoptotic activity of BEX3 in association with a number of additional proteins has been widely supported; however, to the best of our knowledge, very limited data are available on the conformation of any of the members of the BEX family. In this study, we structurally characterized BEX3 using biophysical experimental data. Small angle X-ray scattering and atomic force microscopy revealed that BEX3 forms a specific higher-order oligomer that is consistent with a globular molecule. Solution nuclear magnetic resonance, partial proteinase K digestion, circular dichroism spectroscopy, and fluorescence techniques that were performed on the recombinant protein indicated that the structure of BEX3 is composed of approximately 31% α-helix and 20% β-strand, contains partially folded regions near the N- and C-termini, and a core which is proteolysis-resistant around residues 55-120. The self-oligomerization of BEX3 has been previously reported in cell culture and is consistent with our in vitro data.
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Affiliation(s)
- Katia M. S. Cabral
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diana P. Raymundo
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laura A. G. Sampaio
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laizes Johanson
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Fernando Hill
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio C. L. Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcius S. Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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32
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Rabe M, Zope HR, Kros A. Interplay between Lipid Interaction and Homo-coiling of Membrane-Tethered Coiled-Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9953-9964. [PMID: 26302087 DOI: 10.1021/acs.langmuir.5b02094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The designed coiled-coil-forming peptides E [(EIAALEK)3] and K [(KIAALKE)3] are known to trigger efficient membrane fusion when they are tethered to lipid vesicles in the form of lipopeptides. Knowledge of their secondary structure is a key element in understanding their role in membrane fusion. Special conditions can be found at the interface of the membrane, where the peptides are confined in close proximity to other peptide molecules as well as to the lipid interface. Consequently, different structural states were proposed for the peptides when tethered to this interface. Due to the multitude of possible states, determining the structure solely on the basis of circular dichroism (CD) spectra at a single temperature can be misleading. In addition, it has not yet been possible to unambiguously distinguish between the membrane-bound and the coiled-coil states of these peptides by means of infrared (IR) spectroscopy due to their very similar amide I' bands. Here, the molecular basis of this similarity is investigated by means of site-specific (13)C-labeled FTIR spectroscopy. Structural similarities between the membrane-interacting helix of K and the homo-coiled-coil-forming helix of E are shown to cause the similar spectroscopic properties. Furthermore, the peptide structure is investigated using temperature-dependent CD and IR spectroscopy, and it is shown that the different states can be distinguished on the basis of their thermal behavior. It is shown that the two peptides behave fundamentaly differently when tethered to the lipid membrane, which implies that their role during membrane fusion is different and the mechanism of this process is asymmetric.
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Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Harshal R Zope
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
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33
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Hoang T, Kuljanin M, Smith MD, Jelokhani-Niaraki M. A biophysical study on molecular physiology of the uncoupling proteins of the central nervous system. Biosci Rep 2015; 35:e00226. [PMID: 26182433 PMCID: PMC4613710 DOI: 10.1042/bsr20150130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/04/2015] [Indexed: 01/16/2023] Open
Abstract
Mitochondrial inner membrane uncoupling proteins (UCPs) facilitate transmembrane (TM) proton flux and consequently reduce the membrane potential and ATP production. It has been proposed that the three neuronal human UCPs (UCP2, UCP4 and UCP5) in the central nervous system (CNS) play significant roles in reducing cellular oxidative stress. However, the structure and ion transport mechanism of these proteins remain relatively unexplored. Recently, we reported a novel expression system for obtaining functionally folded UCP1 in bacterial membranes and applied this system to obtain highly pure neuronal UCPs in high yields. In the present study, we report on the structure and function of the three neuronal UCP homologues. Reconstituted neuronal UCPs were dominantly helical in lipid membranes and transported protons in the presence of physiologically-relevant fatty acid (FA) activators. Under similar conditions, all neuronal UCPs also exhibited chloride transport activities that were partially inhibited by FAs. CD, fluorescence and MS measurements and semi-native gel electrophoresis collectively suggest that the reconstituted proteins self-associate in the lipid membranes. Based on SDS titration experiments and other evidence, a general molecular model for the monomeric, dimeric and tetrameric functional forms of UCPs in lipid membranes is proposed. In addition to their shared structural and ion transport features, neuronal UCPs differ in their conformations and proton transport activities (and possibly mechanism) in the presence of different FA activators. The differences in FA-activated UCP-mediated proton transport could serve as an essential factor in understanding and differentiating the physiological roles of UCP homologues in the CNS.
