1
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Lin TC, Shih O, Tsai TY, Yeh YQ, Liao KF, Mansel BW, Shiu YJ, Chang CF, Su AC, Chen YR, Jeng US. Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation. IUCRJ 2024; 11:849-858. [PMID: 39120045 PMCID: PMC11364024 DOI: 10.1107/s2052252524006341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
The aberrant fibrillization of huntingtin exon 1 (Httex1) characterized by an expanded polyglutamine (polyQ) tract is a defining feature of Huntington's disease, a neurodegenerative disorder. Recent investigations underscore the involvement of a small EDRK-rich factor 1a (SERF1a) in promoting Httex1 fibrillization through interactions with its N terminus. By establishing an integrated approach with size-exclusion-column-based small- and wide-angle X-ray scattering (SEC-SWAXS), NMR, and molecular simulations using Rosetta, the analysis here reveals a tight binding of two NT17 fragments of Httex1 (comprising the initial 17 amino acids at the N terminus) to the N-terminal region of SERF1a. In contrast, examination of the complex structure of SERF1a with a coiled NT17-polyQ peptide (33 amino acids in total) indicates sparse contacts of the NT17 and polyQ segments with the N-terminal side of SERF1a. Furthermore, the integrated SEC-SWAXS and molecular-simulation analysis suggests that the coiled NT17 segment can transform into a helical conformation when associated with a polyQ segment exhibiting high helical content. Intriguingly, NT17-polyQ peptides with enhanced secondary structures display diminished interactions with SERF1a. This insight into the conformation-dependent binding of NT17 provides clues to a catalytic association mechanism underlying SERF1a's facilitation of Httext1 fibrillization.
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Affiliation(s)
- Tien Chang Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu 300092, Taiwan
| | - Tien Ying Tsai
- Genomics Research Center, Academia Sinica, Taipei 115024, Taiwan
| | - Yi Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu 300092, Taiwan
| | - Kuei Fen Liao
- National Synchrotron Radiation Research Center, Hsinchu 300092, Taiwan
| | - Bradley W Mansel
- National Synchrotron Radiation Research Center, Hsinchu 300092, Taiwan
| | - Ying Jen Shiu
- National Synchrotron Radiation Research Center, Hsinchu 300092, Taiwan
| | - Chi Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115024, Taiwan
| | - An Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yun Ru Chen
- Genomics Research Center, Academia Sinica, Taipei 115024, Taiwan
| | - U Ser Jeng
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300044, Taiwan
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2
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Skrinda-Melne M, Locs J, Grava A, Dubnika A. Calcium phosphates enhanced with liposomes - the future of bone regeneration and drug delivery. J Liposome Res 2024; 34:507-522. [PMID: 37988074 DOI: 10.1080/08982104.2023.2285973] [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: 06/03/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Effective healing and regeneration of various bone defects is still a major challenge and concern in modern medicine. Calcium phosphates have emerged as extensively studied bone substitute materials due to their structural and chemical resemblance to the mineral phase of bone, along with their versatile properties. Calcium phosphates present promising biological characteristics that make them suitable for bone substitution, but a critical limitation lies in their low osteoinductivity. To supplement these materials with properties that promote bone regeneration, prevent infections, and cure bone diseases locally, calcium phosphates can be biologically and therapeutically modified. A promising approach involves combining calcium phosphates with drug-containing liposomes, renowned for their high biocompatibility and ability to provide controlled and sustained drug delivery. Surprisingly, there is a lack of research focused on liposome-calcium phosphate composites, where liposomes are dispersed within a calcium phosphate matrix. This raises the question of why such studies are limited. In order to provide a comprehensive overview of existing liposome and calcium phosphate composites as bioactive substance delivery systems, the authors review the literature exploring the interactions between calcium phosphates and liposomes. Additionally, it seeks to identify potential interactions between calcium ions and liposomes, which may impact the feasibility of developing liposome-containing calcium phosphate composite materials. Liposome capacity to protect bioactive compounds and facilitate localized treatment can be particularly valuable in scenarios involving bone regeneration, infection prevention, and the management of bone diseases. This review explores the implications of liposomes and calcium phosphate material containing liposomes on drug delivery, bioavailability, and stability, offering insights into their advantages.
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Affiliation(s)
- Marite Skrinda-Melne
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Janis Locs
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Andra Grava
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Arita Dubnika
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
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3
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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.
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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.
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4
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Wang B, Tieleman DP. The structure, self-assembly and dynamics of lipid nanodiscs revealed by computational approaches. Biophys Chem 2024; 309:107231. [PMID: 38569455 DOI: 10.1016/j.bpc.2024.107231] [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: 01/24/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
Nanodisc technology is increasingly being used in structural, biochemical and biophysical studies of membrane proteins. The computational approaches have revealed many important features of nanodisc assembly, structures and dynamics. Therefore, we reviewed the application of computational approaches, especially molecular modeling and molecular dyncamics (MD) simulations, to characterize nanodiscs, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in nanodiscs. More amazing computational studies about nanodiscs are looked forward to in the future.
