1
|
Wang S, Huang CH, Lin TS, Yeh YQ, Fan YS, Wang SW, Tseng HC, Huang SJ, Chang YY, Jeng US, Chang CI, Tzeng SR. Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI. Nat Commun 2024; 15:5461. [PMID: 38937433 PMCID: PMC11211486 DOI: 10.1038/s41467-024-49552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.
Collapse
Affiliation(s)
- Shen Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Te-Sheng Lin
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Qi Yeh
- Soft Matter Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yun-Sheng Fan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Si-Wei Wang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsi-Ching Tseng
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Yu-Yang Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - U-Ser Jeng
- Soft Matter Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
2
|
Yeh HW, Chen PP, Yeh TC, Lin SL, Chen YT, Lin WP, Chen T, Pang JM, Lin KT, Wang LHC, Lin YC, Shih O, Jeng US, Hsia KC, Cheng HC. Cep57 regulates human centrosomes through multivalent interactions. Proc Natl Acad Sci U S A 2024; 121:e2305260121. [PMID: 38857398 PMCID: PMC11194501 DOI: 10.1073/pnas.2305260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/15/2024] [Indexed: 06/12/2024] Open
Abstract
Human Cep57 is a coiled-coil scaffold at the pericentriolar matrix (PCM), controlling centriole duplication and centrosome maturation for faithful cell division. Genetic truncation mutations of Cep57 are associated with the mosaic-variegated aneuploidy (MVA) syndrome. During interphase, Cep57 forms a complex with Cep63 and Cep152, serving as regulators for centrosome maturation. However, the molecular interplay of Cep57 with these essential scaffolding proteins remains unclear. Here, we demonstrate that Cep57 undergoes liquid-liquid phase separation (LLPS) driven by three critical domains (NTD, CTD, and polybasic LMN). In vitro Cep57 condensates catalyze microtubule nucleation via the LMN motif-mediated tubulin concentration. In cells, the LMN motif is required for centrosomal microtubule aster formation. Moreover, Cep63 restricts Cep57 assembly, expansion, and microtubule polymerization activity. Overexpression of competitive constructs for multivalent interactions, including an MVA mutation, leads to excessive centrosome duplication. In Cep57-depleted cells, self-assembly mutants failed to rescue centriole disengagement and PCM disorganization. Thus, Cep57's multivalent interactions are pivotal for maintaining the accurate structural and functional integrity of human centrosomes.
Collapse
Affiliation(s)
- Hung-Wei Yeh
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Po-Pang Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Tzu-Chen Yeh
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Shiou-Lan Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Yue-Ting Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Wan-Ping Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Ting Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Jia Meng Pang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Kai-Ti Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu30013, Taiwan
| | - Kuo-Chiang Hsia
- Institute of Molecular Biology, Academia Sinica, Taipei11529, Taiwan
| | - Hui-Chun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu30013, Taiwan
| |
Collapse
|
3
|
Valério A, Trindade FJ, Penacchio RFS, Cisi B, Damasceno S, Estradiote MB, Rodella CB, Ferlauto AS, Kycia SW, Morelhão SL. Implications of size dispersion on X-ray scattering of crystalline nanoparticles: CeO 2 as a case study. J Appl Crystallogr 2024; 57:793-807. [PMID: 38846767 PMCID: PMC11151675 DOI: 10.1107/s1600576724003108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 04/10/2024] [Indexed: 06/09/2024] Open
Abstract
Controlling the shape and size dispersivity and crystallinity of nanoparticles (NPs) has been a challenge in identifying these parameters' role in the physical and chemical properties of NPs. The need for reliable quantitative tools for analyzing the dispersivity and crystallinity of NPs is a considerable problem in optimizing scalable synthesis routes capable of controlling NP properties. The most common tools are electron microscopy (EM) and X-ray scattering techniques. However, each technique has different susceptibility to these parameters, implying that more than one technique is necessary to characterize NP systems with maximum reliability. Wide-angle X-ray scattering (WAXS) is mandatory to access information on crystallinity. In contrast, EM or small-angle X-ray scattering (SAXS) is required to access information on whole NP sizes. EM provides average values on relatively small ensembles in contrast to the bulk values accessed by X-ray techniques. Besides the fact that the SAXS and WAXS techniques have different susceptibilities to size distributions, SAXS is easily affected by NP-NP interaction distances. Because of all the variables involved, there have yet to be proposed methodologies for cross-analyzing data from two techniques that can provide reliable quantitative results of dispersivity and crystallinity. In this work, a SAXS/WAXS-based methodology is proposed for simultaneously quantifying size distribution and degree of crystallinity of NPs. The most reliable easy-to-access size result for each technique is demonstrated by computer simulation. Strategies on how to compare these results and how to identify NP-NP interaction effects underneath the SAXS intensity curve are presented. Experimental results are shown for cubic-like CeO2 NPs. WAXS size results from two analytical procedures are compared, line-profile fitting of individual diffraction peaks in opposition to whole pattern fitting. The impact of shape dispersivity is also evaluated. Extension of the proposed methodology for cross-analyzing EM and WAXS data is possible.
