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Ecsédi P, Gógl G, Nyitray L. Studying the Structures of Relaxed and Fuzzy Interactions: The Diverse World of S100 Complexes. Front Mol Biosci 2021; 8:749052. [PMID: 34708078 PMCID: PMC8542695 DOI: 10.3389/fmolb.2021.749052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023] Open
Abstract
S100 proteins are small, dimeric, Ca2+-binding proteins of considerable interest due to their associations with cancer and rheumatic and neurodegenerative diseases. They control the functions of numerous proteins by forming protein–protein complexes with them. Several of these complexes were found to display “fuzzy” properties. Examining these highly flexible interactions, however, is a difficult task, especially from a structural biology point of view. Here, we summarize the available in vitro techniques that can be deployed to obtain structural information about these dynamic complexes. We also review the current state of knowledge about the structures of S100 complexes, focusing on their often-asymmetric nature.
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Affiliation(s)
- Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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52
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Sarkar R, Mishra K, Das PK, Ramakrishnan S. Probing Polymer Chain Folding in Solution Using Second Harmonic Light Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12457-12465. [PMID: 34641685 DOI: 10.1021/acs.langmuir.1c02156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Periodically grafted amphiphilic copolymers (PGACs) were earlier shown by us to adopt a zigzag folded conformation in the solid state, which enabled the backbone and pendant segments to segregate and occupy alternate layers in a lamellar structure. The conformational transition from a random coil to a zigzag folded chain in solution is an interesting problem, which is largely unexplored. To examine this, an orthogonally clickable parent polyester was sequentially clicked with two types of poly(ethylene glycol) (PEG) segments: one is a simple PEG and the other is a PEG that carries a dipolar chromophore. These two hydrophilic PEG segments, installed in a periodic and alternating fashion along the hydrocarbon-rich (HC) polyester backbone, ensure that the Janus folded chains are formed upon folding and carry chromophoric dipoles oriented along the same direction, thereby generating a large net dipole. The folding-induced alignment of chromophores in solution was followed using second harmonic light scattering (SHLS), wherein the intensity of the frequency-doubled scattered light (I2ω) is measured. Folding was induced by adding a polar solvent, like methanol, to a chloroform solution of the polymer; methanol desolvates the HC backbone but solubilizes the pendant PEG segments, thus inducing folding. The second harmonic intensity (I2ω) increased initially with methanol concentration and then saturated; in contrast, I2ω remained invariant with the solvent composition in the case of an analogous model chromophore. Furthermore, in a model PGAC carrying chromophore-bearing PEG segments on every repeat unit, I2ω decreased with increasing methanol composition, revealing the formation of a centrosymmetric folded chain, wherein the chromophoric dipoles on either side cancel each other. Thus, this study clearly reveals that the zigzag chain folding of PGACs can be induced by a segment-selective solvent, resulting in the rather elusive directional ordering of chromophoric dipoles in solution.
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Affiliation(s)
- Ramkrishna Sarkar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kamini Mishra
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Puspendu Kumar Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - S Ramakrishnan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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53
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Concentration Dependent Single Chain Properties of Poly(sodium 4-styrenesulfonate) Subjected to Aromatic Interactions with Chlorpheniramine Maleate Studied by Diafiltration and Synchrotron-SAXS. Polymers (Basel) 2021; 13:polym13203563. [PMID: 34685324 PMCID: PMC8538281 DOI: 10.3390/polym13203563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
The polyelectrolyte poly(sodium 4-styrenesulfonate) undergoes aromatic–aromatic interaction with the drug chlorpheniramine, which acts as an aromatic counterion. In this work, we show that an increase in the concentration in the dilute and semidilute regimes of a complex polyelectrolyte/drug 2:1 produces the increasing confinement of the drug in hydrophobic domains, with implications in single chain thermodynamic behavior. Diafiltration analysis at polymer concentrations between 0.5 and 2.5 mM show an increase in the fraction of the aromatic counterion irreversibly bound to the polyelectrolyte, as well as a decrease in the electrostatic reversible interaction forces with the remaining fraction of drug molecules as the total concentration of the system increases. Synchrotron-SAXS results performed in the semidilute regimes show a fractal chain conformation pattern with a fractal dimension of 1.7, similar to uncharged polymers. Interestingly, static and fractal correlation lengths increase with increasing complex concentration, due to the increase in the amount of the confined drug. Nanoprecipitates are found in the range of 30–40 mM, and macroprecipitates are found at a higher system concentration. A model of molecular complexation between the two species is proposed as the total concentration increases, which involves ion pair formation and aggregation, producing increasingly confined aromatic counterions in hydrophobic domains, as well as a decreasing number of charged polymer segments at the hydrophobic/hydrophilic interphase. All of these features are of pivotal importance to the general knowledge of polyelectrolytes, with implications both in fundamental knowledge and potential technological applications considering aromatic-aromatic binding between aromatic polyelectrolytes and aromatic counterions, such as in the production of pharmaceutical formulations.
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54
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Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Res 2021; 49:10166-10177. [PMID: 34432045 PMCID: PMC8517857 DOI: 10.1093/nar/gkab736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.
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Affiliation(s)
- Adrian M Bandera
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Joseph Bartho
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Katja Lammens
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - David Jan Drexler
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Jasmin Kleinschwärzer
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Gregor Witte
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
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55
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Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, Tomilin FN, Fedorov DG, Alexeev Y, Kichkailo AS. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:316-327. [PMID: 34458013 PMCID: PMC8379633 DOI: 10.1016/j.omtn.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Roman V. Moryachkov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina A. Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina V. Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Galina S. Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Olga S. Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V. Krat
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Vladimir N. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey E. Sokolov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Ruslan A. Zukov
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
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56
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Anandan A, Dunstan NW, Ryan TM, Mertens HDT, Lim KYL, Evans GL, Kahler CM, Vrielink A. Conformational flexibility of EptA driven by an interdomain helix provides insights for enzyme-substrate recognition. IUCRJ 2021; 8:732-746. [PMID: 34584735 PMCID: PMC8420757 DOI: 10.1107/s2052252521005613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phospho-ethano-lamine to lipid A by the enzyme phospho-ethano-lamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-do-decyl-β-d-maltoside micelle environment and an open extended structure in an n-do-decyl-phospho-choline micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Nicholas W. Dunstan
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Haydyn D. T. Mertens
- European Molecular Biology Laboratory, Hamburg Unit, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Katherine Y. L. Lim
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Genevieve L. Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
| | - Charlene M. Kahler
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth 6009, Australia
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57
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Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS. Biophys J 2021; 120:3664-3675. [PMID: 34310942 DOI: 10.1016/j.bpj.2021.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 11/23/2022] Open
Abstract
Na+/Ca2+ exchangers (NCXs) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+ sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the NCX of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant interdomain flexibility in the apo state but assume rigid interdomain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N residual dipolar couplings), and small-angle x-ray scattering (SAXS) data in a combined strategy to select an ensemble of conformations in agreement with the experimental data. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, whereas the wide-open interdomain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble toward extended conformers, which could be a key step in the NCXs' allosteric regulation mechanism. This strategy, combining MD with NMR and SAXS, provides a powerful approach to select ensembles of conformations that could be applied to other flexible multidomain systems.
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58
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Fujii S, Sakurai K. Structural Analysis of an Octameric Resorcinarene Self-Assembly in Toluene and its Morphological Transition by Temperature. J Phys Chem Lett 2021; 12:6464-6468. [PMID: 34236861 DOI: 10.1021/acs.jpclett.1c01978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Calix[4]resorcinarene derivatives such as C-undecylcalix[4]resorcinarene self-assemble into a hexameric capsule-like structure. This structure is expected in any apolar solvent, but we recently found a self-assembled octameric form of resorcinarene in toluene. To understand this unexpected form, we performed small-angle X-ray scattering (SAXS) measurements of the octameric self-assembly. In ab initio shape reconstruction and model fitting of the SAXS profile, a core-shell spherical structure resembling a reverse micelle was found in the octameric self-assembly. The shell and core were composed of alkyl chains and resorcinol moieties, respectively. We also evaluated the temperature dependence of the octameric self-assembly. Above 95 °C, the structure began directly decomposing into unimers, implying the partial cleavage of hydrogen bonds in the octamer core. Meanwhile, below 25 °C, the spherical structure of the octamer partially transformed to a cylindrical structure. This morphological transition could be understood by packing parameter theory, which is often applied to suspected micellar structures.
