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Huang X, Wu Z, Zhang B, Yang G, Wang HF, Wang H, Cao Y, Peng F, Li S, Yu H. Formation of Disordered High-Entropy-Alloy Nanoparticles for Highly Efficient Hydrogen Electrocatalysis. Small 2024:e2311631. [PMID: 38513241 DOI: 10.1002/smll.202311631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Indexed: 03/23/2024]
Abstract
Nanoparticles composed of high-entropy alloys (HEA NPs) exhibit remarkable performance in electrocatalytic processes such as hydrogen evolution and oxidations. In this study, two types of quinary HEA NPs of PtRhPdIrRu, are synthesized, featuring disordered and crystallized nanostructures, both with and without a boiling mixture. The disordered HEA NPs (d-HEA NPs) with a size of 3.5 nm is synthesized under intense boiling conditions, attributed to improved heat and mass transfer during reduction of precursors and particle growth. The disordered HEA NPs displayed an exceptionally high turnover frequency of 33.1 s-1 at an overpotential of 50 mV, surpassing commercial Pt NPs in acidic electrolytes by 5.4 times. Additionally, d-HEA NPs exhibited superior stability at a constant electrolyzing current of 50 mA cm-2 compared to commercial Pt NPs. When employed as the anodic catalyst in an H2-O2 fuel cell, d-HEA NPs demonstrated a remarkable high current power density of 15.3 kW per gram of noble metal. Consequently, these findings highlight the potential of d-HEA NPs in electrochemical applications involving hydrogen.
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Affiliation(s)
- Xianfeng Huang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510641, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zenan Wu
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Bo Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Guangxing Yang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Hao-Fan Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Hongjuan Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Yonghai Cao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Feng Peng
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Hao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510641, China
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2
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Liu W, Luo C, Peng X. Phase transitions, conductance fluctuations and distributions in disordered topological insulator stanene. J Phys Condens Matter 2024; 36:165401. [PMID: 38190736 DOI: 10.1088/1361-648x/ad1bf9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024]
Abstract
It is essential to understand to what extent the protected edge states of topological insulators (TIs) can survive against the degradation of the ubiquitous disorders in realistic devices. From a different perspective, disorders can also help to enrich the applications by modulation of the phases in TIs. In this work, the phases and phase transitions in stanene, a two-dimensional TI, have been investigated via the statistical approach based on the random matrix theory. Using a tight binding model with Aderson disorder term and the Landauer-Büttiker formalism, we calculated the conductance of realistic stanene ribbons of tens of nanometers long with random disorders. The calculated phase diagram presents TI in the gap, metal in high energy and ordinary insulator in large disorder region. Increasing the width of the ribbon can significantly enhance the robustness of TI phase against disorders. Due to different underlying symmetries, the metallic phase can be further categorized into unitary and orthogonal classes according to the calculated universal conductance fluctuations. The local density of states is calculated, showing characteristic patterns, which can facilitate the experimental identification of the phases. It is found that different phases have distinguishing statistical distribution of conductance. Whereas at the phase boundary the distribution exhibits intermediate features to show where the phase transition occurs. To reveal the phase evolution process, we further studied the effects of the disorders on respective transmission channels. It is found that when phase transition takes place, the major transmission channels of the old phase are fading and the new channels of the new phase are emerging.