Collapse
Affiliation(s)
- Adriana Valério
- Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Fabiane J. Trindade
- Laboratory of Materials for Energy, Engineering, Modelling and Applied Social Sciences Center, Federal University of ABC, Santo André, São Paulo, Brazil
| | | | - Bria Cisi
- Laboratory of Materials for Energy, Engineering, Modelling and Applied Social Sciences Center, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Sérgio Damasceno
- Laboratory of Materials for Energy, Engineering, Modelling and Applied Social Sciences Center, Federal University of ABC, Santo André, São Paulo, Brazil
| | | | - Cristiane B. Rodella
- Brazilian Synchrotron Light Laboratory – SIRIUS/CNPEM, Campinas, São Paulo, Brazil
| | - Andre S. Ferlauto
- Laboratory of Materials for Energy, Engineering, Modelling and Applied Social Sciences Center, Federal University of ABC, Santo André, São Paulo, Brazil
| | - Stefan W. Kycia
- Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | | |
Collapse
|
4
|
Matsui T, Rajkovic I, Mooers BHM, Liu P, Weiss TM. Adaptable SEC-SAXS data collection for higher quality structure analysis in solution. Protein Sci 2024; 33:e4946. [PMID: 38501481 PMCID: PMC10949327 DOI: 10.1002/pro.4946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 03/20/2024]
Abstract
The two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4-2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enables SEC-SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x-ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC-SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x-ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High-Throughput mode and the Co-Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4-2.
Collapse
Affiliation(s)
- Tsutomu Matsui
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Ivan Rajkovic
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Blaine H. M. Mooers
- Department of Biochemistry and PhysiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Laboratory of Biomolecular Structure and FunctionUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Ping Liu
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| |
Collapse
|
5
|
Narayanan T. Recent advances in synchrotron scattering methods for probing the structure and dynamics of colloids. Adv Colloid Interface Sci 2024; 325:103114. [PMID: 38452431 DOI: 10.1016/j.cis.2024.103114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
Recent progress in synchrotron based X-ray scattering methods applied to colloid science is reviewed. An important figure of merit of these techniques is that they enable in situ investigations of colloidal systems under the desired thermophysical and rheological conditions. An ensemble averaged simultaneous structural and dynamical information can be derived albeit in reciprocal space. Significant improvements in X-ray source brilliance and advances in detector technology have overcome some of the limitations in the past. Notably coherent X-ray scattering techniques have become more competitive and they provide complementary information to laboratory based real space methods. For a system with sufficient scattering contrast, size ranges from nm to several μm and time scales down to μs are now amenable to X-ray scattering investigations. A wide variety of sample environments can be combined with scattering experiments further enriching the science that could be pursued by means of advanced X-ray scattering instruments. Some of these recent progresses are illustrated via representative examples. To derive quantitative information from the scattering data, rigorous data analysis or modeling is required. Development of powerful computational tools including the use of artificial intelligence have become the emerging trend.
Collapse
|
6
|
Tsai YX, Chang NE, Reuter K, Chang HT, Yang TJ, von Bülow S, Sehrawat V, Zerrouki N, Tuffery M, Gecht M, Grothaus IL, Colombi Ciacchi L, Wang YS, Hsu MF, Khoo KH, Hummer G, Hsu STD, Hanus C, Sikora M. Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 2024; 187:1296-1311.e26. [PMID: 38428397 DOI: 10.1016/j.cell.2024.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/18/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Abstract
Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.