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Affiliation(s)
- Shota Fujii
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Kitakyushu, Fukuoka 808-0135, Japan
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59
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Covaceuszach S, Peche L, Konarev P, Lamba D. A combined evolutionary and structural approach to disclose the primary structural determinants essential for proneurotrophins biological functions. Comput Struct Biotechnol J 2021; 19:2891-2904. [PMID: 34094000 PMCID: PMC8144349 DOI: 10.1016/j.csbj.2021.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 12/24/2022] Open
Abstract
The neurotrophins, i.e., Nerve Growth Factor (NGF), Brain-Derived Neurotrophic Factor (BDNF), Neurotrophin 3 (NT3) and Neurotrophin 4 (NT4), are known to play a range of crucial functions in the developing and adult peripheral and central nervous systems. Initially synthesized as precursors, i.e., proneurotrophins (proNTs), that are cleaved to release C-terminal mature forms, they act through two types of receptors, the specific Trk receptors (Tropomyosin-related kinases) and the pan-neurotrophin receptor p75NTR, to initiate survival and differentiative responses. Recently, all the proNTs but proNT4 have been demonstrated to be not just inactive precursors, but signaling ligands that mediate opposing actions in fundamental aspects of the nervous system with respect to the mature counterparts through dual-receptor complexes formation with a member of the VPS10 family and p75NTR. Despite the functional relevance, the molecular determinants underpinning the interactions between the pro-domains and their receptors are still elusive probably due to their intrinsically disordered nature. Here we present an evolutionary approach coupled to an experimental study aiming to uncover the structural and dynamical basis of the biological function displayed by proNGF, proBDNF and proNT3 but missing in proNT4. A bioinformatic analysis allowed to elucidate the functional adaptability of the proNTs family in vertebrates, identifying conserved key structural features. The combined biochemical and SAXS experiments shed lights on the structure and dynamic behavior of the human proNTs in solution, giving insights on the evolutionary conserved structural motifs, essential for the multifaceted roles of proNTs in physiological as well as in pathological contexts.
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Affiliation(s)
- S. Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - L.Y. Peche
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - P.V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
| | - D. Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
- Interuniversity Consortium “Biostructures and Biosystems National Institute”, Roma, Italy
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60
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Marques MA, Landim-Vieira M, Moraes AH, Sun B, Johnston JR, Dieseldorff Jones KM, Cino EA, Parvatiyar MS, Valera IC, Silva JL, Galkin VE, Chase PB, Kekenes-Huskey PM, de Oliveira GAP, Pinto JR. Anomalous structural dynamics of minimally frustrated residues in cardiac troponin C triggers hypertrophic cardiomyopathy. Chem Sci 2021; 12:7308-7323. [PMID: 34163821 PMCID: PMC8171346 DOI: 10.1039/d1sc01886h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022] Open
Abstract
Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction. Here, we report the molecular basis of a human mutation in cTnC's αD-helix (TNNC1-p.C84Y) that impacts conformational dynamics of the D/E central-linker and sampling of discrete states in the N-domain, favoring the "primed" state associated with Ca2+ binding. We demonstrate cTnC's αD-helix normally functions as a central hub that controls minimally frustrated interactions, maintaining evolutionarily conserved rigidity of the N-domain. αD-helix perturbation remotely alters conformational dynamics of the N-domain, compromising its structural rigidity. Transgenic mice carrying this cTnC mutation exhibit altered dynamics of sarcomere function and hypertrophic cardiomyopathy. Together, our data suggest that disruption of evolutionary conserved molecular frustration networks by a myofilament protein mutation may ultimately compromise contractile performance and trigger hypertrophic cardiomyopathy.
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Affiliation(s)
- Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Adolfo H Moraes
- Department of Chemistry, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago Maywood IL USA
| | - Jamie R Johnston
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Karissa M Dieseldorff Jones
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais Belo Horizonte MG Brazil
| | - Michelle S Parvatiyar
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Isela C Valera
- Department of Nutrition, Food and Exercise Sciences, Florida State University Tallahassee FL USA
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School Norfolk VA USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University Tallahassee FL USA
| | | | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro 373 Carlos Chagas Filho Av, Room: E-10 Rio de Janeiro RJ 21941-902 Brazil +55-21-3938-6756
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, College of Medicine 1115 West Call Street, Room: 1370 (lab) - 1350-H (office) Tallahassee FL 32306 USA +1-850-645-0016
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61
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Lebedev DV, Egorov VV, Shvetsov AV, Zabrodskaya YA, Isaev-Ivanov VV, Konevega AL. Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521020103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract
The review describes the application of small-angle scattering (SAS) of neutrons and complementary methods to study the structures of biomacromolecules. Here we cover SAS techniques, such as the contrast variation, the neutron spin-echo, and the solution of direct and inverse problems of three-dimensional reconstruction of the structures of macromolecules from SAS spectra by means of molecular modeling. A special section is devoted to specific objects of research, such as supramolecular complexes, influenza virus nucleoprotein, and chromatin.
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62
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Ding C, Wang S, Zhang Z. Integrating an Enhanced Sampling Method and Small-Angle X-Ray Scattering to Study Intrinsically Disordered Proteins. Front Mol Biosci 2021; 8:621128. [PMID: 34150843 PMCID: PMC8213455 DOI: 10.3389/fmolb.2021.621128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have been paid more and more attention over the past decades because they are involved in a multitude of crucial biological functions. Despite their functional importance, IDPs are generally difficult to investigate because they are very flexible and lack stable structures. Computer simulation may serve as a useful tool in studying IDPs. With the development of computer software and hardware, computational methods, such as molecular dynamics (MD) simulations, are popularly used. However, there is a sampling problem in MD simulations. In this work, this issue is investigated using an IDP called unique long region 11 (UL11), which is the conserved outer tegument component from herpes simplex virus 1. After choosing a proper force field and water model that is suitable for simulating IDPs, integrative modeling by combining an enhanced sampling method and experimental data like small-angle X-ray scattering (SAXS) is utilized to efficiently sample the conformations of UL11. The simulation results are in good agreement with experimental data. This work may provide a general protocol to study structural ensembles of IDPs.
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Affiliation(s)
- Chengtao Ding
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, National Science Center for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | | | - Zhiyong Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, National Science Center for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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63
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Christoff-Tempesta T, Cho Y, Kim DY, Geri M, Lamour G, Lew AJ, Zuo X, Lindemann WR, Ortony JH. Self-assembly of aramid amphiphiles into ultra-stable nanoribbons and aligned nanoribbon threads. NATURE NANOTECHNOLOGY 2021; 16:447-454. [PMID: 33462430 DOI: 10.1038/s41565-020-00840-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Small-molecule self-assembly is an established route for producing high-surface-area nanostructures with readily customizable chemistries and precise molecular organization. However, these structures are fragile, exhibiting molecular exchange, migration and rearrangement-among other dynamic instabilities-and are prone to dissociation upon drying. Here we show a small-molecule platform, the aramid amphiphile, that overcomes these dynamic instabilities by incorporating a Kevlar-inspired domain into the molecular structure. Strong, anisotropic interactions between aramid amphiphiles suppress molecular exchange and elicit spontaneous self-assembly in water to form nanoribbons with lengths of up to 20 micrometres. Individual nanoribbons have a Young's modulus of 1.7 GPa and tensile strength of 1.9 GPa. We exploit this stability to extend small-molecule self-assembly to hierarchically ordered macroscopic materials outside of solvated environments. Through an aqueous shear alignment process, we organize aramid amphiphile nanoribbons into arbitrarily long, flexible threads that support 200 times their weight when dried. Tensile tests of the dry threads provide a benchmark for Young's moduli (between ~400 and 600 MPa) and extensibilities (between ~0.6 and 1.1%) that depend on the counterion chemistry. This bottom-up approach to macroscopic materials could benefit solid-state applications historically inaccessible by self-assembled nanomaterials.