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Affiliation(s)
- Tuan Hoang
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada, N2L 3C5 Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Miljan Kuljanin
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada, N2L 3C5
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada, N2L 3C5 Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada, N2L 3C5 Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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34
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Wu X, Ryder MP, McGuire J, Snider JL, Schilke KF. Sequential and competitive adsorption of peptides at pendant PEO layers. Colloids Surf B Biointerfaces 2015; 130:69-76. [PMID: 25909181 DOI: 10.1016/j.colsurfb.2015.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/05/2015] [Accepted: 04/06/2015] [Indexed: 11/24/2022]
Abstract
Earlier work provided direction for development of responsive drug delivery systems based on modulation of the structure, amphiphilicity, and surface density of bioactive peptides entrapped within pendant polyethylene oxide (PEO) brush layers. In this work, we describe the sequential and competitive adsorption behavior of such peptides at pendant PEO layers. Three cationic peptides were used for this purpose: the arginine-rich, amphiphilic peptide WLBU2, a peptide chemically identical to WLBU2 but of scrambled sequence (S-WLBU2), and the non-amphiphilic peptide poly-L-arginine (PLR). Optical waveguide lightmode spectroscopy (OWLS) was used to quantify the rate and extent of peptide adsorption and elution at surfaces coated with PEO. UV spectroscopy and time-of-flight secondary ion mass spectrometry (TOF-SIMS) were used to quantify the extent of peptide exchange during the course of sequential and competitive adsorption. Circular dichroism (CD) was used to evaluate conformational changes after adsorption of peptide mixtures at PEO-coated silica nanoparticles. Results indicated that amphiphilic peptides are able to displace adsorbed, non-amphiphilic peptides in PEO layers, while non-amphiphilic peptides were not able to displace more amphiphilic peptides. In addition, peptides of greater amphiphilicity dominated the adsorption at the PEO layer from mixtures with less amphiphilic or non-amphiphilic peptides.
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Affiliation(s)
| | - Matthew P Ryder
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Joseph McGuire
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | | | - Karl F Schilke
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA.
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35
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Hoang T, Matovic T, Parker J, Smith MD, Jelokhani-Niaraki M. Role of positively charged residues of the second transmembrane domain in the ion transport activity and conformation of human uncoupling protein-2. Biochemistry 2015; 54:2303-13. [PMID: 25789405 DOI: 10.1021/acs.biochem.5b00177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Residing at the inner mitochondrial membrane, uncoupling protein-2 (UCP2) mediates proton transport from the intermembrane space (IMS) to the mitochondrial matrix and consequently reduces the rate of ATP synthesis in the mitochondria. The ubiquitous expression of UCP2 in humans can be attributed to the protein's multiple physiological roles in tissues, including its involvement in protective mechanisms against oxidative stress, as well as glucose and lipid metabolisms. Currently, the structural properties and ion transport mechanism of UCP2 and other UCP homologues remain poorly understood. UCP2-mediated proton transport is activated by fatty acids and inhibited by di- and triphosphate purine nucleotides. UCP2 also transports chloride and some other small anions. Identification of key amino acid residues of UCP2 in its ion transport pathway can shed light on the protein's ion transport function. On the basis of our previous studies, the second transmembrane helix segment (TM2) of UCP2 exhibited chloride channel activity. In addition, it was suggested that the positively charged residues on TM2 domains of UCPs 1 and 2 were important for their chloride transport activity. On this basis, to further understand the role of these positively charged residues on the ion transport activity of UCP2, we recombinantly expressed four TM2 mutants: R76Q, R88Q, R96Q, and K104Q. The wild type UCP2 and its mutants were purified and reconstituted into liposomes, and their conformation and ion (proton and chloride) transport activity were studied. TM2 Arg residues at the matrix interface of UCP2 proved to be crucial for the protein's anion transport function, and their absence resulted in highly diminished Cl(-) transport rates. On the other hand, the two other positively charged residues of TM2, located at the UCP2-IMS interface, could participate in the salt-bridge formation in the protein and promote the interhelical tight packing in the UCP2. Absence of these residues did not influence Cl(-) transport rates, but disturbed the dense packing in UCP2 and resulted in higher UCP2-mediated proton transport rates in the presence of long chain fatty acids. Overall, the outcome of this study provides a deeper and more detailed molecular image of UCP2's ion transport mechanism.