Collapse
Affiliation(s)
- Yu-Xi Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Ning-En Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Klaus Reuter
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Hao-Ting Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Jing Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany
| | - Vidhi Sehrawat
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Kraków, Poland
| | - Noémie Zerrouki
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France
| | - Matthieu Tuffery
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France
| | - Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany
| | - Isabell Louise Grothaus
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Yong-Sheng Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt, Germany
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Hiroshima 739-8526, Japan.
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France; GHU Psychiatrie et Neurosciences de Paris, 75014 Paris, France.
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Kraków, Poland.
| |
Collapse
|
7
|
Chang YJ, Lin KT, Shih O, Yang CH, Chuang CY, Fang MH, Lai WB, Lee YC, Kuo HC, Hung SC, Yao CK, Jeng US, Chen YR. Sulfated disaccharide protects membrane and DNA damages from arginine-rich dipeptide repeats in ALS. SCIENCE ADVANCES 2024; 10:eadj0347. [PMID: 38394210 PMCID: PMC10889363 DOI: 10.1126/sciadv.adj0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Hexanucleotide repeat expansion in C9ORF72 (C9) is the most prevalent mutation among amyotrophic lateral sclerosis (ALS) patients. The patients carry over ~30 to hundreds or thousands of repeats translated to dipeptide repeats (DPRs) where poly-glycine-arginine (GR) and poly-proline-arginine (PR) are most toxic. The structure-function relationship is still unknown. Here, we examined the minimal neurotoxic repeat number of poly-GR and found that extension of the repeat number led to a loose helical structure disrupting plasma and nuclear membrane. Poly-GR/PR bound to nucleotides and interfered with transcription. We screened and identified a sulfated disaccharide that bound to poly-GR/PR and rescued poly-GR/PR-induced toxicity in neuroblastoma and C9-ALS-iPSC-derived motor neurons. The compound rescued the shortened life span and defective locomotion in poly-GR/PR expressing Drosophila model and improved motor behavior in poly-GR-injected mouse model. Overall, our results reveal structural and toxicity mechanisms for poly-GR/PR and facilitate therapeutic development for C9-ALS.
Collapse
Affiliation(s)
- Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
| | - Kai-Tai Lin
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
| | - Chi-Hua Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Han Fang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Wei-Bin Lai
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Neurology, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | | | - Chi-Kuang Yao
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
8
|
Kenny S, Lai CH, Chiang TS, Brown K, Hewitt CS, Krabill AD, Chang HT, Wang YS, Flaherty DP, Hsu STD, Das C. Altered Protein Dynamics and a More Reactive Catalytic Cysteine in a Neurodegeneration-associated UCHL1 Mutant. J Mol Biol 2024; 436:168438. [PMID: 38185323 DOI: 10.1016/j.jmb.2024.168438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
A mutant of ubiquitin C-terminal hydrolase L1 (UCHL1) detected in early-onset neurodegenerative patients, UCHL1R178Q, showed higher catalytic activity than wild-type UCHL1 (UCHL1WT). Lying within the active-site pocket, the arginine is part of an interaction network that holds the catalytic histidine in an inactive arrangement. However, the structural basis and mechanism of enzymatic activation upon glutamine substitution was not understood. We combined X-ray crystallography, protein nuclear magnetic resonance (NMR) analysis, enzyme kinetics, covalent inhibition analysis, and biophysical measurements to delineate activating factors in the mutant. While the crystal structure of UCHL1R178Q showed nearly the same arrangement of the catalytic residues and active-site pocket, the mutation caused extensive alteration in the chemical environment and dynamics of more than 30 residues, some as far as 15 Å away from the site of mutation. Significant broadening of backbone amide resonances in the HSQC spectra indicates considerable backbone dynamics changes in several residues, in agreement with solution small-angle X-ray scattering (SAXS) analyses which indicate an overall increase in protein flexibility. Enzyme kinetics show the activation is due to a kcat effect despite a slightly weakened substrate affinity. In line with this, the mutant shows a higher second-order rate constant (kinact/Ki) in a reaction with a substrate-derived irreversible inhibitor, Ub-VME, compared to the wild-type enzyme, an observation indicative of a more reactive catalytic cysteine in the mutant. Together, the observations underscore structural plasticity as a factor contributing to enzyme kinetic behavior which can be modulated through mutational effects.
