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Kohl PA, Song C, Fletcher BJ, Best RL, Tchounwou C, Garcia Arceo X, Chung PJ, Miller HP, Wilson L, Choi MC, Li Y, Feinstein SC, Safinya CR. Complexes of tubulin oligomers and tau form a viscoelastic intervening network cross-bridging microtubules into bundles. Nat Commun 2024; 15:2362. [PMID: 38491006 PMCID: PMC10943092 DOI: 10.1038/s41467-024-46438-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: 02/09/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
The axon-initial-segment (AIS) of mature neurons contains microtubule (MT) fascicles (linear bundles) implicated as retrograde diffusion barriers in the retention of MT-associated protein (MAP) tau inside axons. Tau dysfunction and leakage outside of the axon is associated with neurodegeneration. We report on the structure of steady-state MT bundles in varying concentrations of Mg2+ or Ca2+ divalent cations in mixtures containing αβ-tubulin, full-length tau, and GTP at 37 °C in a physiological buffer. A concentration-time kinetic phase diagram generated by synchrotron SAXS reveals a wide-spacing MT bundle phase (Bws), a transient intermediate MT bundle phase (Bint), and a tubulin ring phase. SAXS with TEM of plastic-embedded samples provides evidence of a viscoelastic intervening network (IN) of complexes of tubulin oligomers and tau stabilizing MT bundles. In this model, αβ-tubulin oligomers in the IN are crosslinked by tau's MT binding repeats, which also link αβ-tubulin oligomers to αβ-tubulin within the MT lattice. The model challenges whether the cross-bridging of MTs is attributed entirely to MAPs. Tubulin-tau complexes in the IN or bound to isolated MTs are potential sites for enzymatic modification of tau, promoting nucleation and growth of tau fibrils in tauopathies.
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Affiliation(s)
- Phillip A Kohl
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Chaeyeon Song
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Amorepacific R&I Center, Yongin, 17074, Republic of Korea
| | - Bretton J Fletcher
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Rebecca L Best
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | - Christine Tchounwou
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Ximena Garcia Arceo
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, 93106, USA
| | - Peter J Chung
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Herbert P Miller
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Leslie Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon, 34141, Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
| | - Stuart C Feinstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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2
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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [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: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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3
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Zhang YF, Huang J, Zhang WX, Liu YH, Wang X, Song J, Jin CY, Zhang SY. Tubulin degradation: Principles, agents, and applications. Bioorg Chem 2023; 139:106684. [PMID: 37356337 DOI: 10.1016/j.bioorg.2023.106684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
The microtubule system plays an important role in the mitosis and growth of eukaryotic cells, and it is considered as an appealing and highly successful molecular target for cancer treatment. In fact, microtubule targeting agents, such as paclitaxel and vinblastine, have been approved by FDA for tumor therapy, which have achieved significant therapeutic effects and sales performance. At present, microtubule targeting agents mainly include microtubule-destabilizing agents, microtubule-stabilizing agents, and a few tubulin degradation agents. Although there are few reports about tubulin degradation agents at present, tubulin degradation agents show great potential in overcoming multidrug resistance and reducing neurotoxicity. In addition, some natural drugs could specifically degrade tubulin in tumor cells, but have no effect in normal cells, thus showing a good biosafety profile. Therefore, tubulin degradation agents might exhibit a better application. Currently, some small molecules have been designed to promote tubulin degradation with potent antiproliferative activities, showing the potential for cancer treatment. In this work, we reviewed the reports on tubulin degradation, and focused on the degradation mechanism and important functional groups of chemically synthesized compounds, hoping to provide help for the degradation design of tubulin.
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Affiliation(s)
- Yi-Fan Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Jiao Huang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Xin Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Yun-He Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Xiao Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jian Song
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Cheng-Yun Jin
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China.