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Affiliation(s)
- Ty Christoff-Tempesta
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yukio Cho
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dae-Yoon Kim
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute of Advanced Composite Materials, Korea Institute of Science and Technology, Bondong, Korea
| | - Michela Geri
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guillaume Lamour
- LAMBE, Université Paris-Saclay, University of Evry, CNRS, Evry-Courcouronnes, France
| | - Andrew J Lew
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - William R Lindemann
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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64
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Denz M, Marschall M, Herrmann H, Köster S. Ion type and valency differentially drive vimentin tetramers into intermediate filaments or higher order assemblies. SOFT MATTER 2021; 17:870-878. [PMID: 33237065 DOI: 10.1039/d0sm01659d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Vimentin intermediate filaments, together with actin filaments and microtubules, constitute the cytoskeleton in cells of mesenchymal origin. The mechanical properties of the filaments themselves are encoded in their molecular architecture and depend on their ionic environment. It is thus of great interest to disentangle the influence of both the ion type and their concentration on vimentin assembly. We combine small angle X-ray scattering and fluorescence microscopy and show that vimentin in the presence of the monovalent ions, K+ and Na+, assembles into "standard filaments" with a radius of about 6 nm and 32 monomers per cross-section. In contrast, di- and multivalent ions, independent of type and valency, lead to the formation of thicker filaments associating over time into higher order structures. Hence, our results may indeed be of relevance for living cells, as local ion concentrations in the cytoplasm during certain physiological activities may differ considerably from average intracellular concentrations.
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Affiliation(s)
- Manuela Denz
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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65
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Javor J, Ewoldt JK, Cloonan PE, Chopra A, Luu RJ, Freychet G, Zhernenkov M, Ludwig K, Seidman JG, Seidman CE, Chen CS, Bishop DJ. Probing the subcellular nanostructure of engineered human cardiomyocytes in 3D tissue. MICROSYSTEMS & NANOENGINEERING 2021; 7:10. [PMID: 34567727 PMCID: PMC8433147 DOI: 10.1038/s41378-020-00234-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/13/2020] [Accepted: 12/03/2020] [Indexed: 05/15/2023]
Abstract
The structural and functional maturation of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) is essential for pharmaceutical testing, disease modeling, and ultimately therapeutic use. Multicellular 3D-tissue platforms have improved the functional maturation of hiPSC-CMs, but probing cardiac contractile properties in a 3D environment remains challenging, especially at depth and in live tissues. Using small-angle X-ray scattering (SAXS) imaging, we show that hiPSC-CMs matured and examined in a 3D environment exhibit a periodic spatial arrangement of the myofilament lattice, which has not been previously detected in hiPSC-CMs. The contractile force is found to correlate with both the scattering intensity (R 2 = 0.44) and lattice spacing (R 2 = 0.46). The scattering intensity also correlates with lattice spacing (R 2 = 0.81), suggestive of lower noise in our structural measurement than in the functional measurement. Notably, we observed decreased myofilament ordering in tissues with a myofilament mutation known to lead to hypertrophic cardiomyopathy (HCM). Our results highlight the progress of human cardiac tissue engineering and enable unprecedented study of structural maturation in hiPSC-CMs.
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Affiliation(s)
- Josh Javor
- Department of Mechanical Engineering, Boston University, Boston, MA 02215 USA
| | - Jourdan K. Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - Paige E. Cloonan
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - Anant Chopra
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - Rebeccah J. Luu
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | | | | | - Karl Ludwig
- Department of Physics, Boston University, Boston, MA 02215 USA
- Division of Materials Science, Boston University, Boston, Massachusetts 02215 USA
| | | | | | - Christopher S. Chen
- Department of Mechanical Engineering, Boston University, Boston, MA 02215 USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - David J. Bishop
- Department of Mechanical Engineering, Boston University, Boston, MA 02215 USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
- Department of Physics, Boston University, Boston, MA 02215 USA
- Division of Materials Science, Boston University, Boston, Massachusetts 02215 USA
- Department of Electrical Engineering, Boston University, Boston, MA 02215 USA
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66
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Umerani MJ, Pratakshya P, Chatterjee A, Cerna Sanchez JA, Kim HS, Ilc G, Kovačič M, Magnan C, Marmiroli B, Sartori B, Kwansa AL, Orins H, Bartlett AW, Leung EM, Feng Z, Naughton KL, Norton-Baker B, Phan L, Long J, Allevato A, Leal-Cruz JE, Lin Q, Baldi P, Bernstorff S, Plavec J, Yingling YG, Gorodetsky AA. Structure, self-assembly, and properties of a truncated reflectin variant. Proc Natl Acad Sci U S A 2020; 117:32891-32901. [PMID: 33323484 PMCID: PMC7780002 DOI: 10.1073/pnas.2009044117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.
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Affiliation(s)
- Mehran J. Umerani
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | | | - Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Juana A. Cerna Sanchez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Ho Shin Kim
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, CA 92697
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Albert L. Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Helen Orins
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Andrew W. Bartlett
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Erica M. Leung
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Zhijing Feng
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Kyle L. Naughton
- Department of Physics and Astronomy, University of California, Irvine, CA 92697
| | | | - Long Phan
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - James Long
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Alex Allevato
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Jessica E. Leal-Cruz
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Qiyin Lin
- Irvine Materials Research Institute, University of California, Irvine, CA 92697
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, CA 92697
| | | | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Alon A. Gorodetsky
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
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67
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Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28. Viruses 2020; 13:E15. [PMID: 33374840 PMCID: PMC7823558 DOI: 10.3390/v13010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.
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Affiliation(s)
- Emilio Reyes-Aldrete
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Erik A. Dill
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Cecile Bussetta
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Michal R. Szymanski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Geoffrey Diemer
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Priyank Maindola
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Mark A. White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Wlodzimierz M. Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Marc C. Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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68
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Ruan H, Kiselar J, Zhang W, Li S, Xiong R, Liu Y, Yang S, Lai L. Integrative structural modeling of a multidomain polo-like kinase. Phys Chem Chem Phys 2020; 22:27581-27589. [PMID: 33236741 DOI: 10.1039/d0cp05030j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). While individual domain structures of the KD and the PBD are known, how they interact and assemble into a functional complex remains an open question. The structural model from the KD-PBD-Map205PBM heterotrimeric crystal structure of zebrafish PLK1 represents a major step in understanding the KD and the PBD interactions. However, how these two domains interact when connected by a linker in the full length PLK1 needs further investigation. By integrating different sources of structural data from small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational sampling, here we report an overall architecture for PLK1 multidomain assembly between the KD and the PBD. Our model revealed that the KD uses its C-lobe to interact with the PBD via the site near the phosphopeptide binding site in its auto-inhibitory state in solution. Disruption of this auto-inhibition via site-directed mutagenesis at the KD-PBD interface increases its kinase activity, supporting the functional role of KD-PBD interactions predicted for regulating the PLK1 kinase function. Our results indicate that the full length human PLK1 takes dynamic structures with a variety of domain-domain interfaces in solution.