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Affiliation(s)
- Wenchao Liu
- Hunan Key Laboratory for Micro-Nano Energy Materials and Devices, School of Physics and Optoelectronics, Xiangtan University, Hunan 411105, People's Republic of China
| | - Chaobo Luo
- Hunan Key Laboratory for Micro-Nano Energy Materials and Devices, School of Physics and Optoelectronics, Xiangtan University, Hunan 411105, People's Republic of China
| | - Xiangyang Peng
- Hunan Key Laboratory for Micro-Nano Energy Materials and Devices, School of Physics and Optoelectronics, Xiangtan University, Hunan 411105, People's Republic of China
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3
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Zendle D, Flick C, Halgarth D, Ballou N, Cutting J, Drachen A. The Relationship Between Lockdowns and Video Game Playtime: Multilevel Time-Series Analysis Using Massive-Scale Data Telemetry. J Med Internet Res 2023; 25:e40190. [PMID: 37938889 PMCID: PMC10666013 DOI: 10.2196/40190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/25/2022] [Accepted: 06/09/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND COVID-19 led governments worldwide to enact a variety of containment and closure policies. Substantial attention has been directed toward the idea that these public health measures may have unanticipated negative side effects. One proposed effect relates to video games. There is a nascent evidence base suggesting that individuals played video games for longer and in a more disordered manner during lockdowns and school closures specifically. These increases are commonly framed as a potential health concern in relation to disordered gaming. However, the evidence base regarding changes in gaming during the COVID-19 pandemic is based on self-report and, thus, is susceptible to bias. Therefore, it is unclear what the true consequences of lockdowns were for gaming behavior worldwide. OBJECTIVE The primary objective of this study was to estimate whether any specific lockdown policy led to meaningful increases in the amount of time individuals spent playing video games. METHODS Rather than relying on self-report, we used >251 billion hours of raw gameplay telemetry data from 184 separate countries to assess the behavioral correlates of COVID-19-related policy decisions. A multilevel model estimated the impact of varying enforcement levels of 8 containment and closure policies on the amount of time that individual users spent in-game. Similar models estimated the impact of policy on overall playtime and the number of users within a country. RESULTS No lockdown policy can explain substantial variance in playtime per gamer. School closures were uniquely associated with meaningful increases in total playtime within a country (r2=0.048). However, this was associated with increases in the number of unique individuals playing games (r2=0.057) rather than increases in playtime per gamer (r2<0.001). CONCLUSIONS Previous work using self-report data has suggested that important increases in heavy gaming may occur during pandemics because of containment and closure ("lockdown") procedures. This study contrasts with the previous evidence base and finds no evidence of such a relationship. It suggests that significant further work is needed before increases in disordered or heavy gaming are considered when planning public health policies for pandemic preparedness.
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Affiliation(s)
- David Zendle
- Department of Computer Science, University of York, York, United Kingdom
| | - Catherine Flick
- School of Computer Science and Informatics, De Montfort University, Leicester, United Kingdom
| | - Darel Halgarth
- Department of Computer Science, University of York, York, United Kingdom
| | - Nick Ballou
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London, United Kingdom
| | - Joe Cutting
- Department of Computer Science, University of York, York, United Kingdom
| | - Anders Drachen
- Faculty of Engineering, University of Southern Denmark, Odense, United Kingdom
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4
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Caldas H, Rufo S, Griffith MAR. Non-homogeneous pairing in disordered two-orbital s-wave superconductors. J Phys Condens Matter 2023; 36:055601. [PMID: 37820641 DOI: 10.1088/1361-648x/ad0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
We investigate the effects of non-magnetic disorder in a hybridized two-dimensional two-orbital s-wave superconductor (SC) model. The situation in which electronic orbitals overlap such that the hybridizationVi,jamong them is antisymmetric, under inversion symmetry, was taken into account. The on-site disorder is given by a random impurity potentialW. We find that while the random disorder acts to the detriment of superconductivity, hybridization proceeds to favor it. Accordingly, hybridization plays an important role in two-orbital models of superconductivity, in order to hold the long-range order against the increase of disorder. This makes the present model eligible to describe real materials, since the hybridization may be induced by pressure or doping. In addition, the regime from moderate to strong disorder reveals that the system is broken into SC islands with correlated local order parameters. These correlations persist to distances of several order lattice spacing which corresponds to the size of the SC-Islands.