| | - Sai-Yang Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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Shemesh A, Ghareeb H, Dharan R, Levi-Kalisman Y, Metanis N, Ringel I, Raviv U. Effect of tubulin self-association on GTP hydrolysis and nucleotide exchange reactions. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140869. [PMID: 36400388 DOI: 10.1016/j.bbapap.2022.140869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and the equilibrium of nucleotide exchange. Both reactions are relevant for microtubule (MT) dynamics. We used HPLC to determine the concentrations of GDP and GTP and thereby the GTPase activity of SEC-eluted tubulin dimers in assembly buffer solution, free of glycerol and tubulin aggregates. When GTP hydrolysis was negligible, the nucleotide exchange mechanism was studied by determining the concentrations of tubulin-free and tubulin-bound GTP and GDP. We observed no GTP hydrolysis below the critical conditions for MT assembly (either below the critical tubulin concentration and/or at low temperature), despite the assembly of tubulin 1D curved oligomers and single-rings, showing that their assembly did not involve GTP hydrolysis. Under conditions enabling spontaneous slow MT assembly, a slow pseudo-first-order GTP hydrolysis kinetics was detected, limited by the rate of MT assembly. Cryo-TEM images showed that GTP-tubulin 1D oligomers were curved also at 36 °C. Nucleotide exchange depended on the total tubulin concentration and the molar ratio between tubulin-free GDP and GTP. We used a thermodynamic model of isodesmic tubulin self-association, terminated by the formation of tubulin single-rings to determine the molar fractions of dimers with exposed and buried nucleotide exchangeable sites (E-sites). Our analysis shows that the GDP to GTP exchange reaction equilibrium constant was an order-of-magnitude larger for tubulin dimers with exposed E-sites than for assembled dimers with buried E-sites. This conclusion may have implications on the dynamics at the tip of the MT plus end.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hiba Ghareeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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5
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Fibronectin type III domain-containing protein 5 promotes autophagy via the AMPK/mTOR signaling pathway in hepatocellular carcinoma cells, contributing to nab-paclitaxel chemoresistance. Med Oncol 2022; 40:53. [DOI: 10.1007/s12032-022-01907-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
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6
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Sericin nanoparticles: Future nanocarrier for target-specific delivery of chemotherapeutic drugs. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Shemesh A, Dharan N, Ginsburg A, Dharan R, Levi-Kalisman Y, Ringel I, Raviv U. Mechanism of the Initial Tubulin Nucleation Phase. J Phys Chem Lett 2022; 13:9725-9735. [PMID: 36222421 DOI: 10.1021/acs.jpclett.2c02619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Tubulin nucleation is a highly frequent event in microtubule (MT) dynamics but is poorly understood. In this work, we characterized the structural changes during the initial nucleation phase of dynamic tubulin. Using size-exclusion chromatography-eluted tubulin dimers in an assembly buffer solution free of glycerol and tubulin aggregates enabled us to start from a well-defined initial thermodynamic ensemble of isolated dynamic tubulin dimers and short oligomers. Following a temperature increase, time-resolved X-ray scattering and cryo-transmission electron microscopy during the initial nucleation phase revealed an isodesmic assembly mechanism of one-dimensional (1D) tubulin oligomers (where dimers were added and/or removed one at a time), leading to sufficiently stable two-dimensional (2D) dynamic nanostructures, required for MT assembly. A substantial amount of tubulin octamers accumulated before two-dimensional lattices appeared. Under subcritical assembly conditions, we observed a slower isodesmic assembly mechanism, but the concentration of 1D oligomers was insufficient to form the multistranded 2D nucleus required for MT formation.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nadiv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yael Levi-Kalisman
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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8
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An Overview on Taxol Production Technology and Its Applications as Anticancer Agent. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0063-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Wang B, Chen Z, Liu W, Tan B. Prospects of circular RNAs: the regulators of drug resistance and metastasis in gastric cancer. Am J Transl Res 2022; 14:5760-5772. [PMID: 36105039 PMCID: PMC9452336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Gastric cancer (GC) is one of the most common malignant tumors. Although there are multiple therapeutic methods, the 5-year survival rate for GC remains low primarily due to metastasis and resistance to chemotherapy. GC treatments, which include chemotherapy drugs, targeted drugs, and immunologic drugs, improve the prognosis of advanced GC patients. Nevertheless, resistance to these drugs may result in treatment failure. Tumor metastasis also plays a key role in tumor progression and limits the clinical efficacy of treatments. Recently, it has been reported that circular RNAs (circRNAs), non-coding RNAs, regulate GC drug resistance and metastasis to improve prognosis. In this review, we summarized systematically the underlying mechanisms of circRNA regulation of gastric neoplasm drug resistance and tumor metastasis. Thus we shed light on the potential of circRNAs to function as potential GC biomarkers and therapeutics.