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Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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69
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Thorn DC, Bahraminejad E, Grosas AB, Koudelka T, Hoffmann P, Mata JP, Devlin GL, Sunde M, Ecroyd H, Holt C, Carver JA. Native disulphide-linked dimers facilitate amyloid fibril formation by bovine milk α S2-casein. Biophys Chem 2020; 270:106530. [PMID: 33545456 DOI: 10.1016/j.bpc.2020.106530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/12/2020] [Accepted: 12/12/2020] [Indexed: 12/22/2022]
Abstract
Bovine milk αS2-casein, an intrinsically disordered protein, readily forms amyloid fibrils in vitro and is implicated in the formation of amyloid fibril deposits in mammary tissue. Its two cysteine residues participate in the formation of either intra- or intermolecular disulphide bonds, generating monomer and dimer species. X-ray solution scattering measurements indicated that both forms of the protein adopt large, spherical oligomers at 20 °C. Upon incubation at 37 °C, the disulphide-linked dimer showed a significantly greater propensity to form amyloid fibrils than its monomeric counterpart. Thioflavin T fluorescence, circular dichroism and infrared spectra were consistent with one or both of the dimer isomers (in a parallel or antiparallel arrangement) being predisposed toward an ordered, amyloid-like structure. Limited proteolysis experiments indicated that the region from Ala81 to Lys113 is incorporated into the fibril core, implying that this region, which is predicted by several algorithms to be amyloidogenic, initiates fibril formation of αS2-casein. The partial conservation of the cysteine motif and the frequent occurrence of disulphide-linked dimers in mammalian milks despite the associated risk of mammary amyloidosis, suggest that the dimeric conformation of αS2-casein is a functional, yet amyloidogenic, structure.
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Affiliation(s)
- David C Thorn
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Elmira Bahraminejad
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Aidan B Grosas
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Tomas Koudelka
- Institute of Experimental Medicine, University of Kiel, Kiel 24105, Germany
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Glyn L Devlin
- Victorian Health and Human Services Building Authority, Melbourne, Victoria 3000, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW 2006, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Carl Holt
- Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia.
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70
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Jing B, Ferreira M, Lin K, Li R, Yavitt BM, Qiu J, Fukuto M, Zhu Y. Ultrastructure of Critical-Gel-like Polyzwitterion–Polyoxometalate Complex Coacervates: Effects of Temperature, Salt Concentration, and Shear. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benxin Jing
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Manuela Ferreira
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Kehua Lin
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Benjamin M. Yavitt
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Jie Qiu
- School of Nuclear Science and Technology and State Key Laboratory of Multiphase Flow in Power Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
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71
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Dos Santos APA, da Silva JK, Neri JM, Neves ACO, de Lima DF, Menezes FG. Nucleophilicity of cysteine and related biothiols and the development of fluorogenic probes and other applications. Org Biomol Chem 2020; 18:9398-9427. [PMID: 33200155 DOI: 10.1039/d0ob01754j] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biothiols such as l-cysteine, l-homocysteine, and glutathione play essential roles in many biological processes, and are directly associated with several health conditions. Therefore, the development of fast, selective, sensitive, and inexpensive methods for quantitatively analyzing biothiols in aqueous solution, but especially in biological samples, is a very attractive research field. In this feature review, we have approached the relevance of biothiols' nucleophilicity to develop selective fluorogenic probes. Since biothiols have considerable structural similarity, relevant strategies are in full development, including several fluorescent molecular platforms, specific receptor sites, reaction conditions, and optical responses. All of these features are properly presented and discussed. Biothiol sensing protocols are based on traditional organic chemistry reactions such as (hetero)aromatic nucleophilic substitution, addition, and substitution at carbonyl carbon, conjugate addition, and nucleophilic substitution at saturated carbon, amongst others including combined processes; furthermore, mechanistic aspects are detailed herein, including some interesting historical contexts. The feasibility of related fluorogenic probes is illustrated by analysis in complex matrices such as serum, cells, tissues, and animal models. Applications of these reactions in more complex systems such as sulfhydryl-based peptides and proteins are also presented, aiming at functionalizing and detecting these nucleophiles. Most literature cited in this review is recent; however, some other prominent works are also detailed. It is believed that this review may be accessible for many academic levels and may efficiently contribute not only to popularizing science but also to the rational development of fluorogenic probes for biothiol sensing.
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Affiliation(s)
- Alane P A Dos Santos
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Jordan K da Silva
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Jannyely M Neri
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Ana C O Neves
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Djalan F de Lima
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Fabrício G Menezes
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
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72
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Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020; 19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023] Open
Abstract
Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.
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Key Words
- CLEM, correlated light and electron microscopy
- Crosslinking mass spectrometry
- Cryo-electron microscopy
- Cryo-electron tomography
- EPR, electron paramagnetic resonance
- FRET, Forster resonance energy transfer
- ISB, Integrative structural biology
- Integrative structural biology
- ML, machine learning
- MR, molecular replacement
- MSAs, multiple sequence alignments
- MX, macromolecular crystallography
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Protein docking
- Protein structure prediction
- Quinary interactions
- SAD, single-wavelength anomalous dispersion
- SANS, small angle neutron scattering
- SAXS, small angle X-ray scattering
- X-ray crystallography
- XL-MS, cross-linking mass spectrometry
- cryo-EM SPA, cryo-EM single particle analysis
- cryo-EM, cryo-electron microscopy
- cryo-ET, cryo-electron tomography
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Affiliation(s)
- Samantha J. Ziegler
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Sam J.B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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73
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Wang Y, Li R, Qiao S, Wang J, Liu H, Li Z, Ma H, Yang L, Ruan H, Weng M, Hiscox JA, Stewart JP, Nan Y, Zhang G, Zhou EM. Structural Characterization of Non-structural Protein 9 Complexed With Specific Nanobody Pinpoints Two Important Residues Involved in Porcine Reproductive and Respiratory Syndrome Virus Replication. Front Microbiol 2020; 11:581856. [PMID: 33281776 PMCID: PMC7688669 DOI: 10.3389/fmicb.2020.581856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is a widespread viral disease that has led to huge economic losses for the global swine industry. Non-structural protein 9 (Nsp9) of PRRSV possesses essential RNA-dependent RNA polymerase (RdRp) activity for viral RNA replication. Our previous report showed that Nsp9-specific nanobody, Nb6, was able to inhibit PRRSV replication. In this study, recombinant Nsp9 and Nsp9-Nb6 complex were prepared then characterized using bio-layer interferometry (BLI) and dynamic light scattering (DLS) analyses that demonstrated high-affinity binding of Nb6 to Nsp9 to form a homogeneous complex. Small-angle X-ray scattering (SAXS) characterization analyses revealed that spatial interactions differed between Nsp9 and Nsp9-Nb6 complex molecular envelopes. Enzyme-linked immunosorbent assays (ELISAs) revealed key involvement of Nsp9 residues Ile588, Asp590, and Leu643 and Nb6 residues Tyr62, Trp105, and Pro107 in the Nsp9-Nb6 interaction. After reverse genetics-based techniques were employed to generate recombinant Nsp9 mutant viruses, virus replication efficiencies were assessed in MARC-145 cells. The results revealed impaired viral replication of recombinant viruses bearing I588A and L643A mutations as compared with replication of wild type virus, as evidenced by reduced negative-strand genomic RNA [(−) gRNA] synthesis and attenuated viral infection. Moreover, the isoleucine at position 588 of Nsp9 was conserved across PRRSV genotypes. In conclusion, structural analysis of the Nsp9-Nb6 complex revealed novel amino acid interactions involved in viral RNA replication that will be useful for guiding development of structure-based anti-PRRSV agents.