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Affiliation(s)
- Heron Caldas
- Departamento de Ciências Naturais, Universidade Federal de São João Del Rei, Praça Dom Helvécio 74, 36301-160 São João Del Rei, MG, Brazil
| | - S Rufo
- Beijing Computational Science Research Center, Building 9, East Zone, No. 10 East Xibeiwang Road, Haidian District, Beijing 100193, People's Republic of China
- CeFEMA, Instituto Superior técnico, Universidade de Lisboa, Av. Rovisco Pais, No. 1, 1049-001 Lisboa, Portugal
| | - M A R Griffith
- Beijing Computational Science Research Center, Building 9, East Zone, No. 10 East Xibeiwang Road, Haidian District, Beijing 100193, People's Republic of China
- CeFEMA, Instituto Superior técnico, Universidade de Lisboa, Av. Rovisco Pais, No. 1, 1049-001 Lisboa, Portugal
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5
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Cheng Z, Gao X, Yang C, Brytek-Matera A, He J. Effects of Online and Face-to-Face Intuitive Eating Interventions on Body Image and Eating Behaviors among Women in China: A Feasibility Study. Nutrients 2022; 14:1761. [PMID: 35565730 PMCID: PMC9100518 DOI: 10.3390/nu14091761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Body dissatisfaction and eating disorders have become major global concerns, including in Asian populations. Few studies have examined intervention effects on body dissatisfaction and disordered eating in China, especially for interventions with positive psychological perspectives (e.g., intuitive eating). In this pilot study, 66 women participated in an eight-module intuitive eating intervention delivered online (n = 42; mean age, 30.74 years) and face-to-face (n = 24; mean age, 19.46 years) for 8 weeks. Measures of body image and eating behaviors were used to assess the intervention's feasibility, acceptability, and initial efficacy. Linear mixed models were used to analyze the data. The intervention had significant effects on both groups, promoting positive body image and intuitive eating and reducing negative body image and disordered eating behaviors. The effects of the online and face-to-face interventions did not differ significantly. Thus, whether delivered online or face-to-face, an intuitive eating intervention may effectively improve Chinese women's body image and eating behaviors. However, the efficacy of the intuitive intervention in the Chinese context should be confirmed in future studies with designs in randomized control trials.
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Affiliation(s)
- Ziyue Cheng
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.C.); (X.G.); (C.Y.)
| | - Xueyan Gao
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.C.); (X.G.); (C.Y.)
| | - Chengyang Yang
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.C.); (X.G.); (C.Y.)
| | | | - Jinbo He
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.C.); (X.G.); (C.Y.)
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6
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Abstract
The proteasome system is a large and complex molecular machinery responsible for the degradation of misfolded, damaged, and redundant cellular proteins. When proteasome function is impaired, unwanted proteins accumulate, which can lead to several diseases including age-related and neurodegenerative diseases. Enhancing proteasome-mediated substrate degradation with small molecules may therefore be a valuable strategy for the treatment of various neurodegenerative diseases such as Parkinson's, Alzheimer's, and Huntington's diseases. In this review, we discuss the structure of proteasome and how proteasome's proteolytic activity is associated with aging and various neurodegenerative diseases. We also summarize various classes of compounds that are capable of enhancing, directly or indirectly, proteasome-mediated protein degradation.
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Affiliation(s)
| | - Jetze J. Tepe
- Department of Chemistry and Pharmacology & Toxicology, Michigan State University, East Lansing, MI 48824, USA;
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7
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Henderson ME, Beare J, Sharma S, Bleuel M, Clancy P, Cory DG, Huber MG, Marjerrison CA, Pula M, Sarenac D, Smith EM, Zhernenkov K, Luke GM, Pushin DA. Characterization of a Disordered above Room Temperature Skyrmion Material Co 8Zn 8Mn 4. Materials (Basel) 2021; 14:4689. [PMID: 34443211 PMCID: PMC8399547 DOI: 10.3390/ma14164689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
Topologically nontrivial spin textures host great promise for future spintronic applications. Skyrmions in particular are of burgeoning interest owing to their nanometric size, topological protection, and high mobility via ultra-low current densities. It has been previously reported through magnetic susceptibility, microscopy, and scattering techniques that Co8Zn8Mn4 forms an above room temperature triangular skyrmion lattice. Here, we report the synthesis procedure and characterization of a polycrystalline Co8Zn8Mn4 disordered bulk sample. We employ powder X-ray diffraction and backscatter Laue diffraction as characterization tools of the crystallinity of the samples, while magnetic susceptibility and Small Angle Neutron Scattering (SANS) measurements are performed to study the skyrmion phase. Magnetic susceptibility measurements show a dip anomaly in the magnetization curves, which persists over a range of approximately 305 K-315 K. SANS measurements reveal a rotationally disordered polydomain skyrmion lattice. Applying a symmetry-breaking magnetic field sequence, we were able to orient and order the previously jammed state to yield the prototypical hexagonal diffraction patterns with secondary diffraction rings. This emergence of the skyrmion order serves as a unique demonstration of the fundamental interplay of structural disorder and anisotropy in stabilizing the thermal equilibrium phase.
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Affiliation(s)
- Melissa E. Henderson
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (D.G.C.); (D.S.); (K.Z.); (D.A.P.)