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Affiliation(s)
- Tuan Hoang
- §Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | - Matthew D Smith
- §Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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36
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Cheong JL, Lim J, Toh JKC, Jee JE, Wong LL, Venkataraman S, Lee SS, Lee SG. Effects of incorporation of azido moieties into the hydrophobic core of coiled coil peptides. Chem Commun (Camb) 2015; 51:3793-6. [DOI: 10.1039/c4cc09089f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled peptide folding via the variation of azido content.
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Affiliation(s)
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
| | - Jerry K. C. Toh
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
| | - Joo-Eun Jee
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
| | - Lan Li Wong
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
| | | | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
| | - Song-Gil Lee
- Institute of Bioengineering and Nanotechnology
- Singapore 138669
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37
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Campbell JH, Hoang T, Jelokhani-Niaraki M, Smith MD. Folding and self-association of atTic20 in lipid membranes: implications for understanding protein transport across the inner envelope membrane of chloroplasts. BMC BIOCHEMISTRY 2014; 15:29. [PMID: 25551276 PMCID: PMC4307631 DOI: 10.1186/s12858-014-0029-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/12/2014] [Indexed: 11/24/2022]
Abstract
Background The Arabidopsis thaliana protein atTic20 is a key component of the protein import machinery at the inner envelope membrane of chloroplasts. As a component of the TIC complex, it is believed to form a preprotein-conducting channel across the inner membrane. Results We report a method for producing large amounts of recombinant atTic20 using a codon-optimized strain of E. coli coupled with an autoinduction method of protein expression. This method resulted in the recombinant protein being directed to the bacterial membrane without the addition of a bacterial targeting sequence. Using biochemical and biophysical approaches, we were able to demonstrate that atTic20 homo-oligomerizes in vitro when solubilized in detergents or reconstituted into liposomes. Furthermore, we present evidence that the extramembranous N-terminus of the mature protein displays characteristics that are consistent with it being an intrinsically disordered protein domain. Conclusion Our work strengthens the hypothesis that atTic20 functions similarly to other small α-helical integral membrane proteins, such as Tim23, that are involved in protein transport across membranes. Electronic supplementary material The online version of this article (doi:10.1186/s12858-014-0029-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James H Campbell
- Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada. .,Current address: Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Tuan Hoang
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada. .,Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
| | - Masoud Jelokhani-Niaraki
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada. .,Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada. .,Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
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38
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A novel mechanism of protein thermostability: a unique N-terminal domain confers heat resistance to Fe/Mn-SODs. Sci Rep 2014; 4:7284. [PMID: 25445927 PMCID: PMC4250934 DOI: 10.1038/srep07284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/14/2014] [Indexed: 11/22/2022] Open
Abstract
Superoxide dismutases (SODs), especially thermostable SODs, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent antioxidant properties. A novel thermostable cambialistic SOD from Geobacillus thermodenitrificans NG80-2 exhibits maximum activity at 70°C and high thermostability over a broad range of temperatures (20–80°C). Unlike other reported SODs, this enzyme contains an extra repeat-containing N-terminal domain (NTD) of 244 residues adjacent to the conserved functional SODA domain. Deletion of the NTD dramatically decreased its optimum active temperature (OAT) to 30°C and also impaired its thermostability. Conversely, appending the NTD to a mesophilic counterpart from Bacillus subtilis led to a moderately thermophilic enzyme (OAT changed from 30 to 55°C) with improved heat resistance. Temperature-dependant circular dichroism analysis revealed the enhanced conformational stability of SODs fused with this NTD. Furthermore, the NTD also contributes to the stress resistance of host proteins without altering their metal ion specificity or oligomerisation form except for a slight effect on their pH profile. We therefore demonstrate that the NTD confers outstanding thermostability to the host protein. To our knowledge, this is the first discovery of a peptide capable of remarkably improving protein thermostability and provides a novel strategy for bioengineering thermostable SODs.