Collapse
Affiliation(s)
- Sebastian Kenny
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Tsung-Sheng Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Kwame Brown
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chad S Hewitt
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Aaron D Krabill
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Hao-Ting Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States.
| |
Collapse
|
9
|
Tsai CL, Chang JW, Cheng KY, Lan YJ, Hsu YC, Lin QD, Chen TY, Shih O, Lin CH, Chiang PH, Simenas M, Kalendra V, Chiang YW, Chen CH, Jeng US, Wang SK. Comprehensive characterization of polyproline tri-helix macrocyclic nanoscaffolds for predictive ligand positioning. NANOSCALE ADVANCES 2024; 6:947-959. [PMID: 38298598 PMCID: PMC10825903 DOI: 10.1039/d3na00945a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Multivalent ligands hold promise for enhancing avidity and selectivity to simultaneously target multimeric proteins, as well as potentially modulating receptor signaling in pharmaceutical applications. Essential for these manipulations are nanosized scaffolds that precisely control ligand display patterns, which can be achieved by using polyproline oligo-helix macrocyclic nanoscaffolds via selective binding to protein oligomers and cell surface receptors. This work focuses on synthesis and structural characterization of different-sized polyproline tri-helix macrocyclic (PP3M) scaffolds. Through combined analysis of circular dichroism (CD), small- and wide-angle X-ray scattering (SWAXS), electron spin resonance (ESR) spectroscopy, and molecular modeling, a non-coplanar tri-helix loop structure with partially crossover helix ends is elucidated. This structural model aligns well with scanning tunneling microscopy (STM) imaging. The present work enhances the precision of nanoscale organic synthesis, offering prospects for controlled ligand positioning on scaffolds. This advancement paves the way for further applications in nanomedicine through selective protein interaction, manipulation of cell surface receptor functions, and developments of more complex polyproline-based nanostructures.
Collapse
Affiliation(s)
- Chia-Lung Tsai
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Kum-Yi Cheng
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Yu-Jing Lan
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Yi-Cheng Hsu
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Qun-Da Lin
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Tzu-Yuan Chen
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
| | - Chih-Hsun Lin
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - Po-Hsun Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Mantas Simenas
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Vidmantas Kalendra
- Faculty of Physics, Vilnius University Sauletekio 3 LT-10257 Vilnius Lithuania
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Chun-Hsien Chen
- Department of Chemistry and Centre for Emerging Materials and Advanced Devices, National Taiwan University Taipei 106319 Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center Hsinchu 300092 Taiwan
- Department of Chemical Engineering, National Tsing Hua University Hsinchu 300044 Taiwan
- College of Semiconductor Research, National Tsing Hua University Hsinchu 300044 Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University Hsinchu 300044 Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University Hsinchu 300044 Taiwan
| |
Collapse
|
10
|
Chang JW, Su KH, Pao CW, Tsai JJ, Su CJ, Chen JL, Lyu LM, Kuo CH, Su AC, Yang HC, Lai YH, Jeng US. Arrayed Pt Single Atoms via Phosphotungstic Acids Intercalated in Silicate Nanochannels for Efficient Hydrogen Evolution Reactions. ACS NANO 2024; 18:1611-1620. [PMID: 38166379 PMCID: PMC10795682 DOI: 10.1021/acsnano.3c09656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024]
Abstract
Single-atom catalysts, known for their high activity, have garnered significant interest. Currently, single-atom catalysts were prepared mainly on 2D substrates with random distribution. Here, we report a strategy for preparing arrayed single Pt (Pt1) atoms, which are templated through coordination with phosphotungstic acids (PTA) intercalated inside hexagonally packed silicate nanochannels for a high single Pt-atom loading of ca. 3.0 wt %. X-ray absorption spectroscopy, high-angle annular dark-field scanning transmission electron microscopy, and energy-dispersive X-ray spectroscopy, in conjunction with the density-functional theory calculation, collectively indicate that the Pt single atoms are stabilized via a four-oxygen coordination on the PTA within the nanochannels' inner walls. The critical reduction in the Pt-adsorption energy to nearly the cohesive energy of Pt clustering is attributed to the interaction between PTA and the silicate substrate. Consequently, the transition from single-atom dispersion to clustering of Pt atoms can be controlled by adjusting the number density of PTA intercalated within the silicate nanochannels, specifically when the number ratio of Pt atoms to PTA changes from 3.7 to 18. The 3D organized Pt1-PTA pairs, facilitated by the arrayed silicate nanochannels, demonstrate high and stable efficiency with a hydrogen production rate of ca. 300 mmol/h/gPt─approximately twice that of the best-reported Pt efficiency in polyoxometalate-based photocatalytic systems.