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Affiliation(s)
- Bingyu Wang
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University Shijiazhuang 050017, Hebei, China
| | - Zihao Chen
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University Shijiazhuang 050017, Hebei, China
| | - Wenbo Liu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University Shijiazhuang 050017, Hebei, China
| | - Bibo Tan
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University Shijiazhuang 050017, Hebei, China
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Liu Y, Ao X, Wang Y, Li X, Wang J. Long Non-Coding RNA in Gastric Cancer: Mechanisms and Clinical Implications for Drug Resistance. Front Oncol 2022; 12:841411. [PMID: 35155266 PMCID: PMC8831387 DOI: 10.3389/fonc.2022.841411] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide, with high recurrence and mortality rate. Chemotherapy, including 5-fluorouracil (5-FU), adriamycin (ADR), vincristine (VCR), paclitaxel (PTX), and platinum drugs, remains one of the fundamental methods of GC treatment and has efficiently improved patients’ prognosis. However, most patients eventually develop resistance to chemotherapeutic agents, leading to the failure of clinical treatment and patients’ death. Recent studies suggest that long non-coding RNAs (lncRNAs) are involved in the drug resistance of GC by modulating the expression of drug resistance-related genes via sponging microRNAs (miRNAs). Moreover, lncRNAs also play crucial roles in GC drug resistance via a variety of mechanisms, such as the regulation of the oncogenic signaling pathways, inhibition of apoptosis, induction of autophagy, modulation of cancer stem cells (CSCs), and promotion of the epithelial-to-mesenchymal transition (EMT) process. Some of lncRNAs exhibit great potential as diagnostic and prognostic biomarkers, as well as therapeutic targets for GC patients. Therefore, understanding the role of lncRNAs and their mechanisms in GC drug resistance may provide us with novel insights for developing strategies for individual diagnosis and therapy. In this review, we summarize the recent findings on the mechanisms underlying GC drug resistance regulated by lncRNAs. We also discuss the potential clinical applications of lncRNAs as biomarkers and therapeutic targets in GC.
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Affiliation(s)
- Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
- *Correspondence: Ying Liu,
| | - Xiang Ao
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yu Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiaoge Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
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Misra SK, Pathak K. Naturally occurring heterocyclic anticancer compounds. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2021-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Naturally occurring heterocyclic scaffolds are key ingredients for the development of various therapeutics employed for biomedical applications. Heterocyclic pharmacophores are widely disseminated and have been befallen in almost all categories of drugs for the alleviation of myriad ailments including diabetes, neurodegenerative, psychiatric, microbial infections, disastrous cancers etc. Countless fused heterocyclic anticancerous templates are reported to display antimetabolite, antioxidant, antiproliferative, cytostatic etc. pharmacological actions via targeting different signaling pathways (cell cycle, PI-3kinase/Akt, p53, caspase extrinsic pathway etc.), overexpressive receptors (EGRF, HER2, EGF, VEGF etc.) and physiological enzymes (topoisomerase I and II, cyclin dependent kinase etc.). A compiled description on various natural sources (plants, microbes, marine) containing anticancer agents comprising heterocyclic ring specified with presence of nitrogen (vincristine, vinblastine, indole-3-carbinol, meridianins, piperine, lamellarins etc.), oxygen (paclitaxel, halichondrin B, quercetin, myricetin, kaempferol etc.) and sulphur atoms (brugine, fucoidan, carrageenan etc.) are displayed here along with their molecular level cytotoxic action and therapeutic applications.