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39
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Andersen KK, Otzen DE. Denaturation of α-lactalbumin and myoglobin by the anionic biosurfactant rhamnolipid. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2338-45. [DOI: 10.1016/j.bbapap.2014.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/30/2014] [Accepted: 10/07/2014] [Indexed: 11/26/2022]
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40
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Guo B, Audu CO, Cochran JC, Mierke DF, Pellegrini M. Protein engineering of the N-terminus of NEMO: structure stabilization and rescue of IKKβ binding. Biochemistry 2014; 53:6776-85. [PMID: 25286246 PMCID: PMC4222529 DOI: 10.1021/bi500861x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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NEMO is a scaffolding protein that,
together with the catalytic
subunits IKKα and IKKβ, plays an essential role in the
formation of the IKK complex and in the activation of the canonical
NF-κB pathway. Rational drug design targeting the IKK-binding
site on NEMO would benefit from structural insight, but to date, the
determination of the structure of unliganded NEMO has been hindered
by protein size and conformational heterogeneity. Here we show how
the utilization of a homodimeric coiled-coil adaptor sequence stabilizes
the minimal IKK-binding domain NEMO(44–111) and furthers our
understanding of the structural requirements for IKK binding. The
engineered constructs incorporating the coiled coil at the N-terminus,
C-terminus, or both ends of NEMO(44–111) present high thermal
stability and cooperative melting and, most importantly, restore IKKβ
binding affinity. We examined the consequences of structural content
and stability by circular dichoism and nuclear magnetic resonance
(NMR) and measured the binding affinity of each construct for IKKβ(701–745)
in a fluorescence anisotropy binding assay, allowing us to correlate
structural characteristics and stability to binding affinity. Our
results provide a method for engineering short stable NEMO constructs
to be suitable for structural characterization by NMR or X-ray crystallography.
Meanwhile, the rescuing of the binding affinity implies that a preordered
IKK-binding region of NEMO is compatible with IKK binding, and the
conformational heterogeneity observed in NEMO(44–111) may be
an artifact of the truncation.
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Affiliation(s)
- Bingqian Guo
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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41
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Ronzone E, Wesolowski J, Bauler LD, Bhardwaj A, Hackstadt T, Paumet F. An α-helical core encodes the dual functions of the chlamydial protein IncA. J Biol Chem 2014; 289:33469-80. [PMID: 25324548 DOI: 10.1074/jbc.m114.592063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Chlamydia is an intracellular bacterium that establishes residence within parasitophorous compartments (inclusions) inside host cells. Chlamydial inclusions are uncoupled from the endolysosomal pathway and undergo fusion with cellular organelles and with each other. To do so, Chlamydia expresses proteins on the surface of the inclusion using a Type III secretion system. These proteins, termed Incs, are located at the interface between host and pathogen and carry out the functions necessary for Chlamydia survival. Among these Incs, IncA plays a critical role in both protecting the inclusion from lysosomal fusion and inducing the homotypic fusion of inclusions. Within IncA are two regions homologous to eukaryotic SNARE (soluble N-ethylmaleimide-sensitive factor attachment receptor) domains referred to as SNARE-like domain 1 (SLD1) and SNARE-like domain 2 (SLD2). Using a multidisciplinary approach, we have discovered the functional core of IncA that retains the ability to both inhibit SNARE-mediated fusion and promote the homotypic fusion of Chlamydia inclusions. Circular dichroism and analytical ultracentrifugation experiments show that this core region is composed almost entirely of α-helices and assembles into stable homodimers in solution. Altogether, we propose that both IncA functions are encoded in a structured core domain that encompasses SLD1 and part of SLD2.