Collapse
Affiliation(s)
- Je-Wei Chang
- Department
of Chemical Engineering, National Tsing
Hua University, Hsinchu 300044, Taiwan
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Kuan-Hsuan Su
- Department
of Chemistry, Fu Jen Catholic University, New Taipei City 241037, Taiwan
| | - Chih-Wen Pao
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Jin-Jia Tsai
- Department
of Chemistry, Tunghai University, Taichung 407302, Taiwan
| | - Chun-Jen Su
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Jeng-Lung Chen
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Lian-Ming Lyu
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 300093, Taiwan
| | - Chun-Hong Kuo
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 300093, Taiwan
| | - An-Chung Su
- Department
of Chemical Engineering, National Tsing
Hua University, Hsinchu 300044, Taiwan
| | - Hsiao-Ching Yang
- Department
of Chemistry, Fu Jen Catholic University, New Taipei City 241037, Taiwan
| | - Ying-Huang Lai
- Department
of Chemistry, Tunghai University, Taichung 407302, Taiwan
| | - U-Ser Jeng
- Department
of Chemical Engineering, National Tsing
Hua University, Hsinchu 300044, Taiwan
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 300092, Taiwan
- College
of
Semiconductor Research, National Tsing Hua
University, Hsinchu 300044, Taiwan
| |
Collapse
|
11
|
Xue YJ, Lai ZY, Lu HC, Hong JC, Tsai CL, Huang CL, Huang KH, Lu CF, Lai YY, Hsu CS, Lin JM, Chang JW, Chien SY, Lee GH, Jeng US, Cheng YJ. Unraveling the Structure-Property-Performance Relationships of Fused-Ring Nonfullerene Acceptors: Toward a C-Shaped ortho-Benzodipyrrole-Based Acceptor for Highly Efficient Organic Photovoltaics. J Am Chem Soc 2024; 146:833-848. [PMID: 38113458 DOI: 10.1021/jacs.3c11062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The high-performance Y6-based nonfullerene acceptors (NFAs) feature a C-shaped A-DA'D-A-type molecular architecture with a central electron-deficient thiadiazole (Tz) A' unit. In this work, we designed and synthesized a new A-D-A-type NFA, termed CB16, having a C-shaped ortho-benzodipyrrole-based skeleton of Y6 but with the Tz unit eliminated. When processed with nonhalogenated xylene without using any additives, the binary PM6:CB16 devices display a remarkable power conversion efficiency (PCE) of 18.32% with a high open-circuit voltage (Voc) of 0.92 V, surpassing the performance of the corresponding Y6-based devices. In contrast, similarly synthesized SB16, featuring an S-shaped para-benzodipyrrole-based skeleton, yields a low PCE of 0.15% due to the strong side-chain aggregation of SB16. The C-shaped A-DNBND-A skeleton in CB16 and the Y6-series NFAs constitutes the essential structural foundation for achieving exceptional device performance. The central Tz moiety or other A' units can be employed to finely adjust intermolecular interactions. The single-crystal X-ray structure reveals that ortho-benzodipyrrole-embedded A-DNBND-A plays an important role in the formation of a 3D elliptical network packing for efficient charge transport. Solution structures of the PM6:NFAs detected by small- and wide-angle X-ray scattering (SWAXS) indicate that removing the Tz unit in the C-shaped skeleton could reduce the self-packing of CB16, thereby enhancing the complexing and networking with PM6 in the spin-coating solution and the subsequent device film. Elucidating the structure-property-performance relationships of A-DA'D-A-type NFAs in this work paves the way for the future development of structurally simplified A-D-A-type NFAs.