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Affiliation(s)
- Yan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiaxi Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hongliang Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Zhijun Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hongfang Ma
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lei Yang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Haiyu Ruan
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Maoyang Weng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - James P Stewart
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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74
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Shin J, Singal B, Sony Subramanian Manimekalai M, Wei Chen M, Ragunathan P, Grüber G. Atomic structure of, and valine binding to the regulatory ACT domain of the Mycobacterium tuberculosis Rel protein. FEBS J 2020; 288:2377-2397. [PMID: 33067840 DOI: 10.1111/febs.15600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 12/30/2022]
Abstract
The stringent response, regulated by the bifunctional (p)ppGpp synthetase/hydrolase Rel in mycobacteria, is critical for long-term survival of the drug-tolerant dormant state of Mycobacterium tuberculosis. During amino acid starvation, MtRel senses a drop in amino acid concentration and synthesizes the messengers pppGpp and ppGpp, collectively called (p)ppGpp. Here, we investigate the role of the regulatory 'Aspartokinase, Chorismate mutase and TyrA' (ACT) domain in MtRel. Using NMR spectroscopy approaches, we report the high-resolution structure of dimeric MtRel ACT which selectively binds to valine out of all other branched-chain amino acids tested. A set of MtRel ACT mutants were generated to identify the residues required for maintaining the head-to-tail dimer. Through NMR titrations, we determined the crucial residues for binding of valine and show structural rearrangement of the MtRel ACT dimer in the presence of valine. This study suggests the direct involvement of amino acids in (p)ppGpp accumulation mediated by MtRel independent to interactions with stalled ribosomes. Database Structural data are available in the PDB database under the accession number 6LXG.
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Affiliation(s)
- Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Bharti Singal
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | | | - Ming Wei Chen
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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75
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Han Q, Smith KM, Darmanin C, Ryan TM, Drummond CJ, Greaves TL. Lysozyme conformational changes with ionic liquids: Spectroscopic, small angle x-ray scattering and crystallographic study. J Colloid Interface Sci 2020; 585:433-443. [PMID: 33109332 DOI: 10.1016/j.jcis.2020.10.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/19/2020] [Accepted: 10/07/2020] [Indexed: 01/14/2023]
Abstract
Solvents that support protein functionality are important for biochemical applications, and new solvents are required. Here we employ FTIR and fluorescence spectroscopies, small angle X-ray scattering (SAXS) and X-ray crystallography to understand conformational changes of lysozyme with ionic liquids (ILs) added. Spectroscopic techniques identified that the secondary structure of lysozyme was maintained at the lower IL concentrations of 1 and 5 mol%, though the Tryptophan environment was significantly altered with nitrate-based ILs present. SAXS experiments indicated that the radius of gyration of lysozyme increased with 1 mol% IL present, and then decreased with increasing IL concentrations. The tertiary structure, particularly the loop regions, changed as a function of IL concentration, and this depended on the IL type. The crystallographic structure of lysozyme with the IL of ethylammonium nitrate present confirmed the loop region was extended, and identified three specific binding sites with nitrate ions, and that the positively charged areas were IL sensitive regions. This work provides a detailed understanding of lysozyme conformational changes in the presence of ILs. This approach can be extended to other functionally-important proteins.
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Affiliation(s)
- Qi Han
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Kate M Smith
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, VIC 3086, Australia
| | - Timothy M Ryan
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Calum J Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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76
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Sugrue E, Coombes D, Wood D, Zhu T, Donovan KA, Dobson RCJ. The lid domain is important, but not essential, for catalysis of Escherichia coli pyruvate kinase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:761-772. [PMID: 32978636 DOI: 10.1007/s00249-020-01466-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022]
Abstract
Pyruvate kinase catalyses the final step of the glycolytic pathway in central energy metabolism. The monomeric structure comprises three domains: a catalytic TIM-barrel, a regulatory domain involved in allosteric activation, and a lid domain that encloses the substrates. The lid domain is thought to close over the TIM-barrel domain forming contacts with the substrates to promote catalysis and may be involved in stabilising the activated state when the allosteric activator is bound. However, it remains unknown whether the lid domain is essential for pyruvate kinase catalytic or regulatory function. To address this, we removed the lid domain of Escherichia coli pyruvate kinase type 1 (PKTIM+Reg) using protein engineering. Biochemical analyses demonstrate that, despite the absence of key catalytic residues in the lid domain, PKTIM+Reg retains a low level of catalytic activity and has a reduced binding affinity for the substrate phosphoenolpyruvate. The enzyme retains allosteric activation, but the regulatory profile of the enzyme is changed relative to the wild-type enzyme. Analytical ultracentrifugation and small-angle X-ray scattering data show that, beyond the loss of the lid domain, the PKTIM+Reg structure is not significantly altered and is consistent with the wild-type tetramer that is assembled through interactions at the TIM and regulatory domains. Our results highlight the contribution of the lid domain for facilitating pyruvate kinase catalysis and regulation, which could aid in the development of small molecule inhibitors for pyruvate kinase and related lid-regulated enzymes.
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Affiliation(s)
- Elena Sugrue
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - David Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Tong Zhu
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
| | - Katherine A Donovan
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand. .,Biol21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
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77
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Zhao D, Sheng B, Li H, Wu Y, Xu D, Li C. Glycation from α-dicarbonyl compounds has different effects on the heat-induced aggregation of bovine serum albumin and β-casein. Food Chem 2020; 340:128108. [PMID: 33010643 DOI: 10.1016/j.foodchem.2020.128108] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/24/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
α-Dicarbonyl compounds are generated in large amounts during heat treatment in food production. This work compared the influence of glycation by α-dicarbonyl on the hydrothermal aggregation of bovine serum albumin (BSA) and of β-casein (β-CN). Glycation by α-dicarbonyl compounds was found to be more efficient than glycation by glucose in reducing the free amino groups, surface hydrophobicity and isoelectric point of BSA, thus greatly inhibited the hydrothermal aggregation of BSA. In addition, glycation by α-dicarbonyl greatly transformed the rigid BSA aggregates into flexible structures, based on analysis by fluorescence spectrum, transmission electron microscope and small-angle X-ray scattering. In contrast, both the aggregation process and aggregates conformation of β-CN were found to be minimally affected by glycation, possibly due to the intrinsic disorder of β-CN. This work highlights the substantial influences of α-dicarbonyl on dietary proteins during heat treatment depending on the protein structural characteristics.
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Affiliation(s)
- Di Zhao
- Key Laboratory of Meat Processing, MOA, Key Laboratory of Meat Processing and Quality Control, MOE, Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Bulei Sheng
- Department of Food Science, Aarhus University, Blichers Allé 20, Tjele 8830, Denmark
| | - Hao Li
- Key Laboratory of Meat Processing, MOA, Key Laboratory of Meat Processing and Quality Control, MOE, Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yi Wu
- College of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou 510640, PR China
| | - Dan Xu
- College of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou 510640, PR China
| | - Chunbao Li
- Key Laboratory of Meat Processing, MOA, Key Laboratory of Meat Processing and Quality Control, MOE, Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing 210095, PR China
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78
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Phan-Xuan T, Bogdanova E, Millqvist Fureby A, Fransson J, Terry AE, Kocherbitov V. Hydration-Induced Structural Changes in the Solid State of Protein: A SAXS/WAXS Study on Lysozyme. Mol Pharm 2020; 17:3246-3258. [PMID: 32787275 PMCID: PMC7482395 DOI: 10.1021/acs.molpharmaceut.0c00351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
The stability of biologically produced
pharmaceuticals is the limiting
factor to various applications, which can be improved by formulation
in solid-state forms, mostly via lyophilization. Knowledge about the
protein structure at the molecular level in the solid state and its
transition upon rehydration is however scarce, and yet it most likely
affects the physical and chemical stability of the biological drug.
In this work, synchrotron small- and wide-angle X-ray scattering (SWAXS)
are used to characterize the structure of a model protein, lysozyme,
in the solid state and its structural transition upon rehydration
to the liquid state. The results show that the protein undergoes distortion
upon drying to adopt structures that can continuously fill the space
to remove the protein–air interface that may be formed upon
dehydration. Above a hydration threshold of 35 wt %, the native structure
of the protein is recovered. The evolution of SWAXS peaks as a function
of water content in a broad range of concentrations is discussed in
relation to the structural changes in the protein. The findings presented
here can be used for the design and optimization of solid-state formulations
of proteins with improved stability.