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Affiliation(s)
- Erik Ronzone
- From the Departments of Microbiology and Immunology and
| | | | - Laura D Bauler
- the Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840
| | - Anshul Bhardwaj
- Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 and
| | - Ted Hackstadt
- the Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840
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42
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De Santis E, Faruqui N, Noble JE, Ryadnov MG. Exploitable length correlations in peptide nanofibres. NANOSCALE 2014; 6:11425-11430. [PMID: 25148455 DOI: 10.1039/c4nr03328k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sequence-prescribed biomolecular assemblies find increasing use in the development of novel nanostructured materials. Critical requirements for emerging designs remain in matching form with function. Peptide assembly diversifies form and supports function, but lacks control over both. Herein we exploit length correlations in peptide nanoscale fibres (form) using a model helical template. We establish that different assembly patterns result from a synergistic interplay between peptide length, net charge and folding and supra-molecular cooperativity, while correlating with increases in cell proliferation (function) as a function of peptide length. The revealed correlations offer an efficient rationale for the programming of longitudinally finite and biologically active nanoscale fibres.
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Affiliation(s)
- Emiliana De Santis
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK.
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43
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Mezzina MP, Wetzler DE, Catone MV, Bucci H, Di Paola M, Pettinari MJ. A phasin with many faces: structural insights on PhaP from Azotobacter sp. FA8. PLoS One 2014; 9:e103012. [PMID: 25077609 PMCID: PMC4117528 DOI: 10.1371/journal.pone.0103012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
Phasins are a group of proteins associated to granules of polyhydroxyalkanoates (PHAs). Apart from their structural role as part of the PHA granule cover, different structural and regulatory functions have been found associated to many of them, and several biotechnological applications have been developed using phasin protein fusions. Despite their remarkable functional diversity, the structure of these proteins has not been analyzed except in very few studies. PhaP from Azotobacter sp. FA8 (PhaPAz) is a representative of the prevailing type in the multifunctional phasin protein family. Previous work performed in our laboratory using this protein have demonstrated that it has some very peculiar characteristics, such as its stress protecting effects in recombinant Escherichia coli, both in the presence and absence of PHA. The aim of the present work was to perform a structural characterization of this protein, to shed light on its properties. Its aminoacid composition revealed that it lacks clear hydrophobic domains, a characteristic that appears to be common to most phasins, despite their lipid granule binding capacity. The secondary structure of this protein, consisting of α-helices and disordered regions, has a remarkable capacity to change according to its environment. Several experimental data support that it is a tetramer, probably due to interactions between coiled-coil regions. These structural features have also been detected in other phasins, and may be related to their functional diversity.