Collapse
Affiliation(s)
- Yung-Jing Xue
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Ze-Yu Lai
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Han-Cheng Lu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Jun-Cheng Hong
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Chia-Lin Tsai
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Ching-Li Huang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Kuo-Hsiu Huang
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Chia-Fang Lu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Yu-Ying Lai
- Institute of Polymer Science and Engineering,National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chain-Shu Hsu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Jhih-Min Lin
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300092, Taiwan
| | - Su-Ying Chien
- Instrumentation Center, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300092, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Road, Hsinchu 300044, Taiwan
- College of Semiconductor Research, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yen-Ju Cheng
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| |
Collapse
|
12
|
Hou MH, Wang YC, Yang CS, Liao KF, Chang JW, Shih O, Yeh YQ, Sriramoju MK, Weng TW, Jeng US, Hsu STD, Chen Y. Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING. Nat Commun 2023; 14:8519. [PMID: 38129386 PMCID: PMC10739871 DOI: 10.1038/s41467-023-44052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) signaling pathway plays a critical protective role against viral infections. Metazoan STING undergoes multilayers of regulation to ensure specific signal transduction. However, the mechanisms underlying the regulation of bacterial STING remain unclear. In this study, we determined the crystal structure of anti-parallel dimeric form of bacterial STING, which keeps itself in an inactive state by preventing cyclic dinucleotides access. Conformational transition between inactive and active states of bacterial STINGs provides an on-off switch for downstream signaling. Some bacterial STINGs living in extreme environment contain an insertion sequence, which we show codes for an additional long lid that covers the ligand-binding pocket. This lid helps regulate anti-phage activities. Furthermore, bacterial STING can bind cyclic di-AMP in a triangle-shaped conformation via a more compact ligand-binding pocket, forming spiral-shaped protofibrils and higher-order fibril filaments. Based on the differences between cyclic-dinucleotide recognition, oligomerization, and downstream activation of different bacterial STINGs, we proposed a model to explain structure-function evolution of bacterial STINGs.
Collapse
Grants
- National Science and Technology Council, Taiwan, 109-2311-B241-001 National Science and Technology Council, Taiwan, 111-2311-B-039-001-MY3
- National Science and Technology Council, Taiwan, 111-2811-M-001-125
- National Science and Technology Council, Taiwan, 110-2113-M-001-050-MY3 National Science and Technology Council, Taiwan, 110-2311-B-001-013-MY3 Academia Sinica intramural fund, an Academia Sinica Career Development Award, Academia Sinica, AS-CDA-109-L08 Infectious Disease Research Supporting Grant, AS-IDR-110-08.
Collapse
Affiliation(s)
- Mei-Hui Hou
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Yu-Chuan Wang
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Chia-Shin Yang
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | | | - Tzu-Wen Weng
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
- Department of Chemical Engineering & College of Semiconductor Research, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 402202, Taiwan.
| |
Collapse
|
13
|
Hsu TW, Yang CH, Su CJ, Huang YT, Yeh YQ, Liao KF, Lin TC, Shih O, Lee MT, Su AC, Jeng US. Revealing cholesterol effects on PEGylated HSPC liposomes using AF4-MALS and simultaneous small- and wide-angle X-ray scattering. J Appl Crystallogr 2023; 56:988-993. [PMID: 37555211 PMCID: PMC10405602 DOI: 10.1107/s1600576723005393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/16/2023] [Indexed: 08/10/2023] Open
Abstract
Liposome development is of great interest owing to increasing requirements for efficient drug carriers. The structural features and thermal stability of such liposomes are crucial in drug transport and delivery. Reported here are the results of the structural characterization of PEGylated liposomes via small- and wide-angle X-ray scattering and an asymmetric flow field-flow fractionation (AF4) system coupled with differential refractive-index detection, multi-angle light scattering (MALS) and dynamic light scattering. This integrated analysis of the exemplar PEGylated liposome formed from hydrogenated soy phosphatid-yl-choline (HSPC) with the addition of cholesterol reveals an average hydro-dynamic radius (R h) of 52 nm with 10% polydispersity, a comparable radius of gyration (R g) and a major liposome particle mass of 118 kDa. The local bilayer structure of the liposome is found to have asymmetric electronic density profiles in the inner and outer leaflets, sandwiched by two PEGylated outer layers ca 5 nm thick. Cholesterol was found to effectively intervene in lipid chain packing, resulting in the thickening of the liposome bilayer, an increase in the area per lipid and an increase in liposome size, especially in the fluid phase of the liposome. These cholesterol effects show signs of saturation at cholesterol concentrations above ca 1:5 cholesterol:lipid molar ratio.