- Department of Physics & Astronomy, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - James Beare
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (J.B.); (S.S.); (M.P.); (E.M.S.); (G.M.L.)
| | - Sudarshan Sharma
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (J.B.); (S.S.); (M.P.); (E.M.S.); (G.M.L.)
| | - Markus Bleuel
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (M.B.); (M.G.H.)
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Pat Clancy
- Brockhouse Institute for Materials Research, Hamilton, ON L8S 4M1, Canada; (P.C.); (C.A.M.)
| | - David G. Cory
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (D.G.C.); (D.S.); (K.Z.); (D.A.P.)
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Michael G. Huber
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA; (M.B.); (M.G.H.)
| | - Casey A. Marjerrison
- Brockhouse Institute for Materials Research, Hamilton, ON L8S 4M1, Canada; (P.C.); (C.A.M.)
| | - Mathew Pula
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (J.B.); (S.S.); (M.P.); (E.M.S.); (G.M.L.)
| | - Dusan Sarenac
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (D.G.C.); (D.S.); (K.Z.); (D.A.P.)
| | - Evan M. Smith
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (J.B.); (S.S.); (M.P.); (E.M.S.); (G.M.L.)
| | - Kirill Zhernenkov
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (D.G.C.); (D.S.); (K.Z.); (D.A.P.)
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Graeme M. Luke
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada; (J.B.); (S.S.); (M.P.); (E.M.S.); (G.M.L.)
- Brockhouse Institute for Materials Research, Hamilton, ON L8S 4M1, Canada; (P.C.); (C.A.M.)
| | - Dmitry A. Pushin
- Institute for Quantum Computing, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (D.G.C.); (D.S.); (K.Z.); (D.A.P.)
- Department of Physics & Astronomy, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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8
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Argunhan B, Sakakura M, Afshar N, Kurihara M, Ito K, Maki T, Kanamaru S, Murayama Y, Tsubouchi H, Takahashi M, Takahashi H, Iwasaki H. Cooperative interactions facilitate stimulation of Rad51 by the Swi5-Sfr1 auxiliary factor complex. eLife 2020; 9:52566. [PMID: 32204793 PMCID: PMC7093153 DOI: 10.7554/elife.52566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/13/2020] [Indexed: 01/26/2023] Open
Abstract
Although Rad51 is the key protein in homologous recombination (HR), a major DNA double-strand break repair pathway, several auxiliary factors interact with Rad51 to promote productive HR. We present an interdisciplinary characterization of the interaction between Rad51 and Swi5-Sfr1, a conserved auxiliary factor. Two distinct sites within the intrinsically disordered N-terminus of Sfr1 (Sfr1N) were found to cooperatively bind Rad51. Deletion of this domain impaired Rad51 stimulation in vitro and rendered cells sensitive to DNA damage. By contrast, amino acid-substitution mutants, which had comparable biochemical defects, could promote DNA repair, suggesting that Sfr1N has another role in addition to Rad51 binding. Unexpectedly, the DNA repair observed in these mutants was dependent on Rad55-Rad57, another auxiliary factor complex hitherto thought to function independently of Swi5-Sfr1. When combined with the finding that they form a higher-order complex, our results imply that Swi5-Sfr1 and Rad55-Rad57 can collaboratively stimulate Rad51 in Schizosaccharomyces pombe.