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Affiliation(s)
- Tuan Phan-Xuan
- Biomedical Science, Malmö University, 214 32 Malmö, Sweden.,Biofilms Research Center for Biointerfaces, Malmö University, 214 32 Malmö, Sweden.,Max IV Laboratory, Lund University, 224 84 Lund, Sweden
| | - Ekaterina Bogdanova
- Biomedical Science, Malmö University, 214 32 Malmö, Sweden.,Biofilms Research Center for Biointerfaces, Malmö University, 214 32 Malmö, Sweden
| | | | | | - Ann E Terry
- Max IV Laboratory, Lund University, 224 84 Lund, Sweden
| | - Vitaly Kocherbitov
- Biomedical Science, Malmö University, 214 32 Malmö, Sweden.,Biofilms Research Center for Biointerfaces, Malmö University, 214 32 Malmö, Sweden
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79
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Jensen RK, Jabs F, Miehe M, Mølgaard B, Pfützner W, Möbs C, Spillner E, Andersen GR. Structure of intact IgE and the mechanism of ligelizumab revealed by electron microscopy. Allergy 2020; 75:1956-1965. [PMID: 32037590 DOI: 10.1111/all.14222] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND IgE is the central antibody isotype in TH2-biased immunity and allergic diseases. The structure of intact IgE and the impact of IgE-targeting molecules on IgE however remain elusive. In order to obtain insights into IgE biology and the clinical impact, we aimed for structure determination of IgE and the complex of IgE with the anti-IgE antibody ligelizumab. METHODS Structures of two distinct intact IgE with specificity for cross-reactive carbohydrate determinants and Der p 2 as well as complexes of ligelizumab-Fab with IgE and IgE Fc were assessed by negative stain electron microscopy and solution scattering. Inhibition of IgE binding and displacement of receptor-bound IgE were assessed using cellular assays, basophil activation testing and ELIFAB assays. RESULTS Our data reveal that the investigated IgE molecules share an overall rigid conformation. In contrast to the IgE Fc fragment, the IgE Fc in intact IgE is significantly less asymmetrically bent. The proximal and the distal Fabs are rigidly tethered to the Fc. Binding of ligelizumab to IgE in a 2:1 stoichiometry induces an extended and twofold symmetrical conformation of IgE, which retains a rigid Fab-Fc architecture. Analyses of effector cell activation revealed that ligelizumab inhibits IgE binding without displacing receptor-bound IgE. Together with an interference of CD23 binding, the data underline a functional activity similar to omalizumab. CONCLUSIONS Our data reveal the first structures of intact IgE suggesting that the IgE Fab is fixed relative to the Fc. Furthermore, we provide a structural rationale for the inhibitory mechanism of ligelizumab.
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Affiliation(s)
- Rasmus K. Jensen
- Department of Molecular Biology and Genetics Aarhus University Aarhus Denmark
| | - Frederic Jabs
- Immunological Biotechnology Department of Engineering Aarhus University Aarhus Denmark
| | - Michaela Miehe
- Immunological Biotechnology Department of Engineering Aarhus University Aarhus Denmark
| | - Brian Mølgaard
- Immunological Biotechnology Department of Engineering Aarhus University Aarhus Denmark
| | - Wolfgang Pfützner
- Clinical and Experimental Allergology, Department of Dermatology and Allergology Philipps-Universität Marburg Marburg Germany
| | - Christian Möbs
- Clinical and Experimental Allergology, Department of Dermatology and Allergology Philipps-Universität Marburg Marburg Germany
| | - Edzard Spillner
- Immunological Biotechnology Department of Engineering Aarhus University Aarhus Denmark
| | - Gregers R. Andersen
- Department of Molecular Biology and Genetics Aarhus University Aarhus Denmark
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80
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Sok P, Gógl G, Kumar GS, Alexa A, Singh N, Kirsch K, Sebő A, Drahos L, Gáspári Z, Peti W, Reményi A. MAP Kinase-Mediated Activation of RSK1 and MK2 Substrate Kinases. Structure 2020; 28:1101-1113.e5. [PMID: 32649858 DOI: 10.1016/j.str.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/03/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) control essential eukaryotic signaling pathways. While much has been learned about MAPK activation, much less is known about substrate recruitment and specificity. MAPK substrates may be other kinases that are crucial to promote a further diversification of the signaling outcomes. Here, we used a variety of molecular and cellular tools to investigate the recruitment of two substrate kinases, RSK1 and MK2, to three MAPKs (ERK2, p38α, and ERK5). Unexpectedly, we identified that kinase heterodimers form structurally and functionally distinct complexes depending on the activation state of the MAPK. These may be incompatible with downstream signaling, but naturally they may also form structures that are compatible with the phosphorylation of the downstream kinase at the activation loop, or alternatively at other allosteric sites. Furthermore, we show that small-molecule inhibitors may affect the quaternary arrangement of kinase heterodimers and thus influence downstream signaling in a specific manner.
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Affiliation(s)
- Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Gergő Gógl
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | | | - Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Neha Singh
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Klára Kirsch
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - Anna Sebő
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, USA
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, Magyar Tudósok körútja 2., 1117 Budapest, Hungary.
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81
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Exolysin (ExlA) from Pseudomonas aeruginosa Punctures Holes into Target Membranes Using a Molten Globule Domain. J Mol Biol 2020; 432:4466-4480. [DOI: 10.1016/j.jmb.2020.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
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82
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Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. Proc Natl Acad Sci U S A 2020; 117:14996-15005. [PMID: 32541047 PMCID: PMC7334511 DOI: 10.1073/pnas.1913442117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.
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83
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Wychowaniec JK, Patel R, Leach J, Mathomes R, Chhabria V, Patil-Sen Y, Hidalgo-Bastida A, Forbes RT, Hayes JM, Elsawy MA. Aromatic Stacking Facilitated Self-Assembly of Ultrashort Ionic Complementary Peptide Sequence: β-Sheet Nanofibers with Remarkable Gelation and Interfacial Properties. Biomacromolecules 2020; 21:2670-2680. [DOI: 10.1021/acs.biomac.0c00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacek K. Wychowaniec
- School of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, United Kingdom
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ronak Patel
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - James Leach
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Rachel Mathomes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Vikesh Chhabria
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Yogita Patil-Sen
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Araida Hidalgo-Bastida
- Centre for Biosciences, Department of Life Science, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- Centre for Musculoskeletal Science and Sports Medicine, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- Centre for Advance Materials and Surface Engineering, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
| | - Robert T. Forbes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Joseph M. Hayes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Mohamed A. Elsawy
- School of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, United Kingdom
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Leicester Institute of Pharmaceutical Innovation, Leicester School of Pharmacy, De Monfort University, The Gateway, Leicester LE1 9BH, United Kingdom
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84
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Milton-Harris L, Jeeves M, Walker SA, Ward SE, Mancini EJ. Small molecule inhibits T-cell acute lymphoblastic leukaemia oncogenic interaction through conformational modulation of LMO2. Oncotarget 2020; 11:1737-1748. [PMID: 32477463 PMCID: PMC7233811 DOI: 10.18632/oncotarget.27580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
Ectopic expression in T-cell precursors of LIM only protein 2 (LMO2), a key factor in hematopoietic development, has been linked to the onset of T-cell acute lymphoblastic leukaemia (T-ALL). In the T-ALL context, LMO2 drives oncogenic progression through binding to erythroid-specific transcription factor SCL/TAL1 and sequestration of E-protein transcription factors, normally required for T-cell differentiation. A key requirement for the formation of this oncogenic protein-protein interaction (PPI) is the conformational flexibility of LMO2. Here we identify a small molecule inhibitor of the SCL-LMO2 PPI, which hinders the interaction in vitro through direct binding to LMO2. Biophysical analysis demonstrates that this inhibitor acts through a mechanism of conformational modulation of LMO2. Importantly, this work has led to the identification of a small molecule inhibitor of the SCL-LMO2 PPI, which can provide a starting point for the development of new agents for the treatment of T-ALL. These results suggest that similar approaches, based on the modulation of protein conformation by small molecules, might be used for therapeutic targeting of other oncogenic PPIs.