Collapse
Affiliation(s)
- Ting-Wei Hsu
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Ching-Hsun Yang
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Yin-Tzu Huang
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Tien-Chang Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
| | - Ming-Tao Lee
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
- Department of Physics, National Central University, Zhongli 320317, Taiwan
| | - An-Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 300094, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
- College of Semiconductor Research, National Tsing Hua University, Hsinchu 300044, Taiwan
| |
Collapse
|
14
|
Tsai TY, Chen CY, Lin TW, Lin TC, Chiu FL, Shih O, Chang MY, Lin YC, Su AC, Chen CM, Jeng US, Kuo HC, Chang CF, Chen YR. Amyloid modifier SERF1a interacts with polyQ-expanded huntingtin-exon 1 via helical interactions and exacerbates polyQ-induced toxicity. Commun Biol 2023; 6:767. [PMID: 37479809 PMCID: PMC10361993 DOI: 10.1038/s42003-023-05142-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Abnormal polyglutamine (polyQ) expansion and fibrillization occur in Huntington's disease (HD). Amyloid modifier SERF enhances amyloid formation, but the underlying mechanism is not revealed. Here, the fibrillization and toxicity effect of SERF1a on Htt-exon1 are examined. SERF1a enhances the fibrillization of and interacts with mutant thioredoxin (Trx)-fused Httex1. NMR studies with Htt peptides show that TrxHttex1-39Q interacts with the helical regions in SERF1a and SERF1a preferentially interacts with the N-terminal 17 residues of Htt. Time-course analysis shows that SERF1a induces mutant TrxHttex1 to a single conformation enriched of β-sheet. Co-expression of SERF1a and Httex1-polyQ in neuroblastoma and lentiviral infection of SERF1a in HD-induced polypotent stem cell (iPSC)-derived neurons demonstrates the detrimental effect of SERF1a in HD. Higher level of SERF1a transcript or protein is detected in HD iPSC, transgenic mice, and HD plasma. Overall, this study provides molecular mechanism for SERF1a and mutant Httex1 to facilitate therapeutic development for HD.
Collapse
Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2. Nankang, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chun-Yu Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Wei Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Chang Lin
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
| | - Ming-Yun Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - An-Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Linkou Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan.
| |
Collapse
|
15
|
Kuschnerus IC, Wen H, Ruan J, Zeng X, Su CJ, Jeng US, Opletal G, Barnard AS, Liu M, Nishikawa M, Chang SLY. Complex Dispersion of Detonation Nanodiamond Revealed by Machine Learning Assisted Cryo-TEM and Coarse-Grained Molecular Dynamics Simulations. ACS NANOSCIENCE AU 2023; 3:211-221. [PMID: 37360847 PMCID: PMC10288606 DOI: 10.1021/acsnanoscienceau.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 06/28/2023]
Abstract
Understanding the polydispersity of nanoparticles is crucial for establishing the efficacy and safety of their role as drug delivery carriers in biomedical applications. Detonation nanodiamonds (DNDs), 3-5 nm diamond nanoparticles synthesized through detonation process, have attracted great interest for drug delivery due to their colloidal stability in water and their biocompatibility. More recent studies have challenged the consensus that DNDs are monodispersed after their fabrication, with their aggregate formation poorly understood. Here, we present a novel characterization method of combining machine learning with direct cryo-transmission electron microscopy imaging to characterize the unique colloidal behavior of DNDs. Together with small-angle X-ray scattering and mesoscale simulations we show and explain the clear differences in the aggregation behavior between positively and negatively charged DNDs. Our new method can be applied to other complex particle systems, which builds essential knowledge for the safe implementation of nanoparticles in drug delivery.