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Affiliation(s)
- Shashi Kiran Misra
- University Institute of Pharmacy, Chhatrapati Shahu Ji Maharaj University , Kanpur , 208026 , India
| | - Kamla Pathak
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences , Saifai , Etawah , 206130 , Uttar Pradesh , India
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12
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Dharan R, Shemesh A, Millgram A, Zalk R, Frank GA, Levi-Kalisman Y, Ringel I, Raviv U. Hierarchical Assembly Pathways of Spermine-Induced Tubulin Conical-Spiral Architectures. ACS NANO 2021; 15:8836-8847. [PMID: 33900736 DOI: 10.1021/acsnano.1c01374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tubulin, an essential cytoskeletal protein, assembles into various morphologies by interacting with an array of cellular factors. One of these factors is the endogenous polyamine spermine, which may promote and stabilize tubulin assemblies. Nevertheless, the assembled structures and their formation pathways are poorly known. Here we show that spermine induced the in vitro assembly of tubulin into several hierarchical architectures based on a tubulin conical-spiral subunit. Using solution X-ray scattering and cryo-TEM, we found that with progressive increase of spermine concentration tubulin dimers assembled into conical-frustum-spirals of increasing length, containing up to three helical turns. The subunits with three helical turns were then assembled into tubules through base-to-top packing and formed antiparallel bundles of tubulin conical-spiral tubules in a distorted hexagonal symmetry. Further increase of the spermine concentration led to inverted tubulin tubules assembled in hexagonal bundles. Time-resolved experiments revealed that tubulin assemblies formed at higher spermine concentrations assembled from intermediates, similar to those formed at low spermine concentrations. These results are distinct from the classical transition between twisted ribbons, helical, and tubular assemblies, and provide insight into the versatile morphologies that tubulin can form. Furthermore, they may contribute to our understanding of the interactions that control the composition and construction of protein-based biomaterials.
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Affiliation(s)
- Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Karem, Jerusalem 9112102, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Abigail Millgram
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Ran Zalk
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Gabriel A Frank
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Yael Levi-Kalisman
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Karem, Jerusalem 9112102, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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13
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Lee J, Song C, Lee J, Miller HP, Cho H, Gim B, Li Y, Feinstein SC, Wilson L, Safinya CR, Choi MC. Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001240. [PMID: 32794304 DOI: 10.1002/smll.202001240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/14/2020] [Indexed: 06/11/2023]
Abstract
By virtue of their native structures, tubulin dimers are protein building blocks that are naturally preprogrammed to assemble into microtubules (MTs), which are cytoskeletal polymers. Here, polycation-directed (i.e., electrostatically tunable) assembly of tubulins is demonstrated by conformational changes to the tubulin protofilament in longitudinal and lateral directions, creating tubulin double helices and various tubular architectures. Synchrotron small-angle X-ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single- and double-layered double-helix tubulin tubules. The phase transitions from MTs to the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and to MT diameter (≈25 nm). This work suggests the feasibility of using polycations that have scissor- and glue-like properties to achieve "programmable breakdown" of protein nanotubes, tearing MTs into double-stranded tubulins and building up previously undiscovered nanostructures. Importantly, a new role of tubulins is defined as 2D shape-controllable building blocks for supramolecular architectures. These findings provide insight into the design of protein-based functional materials, for example, as metallization templates for nanoscale electronic devices, molecular screws, and drug delivery vehicles.
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Affiliation(s)
- Juncheol Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
| | - Chaeyeon Song
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
| | - Jimin Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
| | - Herbert P Miller
- Molecular, Cellular and Developmental Biology Department and Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Hasaeam Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
| | - Bopil Gim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA, 93106, USA
| | - Stuart C Feinstein
- Molecular, Cellular and Developmental Biology Department and Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Leslie Wilson
- Molecular, Cellular and Developmental Biology Department and Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Cyrus R Safinya
- Materials, Physics, Molecular, Cellular and Developmental Biology Departments, University of California, Santa Barbara, CA, 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, South Korea
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14
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Li L, Zhang Q, Lei X, Huang Y, Hu J. MAP4 as a New Candidate in Cardiovascular Disease. Front Physiol 2020; 11:1044. [PMID: 32982783 PMCID: PMC7479186 DOI: 10.3389/fphys.2020.01044] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 12/30/2022] Open
Abstract
Microtubule and mitochondrial dysfunction have been implicated in the pathogenesis of cardiovascular diseases (CVDs), including cardiac hypertrophy, fibrosis, heart failure, and hypoxic/ischemic related heart dysfunction. Microtubule dynamics instability leads to disrupted cell homeostasis and cell shape, decreased cell survival, and aberrant cell division and cell cycle, while mitochondrial dysfunction contributes to abnormal metabolism and calcium flux, increased cell death, oxidative stress, and inflammation, both of which causing cell and tissue dysfunction followed by CVDs. A cytosolic skeleton protein, microtubule-associated protein 4 (MAP4), belonging to the family of microtubule-associated proteins (MAPs), is widely expressed in non-neural cells and possesses an important role in microtubule dynamics. Increased MAP4 phosphorylation results in microtubule instability. In addition, MAP4 also expresses in mitochondria and reveals a crucial role in maintaining mitochondrial homeostasis. Phosphorylated MAP4 promotes mitochondrial apoptosis, followed by cardiac injury. The aim of the present review is to highlight the novel role of MAP4 as a potential candidate in multiple cardiovascular pathologies.