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Affiliation(s)
- Leanne Milton-Harris
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sarah A Walker
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9QJ, United Kingdom
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Erika J Mancini
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
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85
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Feger G, Angelov B, Angelova A. Prediction of Amphiphilic Cell-Penetrating Peptide Building Blocks from Protein-Derived Amino Acid Sequences for Engineering of Drug Delivery Nanoassemblies. J Phys Chem B 2020; 124:4069-4078. [PMID: 32337991 DOI: 10.1021/acs.jpcb.0c01618] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amphiphilic molecules, forming self-assembled nanoarchitectures, are typically composed of hydrophobic and hydrophilic domains. Peptide amphiphiles can be designed from two, three, or four building blocks imparting novel structural and functional properties and affinities for interaction with cellular membranes or intracellular organelles. Here we present a combined numerical approach to design amphiphilic peptide scaffolds that are derived from the human nuclear Ki-67 protein. Ki-67 acts, like a biosurfactant, as a steric and electrostatic charge barrier against the collapse of mitotic chromosomes. The proposed predictive design of new Ki-67 protein-derived amphiphilic amino acid sequences exploits the computational outcomes of a set of web-accessible predictors, which are based on machine learning methods. The ensemble of such artificial intelligence algorithms, involving support vector machine (SVM), random forest (RF) classifiers, and neural networks (NN), enables the nanoengineering of a broad range of innovative peptide materials for therapeutic delivery in various applications. Amphiphilic cell-penetrating peptides (CPP), derived from natural protein sequences, may spontaneously form self-assembled nanocarriers characterized by enhanced cellular uptake. Thanks to their inherent low immunogenicity, they may enable the safe delivery of therapeutic molecules across the biological barriers.
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Affiliation(s)
- Guillaume Feger
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay UMR8612, F-92296 Châtenay-Malabry, France
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay UMR8612, F-92296 Châtenay-Malabry, France
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86
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Metrick CM, Koenigsberg AL, Heldwein EE. Conserved Outer Tegument Component UL11 from Herpes Simplex Virus 1 Is an Intrinsically Disordered, RNA-Binding Protein. mBio 2020; 11:e00810-20. [PMID: 32371601 PMCID: PMC7403781 DOI: 10.1128/mbio.00810-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 12/23/2022] Open
Abstract
A distinguishing morphological feature of all herpesviruses is the multiprotein tegument layer located between the nucleocapsid and lipid envelope of the virion. Tegument proteins play multiple roles in viral replication, including viral assembly, but we do not yet understand their individual functions or how the tegument is assembled and organized. UL11, the smallest tegument protein, is important for several distinct processes in replication, including efficient virion morphogenesis and cell-cell spread. However, the mechanistic understanding of its role in these and other processes is limited in part by the scant knowledge of its biochemical and structural properties. Here, we report that UL11 from herpes simplex virus 1 (HSV-1) is an intrinsically disordered, conformationally dynamic protein that undergoes liquid-liquid phase separation (LLPS) in vitro Intrinsic disorder may underlie the ability of UL11 to exert multiple functions and bind multiple partners. Sequence analysis suggests that not only all UL11 homologs but also all HSV-1 tegument proteins contain intrinsically disordered regions of different lengths. The presence of intrinsic disorder, and potentially, the ability to form LLPS, may thus be a common feature of the tegument proteins. We hypothesize that tegument assembly may involve the formation of a biomolecular condensate, driven by the heterogeneous mixture of intrinsically disordered tegument proteins.IMPORTANCE Herpesvirus virions contain a unique tegument layer sandwiched between the capsid and lipid envelope and composed of multiple copies of about two dozen viral proteins. However, little is known about the structure of the tegument or how it is assembled. Here, we show that a conserved tegument protein UL11 from herpes simplex virus 1, a prototypical alphaherpesvirus, is an intrinsically disordered protein that undergoes liquid-liquid phase separation in vitro Through sequence analysis, we find intrinsically disordered regions of different lengths in all HSV-1 tegument proteins. We hypothesize that intrinsic disorder is a common characteristic of tegument proteins and propose a new model of tegument as a biomolecular condensate.
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Affiliation(s)
- Claire M Metrick
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Biochemistry, Tufts School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Andrea L Koenigsberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Tufts School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Ekaterina E Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
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87
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Phosphoprotein Biosensors for Monitoring Pathological Protein Structural Changes. Trends Biotechnol 2020; 38:519-531. [DOI: 10.1016/j.tibtech.2019.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022]
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88
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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89
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do Amaral MJ, Araujo TS, Díaz NC, Accornero F, Polycarpo CR, Cordeiro Y, Cabral KM, Almeida MS. Phase Separation and Disorder-to-Order Transition of Human Brain Expressed X-Linked 3 (hBEX3) in the Presence of Small Fragments of tRNA. J Mol Biol 2020; 432:2319-2348. [DOI: 10.1016/j.jmb.2020.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/10/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022]
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90
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Sevinis Ozbulut EB, Seven S, Bilge K, Akkas T, Tas CE, Yildiz B, Atilgan C, Menceloglu YZ, Unal S. Blends of highly branched and linear poly(arylene ether sulfone)s: Multiscale effect of the degree of branching on the morphology and mechanical properties. POLYMER 2020. [DOI: 10.1016/j.polymer.2019.122114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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91
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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92
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Théobald-Dietrich A, de Wijn R, Rollet K, Bluhm A, Rudinger-Thirion J, Paulus C, Lorber B, Thureau A, Frugier M, Sauter C. Structural Analysis of RNA by Small-Angle X-ray Scattering. Methods Mol Biol 2020; 2113:189-215. [PMID: 32006316 DOI: 10.1007/978-1-0716-0278-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.