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Affiliation(s)
- Beibei Wang
- Centre for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China.
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary T2N 1N4, Canada.
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5
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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.
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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
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6
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Dong Y, Fu L, Song J, Zhang S, Li X, Fang W, Cui Q, Gao L. Thermodynamic Driving Forces for Divalent Cations Binding to Zwitterionic Phospholipid Membranes. J Phys Chem Lett 2022; 13:11237-11244. [PMID: 36448843 DOI: 10.1021/acs.jpclett.2c03019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We calculated the free energies for calcium, magnesium, and zinc ions binding to a zwitterionic phospholipid bilayer by using molecular dynamics simulations and the enhanced umbrella sampling technique. By decomposing the free energy into entropic and enthalpic contributions, we found that Ca2+ has the highest binding affinity and that the overall process is endothermic combined with a secondary exothermic process at higher ion concentrations. The relatively low dehydration free energy of Ca2+ allows it to release coordinated water upon binding to the membrane. The dehydrated Ca2+ further coordinates with lipids, resulting in a weaker influence on the water orientation and increased entropy. However, when sufficient Ca2+ ions are adsorbed, the concentrated cation layer induces a positive electrostatic field, which enhances the energy barrier for further ion binding and orients the adjacent water, resulting in decreased entropy. In contrast, binding of Mg2+ and Zn2+ is exothermic and less favored because they remain fully hydrated when interacting with lipids.
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Affiliation(s)
- Yi Dong
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts02215, United States
| | - Junjie Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
| | - Shan Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
| | - Xiangyuan Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts02215, United States
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, 19 Xin-Jie-Kou-Wai Street, Beijing100875, China
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7
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Deplazes E, Tafalla BD, Murphy C, White J, Cranfield CG, Garcia A. Calcium Ion Binding at the Lipid-Water Interface Alters the Ion Permeability of Phospholipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:14026-14033. [PMID: 34784471 DOI: 10.1021/acs.langmuir.1c02016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Calcium ions (Ca2+) play a fundamental role in membrane-associated physiological processes. Ca2+ can also significantly modulate the physicochemical properties of phospholipid bilayers, but whether this occurs at physiologically relevant concentrations is difficult to determine because of the uncertainty in the reported affinity of Ca2+ for phospholipid bilayers. In this article, we determine the apparent affinity of Ca2+ for zwitterionic phospholipid bilayers using tethered bilayer lipid membranes (tBLMs) used in conjunction with swept-frequency electrical impedance spectroscopy (EIS). We report that Ca2+ binds to phospholipid bilayers at physiologically relevant concentrations and modulates membrane permeability. We present direct experimental evidence that this effect is governed by specific interactions with select lipid headgroup moieties, which is supported by data from molecular dynamics (MD) simulations. This is the first reported use of tBLM/EIS to estimate cation-membrane affinity. Combined with MD simulations, this technique provides a novel methodology to elucidate the molecular details of cation-membrane interactions at the water-phospholipid interface.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Christopher Murphy
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jacqueline White
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
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8
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Chen EHL, Lin KM, Sang JC, Ho MR, Lee CH, Shih O, Su CJ, Yeh YQ, Jeng US, Chen RPY. Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein. IUBMB Life 2021; 74:780-793. [PMID: 34288372 DOI: 10.1002/iub.2528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/06/2022]
Abstract
Prion protein is composed of a structure-unsolved N-terminal domain and a globular C-terminal domain. Under limited trypsin digestion, mouse recombinant prion protein can be cleaved into two parts at residue Lys105. Here, we termed these two fragments as the N-domain (sequence 23-105) and the C-domain (sequence 106-230). In this study, the structural properties of the N-domain, the C-domain, and the full-length protein were explored using small-angle X-ray scattering, analytical ultracentrifugation, circular dichroism spectroscopy, and the 8-anilino-1-naphthalenesulfonic acid binding assay. The conformation and size of the prion protein were found to change sensitively under the solvent conditions. The positive residues in the sequence 23-99 of the N-domain were found to be responsible for the enhanced flexibility with the salt concentration reduced below 5 mM. The C-domain containing a hydrophobic patch tends to unfold and aggregate during a salt-induced structural collapse. The N-domain collapsed together with the C-domain at pH 5.2, whereas it collapsed independently at pH 4.2. The positively charged cluster (sequence 100-105) in the N-domain contributed to protecting the exposed hydrophobic surface of the C-domain.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-Ming Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jason C Sang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chih-Hsuan Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan.,Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