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Affiliation(s)
- Mariela P. Mezzina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Diana E. Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Mariela V. Catone
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Hernan Bucci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - M. Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
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44
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Wu X, Ryder MP, McGuire J, Schilke KF. Concentration effects on peptide elution from pendant PEO layers. Colloids Surf B Biointerfaces 2014; 118:210-7. [PMID: 24780434 DOI: 10.1016/j.colsurfb.2014.03.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 03/28/2014] [Accepted: 03/30/2014] [Indexed: 11/29/2022]
Abstract
In earlier work, we have provided direction for development of responsive drug delivery systems based on modulation of structure and amphiphilicity of bioactive peptides entrapped within pendant polyethylene oxide (PEO) brush layers. Amphiphilicity promotes retention of the peptides within the hydrophobic inner region of the PEO brush layer. In this work, we describe the effects of peptide surface density on the conformational changes caused by peptide-peptide interactions, and show that this phenomenon substantially affects the rate and extent of peptide elution from PEO brush layers. Three cationic peptides were used in this study: the arginine-rich amphiphilic peptide WLBU2, the chemically identical but scrambled peptide S-WLBU2, and the non-amphiphilic homopolymer poly-l-arginine (PLR). Circular dichroism (CD) was used to evaluate surface density effects on the structure of these peptides at uncoated (hydrophobic) and PEO-coated silica nanoparticles. UV spectroscopy and a quartz crystal microbalance with dissipation monitoring (QCM-D) were used to quantify changes in the extent of peptide elution caused by those conformational changes. For amphiphilic peptides at sufficiently high surface density, peptide-peptide interactions result in conformational changes which compromise their resistance to elution. In contrast, elution of a non-amphiphilic peptide is substantially independent of its surface density, presumably due to the absence of peptide-peptide interactions. The results presented here provide a strategy to control the rate and extent of release of bioactive peptides from PEO layers, based on modulation of their amphiphilicity and surface density.
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Affiliation(s)
- Xiangming Wu
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Matthew P Ryder
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Joseph McGuire
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Karl F Schilke
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA.
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45
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Mahajan M, Bhattacharjya S. Designed di-heme binding helical transmembrane protein. Chembiochem 2014; 15:1257-62. [PMID: 24829076 DOI: 10.1002/cbic.201402142] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 01/03/2023]
Abstract
De novo designing of functional membrane proteins is fundamental in terms of understanding the structure, folding, and stability of membrane proteins. In this work, we report the design and characterization of a transmembrane protein, termed HETPRO (HEme-binding Transmembrane PROtein), that binds two molecules of heme in a membrane and catalyzes oxidation/reduction reactions. The primary structure of HETPRO has been optimized in a guided fashion, from an antimicrobial peptide, for transmembrane orientation, defined 3D structure, and functions. HETPRO assembles into a tetrameric form, from an apo dimeric helical structure, in complex with cofactor in detergent micelles. The NMR structure of the apo HETPRO in micelles reveals an antiparallel helical dimer that inserts into the nonpolar core of detergent micelles. The well-defined structure of HETPRO and its ability to bind to heme moieties could be utilized to develop a functional membrane protein mimic for electron transport and photosystems.
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Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore-637551 (Singapore)
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46
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Hagen S, Mattay D, Räuber C, Müller KM, Arndt KM. Characterization and inhibition of AF10-mediated interaction. J Pept Sci 2014; 20:385-97. [PMID: 24692230 DOI: 10.1002/psc.2626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022]
Abstract
The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics.