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Affiliation(s)
- Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Negar Afshar
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Misato Kurihara
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kentaro Ito
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Takahisa Maki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Shuji Kanamaru
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuto Murayama
- Center for Frontier Research, National Institute of Genetics, Shizuoka, Japan
| | - Hideo Tsubouchi
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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9
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Engilberge S, Rennie ML, Crowley PB. Calixarene capture of partially unfolded cytochrome c. FEBS Lett 2019; 593:2112-2117. [PMID: 31254353 DOI: 10.1002/1873-3468.13512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/20/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
Supramolecular receptors such as water-soluble calixarenes are in development as 'molecular glues' for protein assembly. Here, we obtained cocrystals of sulfonato-calix[6]arene (sclx6 ) and yeast cytochrome c (cytc) in the presence of imidazole. A crystal structure at 2.65 Å resolution reveals major structural rearrangement and disorder in imidazole-bound cytc. The largest protein-calixarene interface involves 440 Å2 of the protein surface with key contacts at Arg13, Lys73, and Lys79. These lysines participate in alkaline transitions of cytc and are part of Ω-loop D, which is substantially restructured in the complex with sclx6 . The structural modification also includes Ω-loop C, which is disordered (residues 41-55 inclusive). These results suggest the possibility of using supramolecular scaffolds to trap partially disordered proteins.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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10
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McPherson A, Larson SB. Investigation into the binding of dyes within protein crystals. Acta Crystallogr F Struct Biol Commun 2018; 74:593-602. [PMID: 30198893 PMCID: PMC6130428 DOI: 10.1107/s2053230x18010300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 11/10/2022] Open
Abstract
It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins. Four protein crystals were investigated by X-ray diffraction to ascertain the mode of binding. These were crystals of lysozyme, thaumatin, trypsin inhibited with benzamidine and satellite tobacco mosaic virus. In 30 X-ray analyses of protein crystal-dye complexes, in only three difference Fourier maps was any difference electron density present that was consistent with the binding of dye molecules, and even in these three cases (thaumatin plus thioflavin T, xylene cyanol and m-cresol purple) the amount of dye observed was inadequate to explain the intense color of the crystals. It was concluded that the dye molecules, which are clearly inside the crystals, are disordered but are paradoxically tightly bound to the protein. It is speculated that the dyes, which exhibit large hydrophobic cores and peripheral charged groups, may interact with the crystalline proteins in the manner of conventional detergents.
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Affiliation(s)
- Alexander McPherson
- Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
| | - Steven B. Larson
- Molecular Biology and Biochemistry, University of California Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900, USA
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11
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Bozoky Z, Krzeminski M, Chong PA, Forman-Kay JD. Structural changes of CFTR R region upon phosphorylation: a plastic platform for intramolecular and intermolecular interactions. FEBS J 2013; 280:4407-16. [PMID: 23826884 PMCID: PMC4160016 DOI: 10.1111/febs.12422] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/24/2013] [Accepted: 07/02/2013] [Indexed: 11/29/2022]
Abstract
Chloride channel gating and trafficking of the cystic fibrosis transmembrane conductance regulator (CFTR) are regulated by phosphorylation. Intrinsically disordered segments of the protein are responsible for phospho‐regulation, particularly the regulatory (R) region that is a target for several kinases and phosphatases. The R region remains disordered following phosphorylation, with different phosphorylation states sampling various conformations. Recent studies have demonstrated the crucial role that intramolecular and intermolecular interactions of the R region play in CFTR regulation. Different partners compete for the same binding segment, with the R region containing multiple overlapping binding elements. The non‐phosphorylated R region interacts with the nucleotide binding domains and inhibits channel activity by blocking heterodimerization. Phosphorylation shifts the equilibrium such that the R region is excluded from the dimer interface, facilitating gating and processing by stimulating R region interactions with other domains and proteins. The dynamic conformational sampling and transient binding of the R region to multiple partners enables complex control of CFTR channel activity and trafficking.
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Affiliation(s)
- Zoltan Bozoky
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
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12
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Williams RW, Xue B, Uversky VN, Dunker AK. Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. Intrinsically Disord Proteins 2013; 1:e25724. [PMID: 28516017 PMCID: PMC5424788 DOI: 10.4161/idp.25724] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/11/2013] [Indexed: 11/19/2022]
Abstract
The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information.
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Affiliation(s)
- Robert W Williams
- Department of Biomedical Informatics; Uniformed Services University; Bethesda, MD USA
| | - Bin Xue
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA.,Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Indiana School of Medicine; Indianapolis, IN USA
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Abstract
The left-handed polyproline II (PPII) helix gives rise to a circular dichroism spectrum that is remarkably similar to that of unfolded proteins. This similarity has been used as the basis for the hypothesis that unfolded proteins possess considerable PPII helical content. It has long been known that homopolymers of lysine adopt the PPII helical conformation at neutral pH, presumably a result of electrostatic repulsion between side chains. It is shown here that a seven-residue lysine peptide also adopts the PPII conformation. In contrast with homopolymers of lysine, this short peptide is shown to retain PPII helical character under conditions in which side-chain charges are heavily screened or even neutralized. The most plausible explanation for these observations is that the peptide backbone favors the PPII conformation to maximize favorable interactions with solvent. These data are evidence that unfolded proteins do indeed possess PPII content, indicating that the ensemble of unfolded states is significantly smaller than is commonly assumed.
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Affiliation(s)
- Adam L Rucker
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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