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Affiliation(s)
- Lingfei Li
- Department of Dermatology, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qiong Zhang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xia Lei
- Department of Dermatology, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuesheng Huang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jiongyu Hu
- State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University (Army Medical University), Chongqing, China.,Department of Endocrinology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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15
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Kim J, Lee J, Lee J, Keum H, Kim Y, Kim Y, Yu B, Lee SY, Tanaka J, Jon S, Choi MC. Tubulin-Based Nanotubes as Delivery Platform for Microtubule-Targeting Agents. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002902. [PMID: 32579276 DOI: 10.1002/adma.202002902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Tubulin-based nanotubes (TNTs) to deliver microtubule-targeting agents (MTAs) for clinical oncology are reported. Three MTAs, docetaxel (DTX), laulimalide (LMD), and monomethyl auristatin E (MMAE), which attach to different binding sites in a tubulin, are loaded onto TNTs and cause structural changes in them, including shape anisotropy and tubulin layering. This drug-driven carrier transformation leads to changes in the drug-loading efficiency and stability characteristics of the carrier. TNTs coloaded with DTX and LMD efficiently deliver dual drug cargoes to cellular tubulins by the endolysosomal pathway, and results in synergistic anticancer and antiangiogenic action of the drugs in vitro. In in vivo tests, TNTs loaded with a microtubule-destabilizing agent MMAE suppress the growth of tumors with much higher efficacy than free MMAE did. This work suggests a new concept of using a drug's target protein as a carrier. The findings demonstrate that the TNTs developed here can be used universally as a delivery platform for many MTAs.
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Affiliation(s)
- Jinjoo Kim
- Department of Biological Sciences, Center for Precision Bio-Nanomedicine, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Juncheol Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Jimin Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Hyeongseop Keum
- Department of Biological Sciences, Center for Precision Bio-Nanomedicine, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Yumi Kim
- Department of Biological Sciences, Center for Precision Bio-Nanomedicine, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Yujin Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Byeongjun Yu
- Department of Biological Sciences, Center for Precision Bio-Nanomedicine, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Sang Yeop Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Sangyong Jon
- Department of Biological Sciences, Center for Precision Bio-Nanomedicine, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Daejeon, 34141, Korea
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16
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Discovery of isopenicin A, a meroterpenoid as a novel inhibitor of tubulin polymerization. Biochem Biophys Res Commun 2020; 525:303-307. [DOI: 10.1016/j.bbrc.2020.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 01/09/2023]
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17
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Safinya CR, Chung PJ, Song C, Li Y, Miller HP, Choi MC, Raviv U, Ewert KK, Wilson L, Feinstein SC. Minireview - Microtubules and Tubulin Oligomers: Shape Transitions and Assembly by Intrinsically Disordered Protein Tau and Cationic Biomolecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:15970-15978. [PMID: 31539262 PMCID: PMC6988848 DOI: 10.1021/acs.langmuir.9b02208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this minireview, which is part of a special issue in honor of Jacob N. Israelachvili's remarkable research career on intermolecular forces and interfacial science, we present studies of structures, phase behavior, and forces in reaction mixtures of microtubules (MTs) and tubulin oligomers with either intrinsically disordered protein (IDP) Tau, cationic vesicles, or the polyamine spermine (4+). Bare MTs consist of 13 protofilaments (PFs), on average, where each PF is made of a linear stack of αβ-tubulin dimers (i.e., tubulin oligomers). We begin with a series of experiments which demonstrate the flexibility of PFs toward shape changes in response to local environmental cues. First, studies show that MT-associated protein (MAP) Tau controls the diameter of microtubules upon binding to the outer surface, implying a shape change in the cross-sectional area of PFs forming the MT perimeter. The diameter of a MT may also be controlled by the charge density of a lipid bilayer membrane that coats the outer surface. We further describe an experimental study where it is unexpectedly found that the biologically relevant polyamine spermine (+4e) is able to depolymerize taxol-stabilized microtubules with efficiency that increases with decreasing temperature. This MT destabilization drives a dynamical structural transition where inside-out curving of PFs, during the depolymerization peeling process, is followed by reassembly of ring-like curved PF building blocks into an array of helical inverted tubulin tubules. We finally turn to a very recent study on pressure-distance measurements in bundles of MTs employing the small-angle X-ray scattering (SAXS)-osmotic pressure technique, which complements the surface-forces-apparatus technique developed by Jacob N. Israelachvili. These latter studies are among the very few which are beginning to shed light on the precise nature of the interactions between MTs mediated by MAP Tau in 37 °C reaction mixtures containing GTP and lacking taxol.