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9
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Lin S, Su K, Yeh Y, Jeng U, Wu C, Yang H. Molecular dynamics simulation combined with small‐angle X‐ray/neutron scattering defining
solution‐state
protein structures. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shang‐Wei Lin
- Department of Chemistry Fu Jen Catholic University New Taipei City Taiwan
| | - Kuan‐Hsuan Su
- Department of Chemistry Fu Jen Catholic University New Taipei City Taiwan
| | - Yi‐Qi Yeh
- National Synchrotron Radiation Research Center Hsinchu Science Park Hsinchu Taiwan
| | - U‐Ser Jeng
- National Synchrotron Radiation Research Center Hsinchu Science Park Hsinchu Taiwan
- Department of Chemical Engineering National Tsing Hua University Hsinchu Taiwan
| | - Chun‐Ming Wu
- National Synchrotron Radiation Research Center Hsinchu Science Park Hsinchu Taiwan
| | - Hsiao‐Ching Yang
- Department of Chemistry Fu Jen Catholic University New Taipei City Taiwan
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10
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Akutsu H. Structure and dynamics of phospholipids in membranes elucidated by combined use of NMR and vibrational spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183352. [DOI: 10.1016/j.bbamem.2020.183352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022]
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11
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Sahoo A, Matysiak S. Microscopic Picture of Calcium-Assisted Lipid Demixing and Membrane Remodeling Using Multiscale Simulations. J Phys Chem B 2020; 124:7327-7335. [PMID: 32786720 DOI: 10.1021/acs.jpcb.0c03067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The specificity of anionic phospholipids-calcium ion interaction and lipid demixing has been established as a key regulatory mechanism in several cellular signaling processes. The mechanism and implications of this calcium-assisted demixing have not been elucidated from a microscopic point of view. Here, we present an overview of atomic interactions between calcium and phospholipids that can drive nonideal mixing of lipid molecules in a model lipid bilayer composed of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) lipids with computer simulations at multiple resolutions. Lipid nanodomain formation and growth were driven by calcium-enabled lipid bridging of the charged phosphatidylserine (PS) headgroups, which were favored against inter-POPS dipole interactions. Consistent with several experimental studies of calcium-associated membrane sculpting, our analyses also suggest modifications in local membrane curvature and cross-leaflet couplings as a response to such induced lateral heterogeneity. In addition, reverse mapping to a complementary atomistic description revealed structural insights in the presence of anionic nanodomains, at timescales not accessed by previous computational studies. This work bridges information across multiple scales to reveal a mechanistic picture of calcium ion's impact on membrane biophysics.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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12
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Liao CC, Shankar S, Pi WC, Chang CC, Ahmed GR, Chen WY, Hsia KC. Karyopherin Kap114p-mediated trans-repression controls ribosomal gene expression under saline stress. EMBO Rep 2020; 21:e48324. [PMID: 32484313 DOI: 10.15252/embr.201948324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Nuclear accessibility of transcription factors controls gene expression, co-regulated by Ran-dependent nuclear localization and a competitive regulatory network. Here, we reveal that nuclear import factor-facilitated transcriptional repression attenuates ribosome biogenesis under chronic salt stress. Kap114p, one of the karyopherin-βs (Kap-βs) that mediates nuclear import of yeast TATA-binding protein (yTBP), exhibits a yTBP-binding affinity four orders of magnitude greater than its counterparts and suppresses binding of yTBP with DNA. Our crystal structure of Kap114p reveals an extensively negatively charged concave surface, accounting for high-affinity basic-protein binding. KAP114 knockout in yeast leads to a high-salt growth defect, with transcriptomic analyses revealing that Kap114p modulates expression of genes associated with ribosomal biogenesis by suppressing yTBP binding to target promoters, a trans-repression mechanism we attribute to reduced nuclear Ran levels under salinity stress. Our findings reveal that Ran integrates the nuclear transport pathway and transcription regulatory network, allowing yeast to respond to environmental stresses.
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Affiliation(s)
- Chung-Chi Liao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sahana Shankar
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chia Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Chiang Hsia
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
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13
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Su CJ, Lee MT, Liao KF, Shih O, Jeng US. Interplay of entropy and enthalpy in peptide binding to zwitterionic phospholipid membranes as revealed from membrane thinning. Phys Chem Chem Phys 2018; 20:26830-26836. [DOI: 10.1039/c8cp02861c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Melittin binding affinity enhances linearly with the membrane thermal thinning rate of the three phosphocholine-based ULVs of diCn:1PC.
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Affiliation(s)
- Chun-Jen Su
- National Synchrotron Radiation Research Center
- Hsinchu Science Park
- Hsinchu 30076
- Taiwan
| | - Ming-Tao Lee
- National Synchrotron Radiation Research Center
- Hsinchu Science Park
- Hsinchu 30076
- Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center
- Hsinchu Science Park
- Hsinchu 30076
- Taiwan
| | - Orion Shih
- 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
| |
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