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Affiliation(s)
- Anne Théobald-Dietrich
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Raphaël de Wijn
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Kévin Rollet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexandra Bluhm
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Caroline Paulus
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Bernard Lorber
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | | | - Magali Frugier
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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93
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Sagar A, Svergun D, Bernadó P. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering. Methods Mol Biol 2020; 2141:249-269. [PMID: 32696361 DOI: 10.1007/978-1-0716-0524-0_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small-angle X-ray scattering (SAXS) is a low-resolution method for the structural characterization of biological macromolecules in solution. Information about the overall structural features provided by SAXS is highly complementary to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, which are high-resolution methods. SAXS not only provides the shape, oligomeric state, and quaternary structure of folded proteins and protein complexes but also allows for quantitative analysis of flexible biomolecules. In this chapter, the most relevant SAXS procedures for structural characterization of flexible macromolecules, including intrinsically disordered proteins (IDPs), are presented. The sample requirements for SAXS experiments on protein solutions and the sequence of steps in data collection and processing are described. The use of the advanced data analysis tools to quantitatively characterize flexible proteins is presented in detail. Typical experimental issues and potential problems encountered during SAXS data measurements and analyses are discussed.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
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94
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Buchanan JK, Zhang Y, Holmes G, Covington AD, Prabakar S. Role of X‐ray Scattering Techniques in Understanding the Collagen Structure of Leather. ChemistrySelect 2019. [DOI: 10.1002/slct.201902908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jenna K. Buchanan
- Leather and Shoe Research Association of New Zealand, P.O. Box 8094 Palmerston North 4472 New Zealand
| | - Yi Zhang
- Leather and Shoe Research Association of New Zealand, P.O. Box 8094 Palmerston North 4472 New Zealand
| | - Geoff Holmes
- Leather and Shoe Research Association of New Zealand, P.O. Box 8094 Palmerston North 4472 New Zealand
| | - Anthony D. Covington
- Institute for Creative Leather TechnologiesThe University of NorthamptonUniversity Drive Northampton NN1 5PH United Kingdom
| | - Sujay Prabakar
- Leather and Shoe Research Association of New Zealand, P.O. Box 8094 Palmerston North 4472 New Zealand
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95
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Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:8-17. [PMID: 31989063 PMCID: PMC6984960 DOI: 10.1016/j.cobme.2019.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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96
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Shtykova EV, Petoukhov MV, Mozhaev AA, Deyev IE, Dadinova LA, Loshkarev NA, Goryashchenko AS, Bocharov EV, Jeffries CM, Svergun DI, Batishchev OV, Petrenko AG. The dimeric ectodomain of the alkali-sensing insulin receptor-related receptor (ectoIRR) has a droplike shape. J Biol Chem 2019; 294:17790-17798. [PMID: 31615897 PMCID: PMC6879334 DOI: 10.1074/jbc.ra119.010390] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/10/2019] [Indexed: 09/10/2023] Open
Abstract
Insulin receptor-related receptor (IRR) is a receptor tyrosine kinase of the insulin receptor family and functions as an extracellular alkali sensor that controls metabolic alkalosis in the regulation of the acid-base balance. In the present work, we sought to analyze structural features of IRR by comparing them with those of the insulin receptor, which is its closest homolog but does not respond to pH changes. Using small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM), we investigated the overall conformation of the recombinant soluble IRR ectodomain (ectoIRR) at neutral and alkaline pH. In contrast to the well-known inverted U-shaped (or λ-shaped) conformation of the insulin receptor, the structural models reconstructed at different pH values revealed that the ectoIRR organization has a "droplike" shape with a shorter distance between the fibronectin domains of the disulfide-linked dimer subunits within ectoIRR. We detected no large-scale pH-dependent conformational changes of ectoIRR in both SAXS and AFM experiments, an observation that agreed well with previous biochemical and functional analyses of IRR. Our findings indicate that ectoIRR's sensing of alkaline conditions involves additional molecular mechanisms, for example engagement of receptor juxtamembrane regions or the surrounding lipid environment.
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Affiliation(s)
- Eleonora V Shtykova
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow 119333, Russia
| | - Maxim V Petoukhov
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow 119333, Russia
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow 119071, Russia
| | - Andrey A Mozhaev
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow 119333, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Igor E Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Liubov A Dadinova
- A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow 119333, Russia
| | - Nikita A Loshkarev
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow 119071, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141701, Russia
| | - Alexander S Goryashchenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141701, Russia
| | - Cy M Jeffries
- European Molecular Biology Laboratory, EMBL Hamburg Unit, 22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, EMBL Hamburg Unit, 22607 Hamburg, Germany
| | - Oleg V Batishchev
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow 119071, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141701, Russia
| | - Alexander G Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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97
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Hsu DJ, Leshchev D, Rimmerman D, Hong J, Kelley MS, Kosheleva I, Zhang X, Chen LX. X-ray snapshots reveal conformational influence on active site ligation during metalloprotein folding. Chem Sci 2019; 10:9788-9800. [PMID: 32055348 PMCID: PMC6993610 DOI: 10.1039/c9sc02630d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
Cytochrome c (cyt c) has long been utilized as a model system to study metalloprotein folding dynamics and the interplay between active site ligation and tertiary structure. However, recent reports regarding the weakness of the native Fe(ii)-S bond (Fe-Met80) call into question the role of the active site ligation in the protein folding process. In order to investigate the interplay between protein conformation and active site structures, we directly tracked the evolution of both during a photolysis-induced folding reaction using X-ray transient absorption spectroscopy and time-resolved X-ray solution scattering techniques. We observe an intermediate Fe-Met80 species appearing on ∼2 μs timescale, which should not be sustained without stabilization from the folded protein structure. We also observe the appearance of a new active site intermediate: a weakly interacting Fe-H2O state. As both intermediates require stabilization of weak metal-ligand interactions, we surmise the existence of a local structure within the unfolded protein that protects and limits the movement of the ligands, similar to the entatic state found in the native cyt c fold. Furthermore, we observe that in some of the unfolded ensemble, the local stabilizing structure is lost, leading to expansion of the unfolded protein structure and misligation to His26/His33 residues.
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Affiliation(s)
- Darren J Hsu
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Denis Leshchev
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Dolev Rimmerman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Jiyun Hong
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Matthew S Kelley
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Irina Kosheleva
- Center for Advanced Radiation Sources , The University of Chicago , Illinois 60637 , USA
| | - Xiaoyi Zhang
- X-ray Sciences Division of the Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , USA
| | - Lin X Chen
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
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98
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Jing B, Ferreira M, Gao Y, Wood C, Li R, Fukuto M, Liu T, Zhu Y. Unconventional Complex Coacervation between Neutral Polymer and Inorganic Polyoxometalate in Aqueous Solution via Direct Water Mediation. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Benxin Jing
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Manuela Ferreira
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Yunyi Gao
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Christopher Wood
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Tianbo Liu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
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99
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Rodríguez-Zamora P. Conjugation of NMR and SAXS for flexible and multidomain protein structure determination: From sample preparation to model refinement. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:140-144. [PMID: 31445067 DOI: 10.1016/j.pbiomolbio.2019.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the protein with lower resolution, but revealing domain positions. Different conjugation methodologies use the complementarity of both techniques' independent constraints to achieve comprehensive protein structure determination and resolve dynamics at a moderate computational expense.
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Affiliation(s)
- P Rodríguez-Zamora
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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100
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Gielnik M, Pietralik Z, Zhukov I, Szymańska A, Kwiatek WM, Kozak M. PrP (58-93) peptide from unstructured N-terminal domain of human prion protein forms amyloid-like fibrillar structures in the presence of Zn 2+ ions. RSC Adv 2019; 9:22211-22219. [PMID: 35519468 PMCID: PMC9066832 DOI: 10.1039/c9ra01510h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/07/2019] [Indexed: 12/12/2022] Open
Abstract
Many transition metal ions modulate the aggregation of different amyloid peptides. Substoichiometric zinc concentrations can inhibit aggregation, while an excess of zinc can accelerate the formation of cytotoxic fibrils. In this study, we report the fibrillization of the octarepeat domain to amyloid-like structures. Interestingly, this self-assembling process occurred only in the presence of Zn(ii) ions. The formed peptide aggregates are able to bind amyloid specific dyes thioflavin T and Congo red. Atomic force microscopy and transmission electron microscopy revealed the formation of long, fibrillar structures. X-ray diffraction and Fourier transform infrared spectroscopy studies of the formed assemblies confirmed the presence of cross-β structure. Two-component analysis of synchrotron radiation SAXS data provided the evidence for a direct decrease in monomeric peptide species content and an increase in the fraction of aggregates as a function of Zn(ii) concentration. These results could shed light on Zn(ii) as a toxic agent and on the metal ion induced protein misfolding in prion diseases.
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Affiliation(s)
- Maciej Gielnik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Zuzanna Pietralik
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences PL 02-106 Warszawa Poland
- NanoBioMedical Centre, Adam Mickiewicz University PL 61-614 Poznań Poland
| | - Aneta Szymańska
- Department of Biomedical Chemistry, Faculty of Chemistry, Gdańsk University PL 80-308 Gdańsk Poland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics Polish Academy of Sciences PL 31-342 Krakow Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University Uniwersytetu Poznańskiego 2 PL 61-614 Poznań Poland
- Joint Laboratory for SAXS Studies, Faculty of Physics, Adam Mickiewicz University PL 61-614 Poznań Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University PL 30-392 Kraków Poland
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