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Affiliation(s)
- Cyrus R. Safinya
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Peter J. Chung
- James Franck Institute and Department of Chemistry, University of Chicago, Illinois 60637, USA
| | - Chaeyeon Song
- Amorepacific Corporation R&D Center, Yongin 17074, Republic of Korea
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Herbert P. Miller
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Kai K. Ewert
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Leslie Wilson
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
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18
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Amselem S. Remote Controlled Autonomous Microgravity Lab Platforms for Drug Research in Space. Pharm Res 2019; 36:183. [PMID: 31741058 DOI: 10.1007/s11095-019-2703-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022]
Abstract
Research conducted in microgravity conditions has the potential to yield new therapeutics, as advances can be achieved in the absence of phenomena such as sedimentation, hydrostatic pressure and thermally-induced convection. The outcomes of such studies can significantly contribute to many scientific and technological fields, including drug discovery. This article reviews the existing traditional microgravity platforms as well as emerging ideas for enabling microgravity research focusing on SpacePharma's innovative autonomous remote-controlled microgravity labs that can be launched to space aboard nanosatellites to perform drug research in orbit. The scientific literature is reviewed and examples of life science fields that have benefited from studies in microgravity conditions are given. These include the use of microgravity environment for chemical applications (protein crystallization, drug polymorphism, self-assembly of biomolecules), pharmaceutical studies (microencapsulation, drug delivery systems, behavior and stability of colloidal formulations, antibiotic drug resistance), and biological research, including accelerated models for aging, investigation of bacterial virulence , tissue engineering using organ-on-chips in space, enhanced stem cells proliferation and differentiation.
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Affiliation(s)
- Shimon Amselem
- SpacePharma R&D Israel LTD, 1st Aba Even Av, 4672519, Herzliya Pituach, Israel. .,SpacePharma SA, Rue l'Armeratte 3, 2950, Courgenay, Switzerland.
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19
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Niu L, Yang J, Yan W, Yu Y, Zheng Y, Ye H, Chen Q, Chen L. Reversible binding of the anticancer drug KXO1 (tirbanibulin) to the colchicine-binding site of β-tubulin explains KXO1's low clinical toxicity. J Biol Chem 2019; 294:18099-18108. [PMID: 31628188 DOI: 10.1074/jbc.ra119.010732] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
KXO1 (tirbanibulin or KX2-391) is as a non-ATP-competitive inhibitor of SRC proto-oncogene nonreceptor tyrosine kinase (SRC) and is being clinically investigated for the management of various cancers and actinic keratosis. Recently, KXO1 has also been shown to strongly inhibit tubulin. Interestingly, unlike conventional tubulin-targeting drugs, KXO1 has exhibited low toxicity in preclinical and clinical studies, but the reason for this remains elusive, as are the KXO1-binding site and other details of the interaction of KXO1 with tubulin. Here, cell-based experiments revealed that KXO1 induces tubulin depolymerization and G2/M phase cell cycle arrest at low nanomolar concentrations, similar to colchicine, used as a positive control. Results from biochemical experiments, including an N,N-ethylenebis(iodoacetamide) competition assay, disclosed that KXO1 binds to the colchicine-binding site on β-tubulin, further confirmed by the crystal structure of the tubulin-KXO1 complex at 2.5-Å resolution. A high-quality electron density map of the crystallographic data enabled us to unambiguously determine the position and orientation of KXO1 in the colchicine-binding site, revealing the detailed interactions between KXO1 and tubulin. We also found that KXO1 binds reversibly to purified tubulin, induces a totally reversible cellular effect (G2/M cell cycle arrest), and possesses no cellular toxicity 5 days after drug washout, explaining KXO1's low toxicity. In summary, we show that KXO1 binds to the colchicine-binding site of tubulin and resolved the crystal structure of the tubulin-KXO1 complex. Importantly, KXO1's reversible binding to tubulin explains its clinically low toxicity, an insight that could guide further clinical applications of KXO1.