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Affiliation(s)
- Sven Hagen
- Molecular Biotechnology, University of Potsdam, Potsdam/Golm, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Institute for Biology III, University of Freiburg, Freiburg, Germany
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47
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Kirwan JP, Hodges RS. Transmission of stability information through the N-domain of tropomyosin is interrupted by a stabilizing mutation (A109L) in the hydrophobic core of the stability control region (residues 97-118). J Biol Chem 2013; 289:4356-66. [PMID: 24362038 PMCID: PMC3924298 DOI: 10.1074/jbc.m113.507236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tropomyosin (Tm) is an actin-binding, thin filament, two-stranded α-helical coiled-coil critical for muscle contraction and cytoskeletal function. We made the first identification of a stability control region (SCR), residues 97-118, in the Tm sequence that controls overall protein stability but is not required for folding. We also showed that the individual α-helical strands of the coiled-coil are stabilized by Leu-110, whereas the hydrophobic core is destabilized in the SCR by Ala residues at three consecutive d positions. Our hypothesis is that the stabilization of the individual α-helices provides an optimum stability and allows functionally beneficial dynamic motion between the α-helices that is critical for the transmission of stabilizing information along the coiled-coil from the SCR. We prepared three recombinant (rat) Tm(1-131) proteins, including the wild type sequence, a destabilizing mutation L110A, and a stabilizing mutation A109L. These proteins were evaluated by circular dichroism (CD) and differential scanning calorimetry. The single mutation L110A destabilizes the entire Tm(1-131) molecule, showing that the effect of this mutation is transmitted 165 Å along the coiled-coil in the N-terminal direction. The single mutation A109L prevents the SCR from transmitting stabilizing information and separates the coiled-coil into two domains, one that is ∼9 °C more stable than wild type and one that is ∼16 °C less stable. We know of no other example of the substitution of a stabilizing Leu residue in a coiled-coil hydrophobic core position d that causes this dramatic effect. We demonstrate the importance of the SCR in controlling and transmitting the stability signal along this rodlike molecule.
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Affiliation(s)
- J Paul Kirwan
- From the Program in Structural Biology and Biophysics, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045
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48
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Hoang T, Smith MD, Jelokhani-Niaraki M. Expression, folding, and proton transport activity of human uncoupling protein-1 (UCP1) in lipid membranes: evidence for associated functional forms. J Biol Chem 2013; 288:36244-58. [PMID: 24196960 DOI: 10.1074/jbc.m113.509935] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uncoupling protein-1 (UCP1) is abundantly expressed in the mitochondrial inner membrane of brown adipose tissues and has an important role in heat generation, mediated by its proton transport function. The structure and function of UCP1 are not fully understood, partially due to the difficulty in obtaining native-like folded proteins in vitro. In this study, using the auto-induction method, we have successfully expressed UCP1 in Escherichia coli membranes in high yield. Overexpressed UCP1 in bacterial membranes was extracted using mild detergents and reconstituted into phospholipid bilayers for biochemical studies. UCP1 was folded in octyl glucoside, as indicated by its high helical content and binding to ATP, a known UCP1 proton transport inhibitor. Reconstituted UCP1 in phospholipid vesicles also exhibited highly helical structures and proton transport that is activated by fatty acids and inhibited by purine nucleotides. Self-associated functional forms of UCP1 in lipid membranes were observed for the first time. The self-assembly of UCP1 into tetramers was unambiguously characterized by circular dichroism and fluorescence spectroscopy, analytical ultracentrifugation, and semi-native gel electrophoresis. In addition, the mitochondrial lipid cardiolipin stabilized the structure of associated UCP1 and enhanced the proton transport activity of the protein. The existence of the functional oligomeric states of UCP1 in the lipid membranes has important implications for understanding the structure and proton transport mechanism of this protein in brown adipose tissues as well as structure-function relationships of other mammalian UCPs in other tissues.
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49
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Quistgaard EM, Löw C, Moberg P, Guettou F, Maddi K, Nordlund P. Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31. PLoS One 2013; 8:e71111. [PMID: 23967155 PMCID: PMC3742741 DOI: 10.1371/journal.pone.0071111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022] Open
Abstract
Two members of the B-cell associated 31 (BAP31) family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED), which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional α-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.
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Affiliation(s)
- Esben M. Quistgaard
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (EMQ); (PN)
| | - Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fatma Guettou
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Karthik Maddi
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (EMQ); (PN)
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50
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Myrset HR, Fæste CK, Kristiansen PE, Dooper MM. Mapping of the Immunodominant Regions of Shrimp Tropomyosin Pan b 1 by Human IgE-Binding and IgE Receptor Crosslinking Studies. Int Arch Allergy Immunol 2013; 162:25-38. [DOI: 10.1159/000350791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
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