Collapse
Affiliation(s)
- Inga C. Kuschnerus
- School
of Materials Science and Engineering, University
of New South Wales, Sydney, New South Wales 2052, Australia
- Electron
Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Haotian Wen
- School
of Materials Science and Engineering, University
of New South Wales, Sydney, New South Wales 2052, Australia
| | - Juanfang Ruan
- Electron
Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Xinrui Zeng
- School
of Materials Science and Engineering, University
of New South Wales, Sydney, New South Wales 2052, Australia
| | - Chun-Jen Su
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30076, Taiwan
| | - U-Ser Jeng
- National
Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu 30076, Taiwan
- Department
of Chemical Engineering, National Tsing
Hua University, Hsinchu 30013, Taiwan
| | | | - Amanda S. Barnard
- School
of
Computing, Australian National University, Acton, Australian Capital
Territory 2601, Australia
| | - Ming Liu
- Daicel
Corporation, Osaka 530-0011, Japan
| | | | - Shery L. Y. Chang
- School
of Materials Science and Engineering, University
of New South Wales, Sydney, New South Wales 2052, Australia
- Electron
Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
16
|
Nguyen HTV, Chen X, Parada C, Luo AC, Shih O, Jeng US, Huang CY, Shih YL, Ma C. Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome. Nat Commun 2023; 14:1903. [PMID: 37019934 PMCID: PMC10076392 DOI: 10.1038/s41467-023-37543-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
The synthesis of the cell-wall peptidoglycan during bacterial cell division is mediated by a multiprotein machine, called the divisome. The essential membrane protein complex of FtsB, FtsL and FtsQ (FtsBLQ) is at the heart of the divisome assembly cascade in Escherichia coli. This complex regulates the transglycosylation and transpeptidation activities of the FtsW-FtsI complex and PBP1b via coordination with FtsN, the trigger for the onset of constriction. Yet the underlying mechanism of FtsBLQ-mediated regulation is largely unknown. Here, we report the full-length structure of the heterotrimeric FtsBLQ complex, which reveals a V-shaped architecture in a tilted orientation. Such a conformation could be strengthened by the transmembrane and the coiled-coil domains of the FtsBL heterodimer, as well as an extended β-sheet of the C-terminal interaction site involving all three proteins. This trimeric structure may also facilitate interactions with other divisome proteins in an allosteric manner. These results lead us to propose a structure-based model that delineates the mechanism of the regulation of peptidoglycan synthases by the FtsBLQ complex.
Collapse
Affiliation(s)
- Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Claudia Parada
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - An-Chi Luo
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30044, Taiwan
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Yu-Ling Shih
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
| |
Collapse
|
17
|
Cancer-targeted fucoidan‑iron oxide nanoparticles for synergistic chemotherapy/chemodynamic theranostics through amplification of P-selectin and oxidative stress. Int J Biol Macromol 2023; 235:123821. [PMID: 36870633 DOI: 10.1016/j.ijbiomac.2023.123821] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 03/06/2023]
Abstract
A combination of chemotherapy and chemodynamic therapy (CDT) is being developed to improve the theranostic efficacy and biological safety of current therapies. However, most CDT agents are restricted due to complex issues such as multiple components, low colloidal stability, carrier-associated toxicity, insufficient reactive oxygen species generation, and poor targeting efficacy. To overcome these problems, a novel nanoplatform composed of fucoidan (Fu) and iron oxide (IO) nanoparticles (NPs) was developed to achieve chemotherapy combined with CDT synergistic treatment with a facile self-assembling manner, and the NPs were made up of Fu and IO, in which the Fu was not only used as a potential chemotherapeutic but was also designed to stabilize the IO and target P-selectin-overexpressing lung cancer cells, thereby producing oxidative stress and thus synergizing the CDT efficacy. The Fu-IO NPs exhibited a suitable diameter below 300 nm, which favored their cellular uptake by cancer cells. Microscopic and MRI data confirmed the lung cancer cellular uptake of the NPs due to active Fu targeting. Moreover, Fu-IO NPs induced efficient apoptosis of lung cancer cells, and thus offer significant anti-cancer functions by potential chemotherapeutic-CDT.
Collapse
|