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Affiliation(s)
- Lu Niu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Jianhong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Wei Yan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Yamei Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Yunhua Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Haoyu Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China
| | - Qiang Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China; Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, People's Republic of China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China.
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20
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Yang J, Yan W, Li Y, Niu L, Ye H, Chen L. The Natural Compound Withaferin A Covalently Binds to Cys239 of β-Tubulin to Promote Tubulin Degradation. Mol Pharmacol 2019; 96:711-719. [PMID: 31585985 DOI: 10.1124/mol.119.117812] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/28/2019] [Indexed: 02/05/2023] Open
Abstract
Withaferin A (WIT) is a natural product possessing a wide range of pharmacologic activities. Previous studies have reported covalent binding of WIT to tubulin and down-of tubulin protein levels although the underlying mechanisms remain to be established. In the current investigation, we showed that WIT induces down-regulation of tubulin in a post-transcriptional manner, suggestive of direct and potent activity in tubulin degradation. The N,N'-ethylene bis(iodoacetamide) assay and competitive binding experiments with four colchicine site-targeted tubulin inhibitors further revealed that WIT interacts with the colchicine site of tubulin to promote degradation. WIT irreversibly inhibited tubulin polymerization, and mass spectrometry results disclosed binding to cysteine at position 239 (Cys239) and Cys303 sites of β-tubulin. Interestingly, WIT promoted degradation of the β-tubulin isoforms containing Cys239 [β2, β4, and β5(β)] but had no effect on those containing Ser239 (β3 and β6). Moreover, a C239S but not C303S mutation in β-tubulin completely abolished the degradation effect of WIT, suggesting that the Cys239-WIT covalent bond accounts for this activity. Our collective results clearly demonstrate that covalent interactions between WIT and Cys239 of β-tubulin promote tubulin degradation, supporting its potential utility as a therapeutic compound. SIGNIFICANCE STATEMENT: Withaferin A, a natural product possessing a wide range of pharmacologic activities, covalently binds to Cys239 of β-tubulin near the colchicine site, and the WIT-Cys239 covalent bond accounts for WIT-induced tubulin degradation, fully clarifying the underlying mechanisms and supporting its potential utility a therapeutic compound.
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Affiliation(s)
- Jianhong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
| | - Wei Yan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
| | - Yong Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
| | - Lu Niu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
| | - Haoyu Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu, People's Republic of China
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21
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Xu M, Zeng R, Xiang J, Yan Q. Shaping Protein Amphiphilic Assemblies via Allosteric Effect: From 1D Nanofilament to 2D Rectangular Nanosheet. J Am Chem Soc 2019; 141:13724-13728. [DOI: 10.1021/jacs.9b05946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Miaomiao Xu
- State Key Laboratory
of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Rongjin Zeng
- State Key Laboratory
of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Jun Xiang
- Department of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Qiang Yan
- State Key Laboratory
of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
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22
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Progress in research on paclitaxel and tumor immunotherapy. Cell Mol Biol Lett 2019; 24:40. [PMID: 31223315 PMCID: PMC6567594 DOI: 10.1186/s11658-019-0164-y] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Paclitaxel is a well-known anticancer agent with a unique mechanism of action. It is considered to be one of the most successful natural anticancer drugs available. This study summarizes the recent advances in our understanding of the sources, the anticancer mechanism, and the biosynthetic pathway of paclitaxel. With the advancement of biotechnology, improvements in endophytic fungal strains, and the use of recombination techniques and microbial fermentation engineering, the yield of extracted paclitaxel has increased significantly. Recently, paclitaxel has been found to play a large role in tumor immunity, and it has a great potential for use in many cancer treatments.
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23
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Chen T, Guo Y, Shan J, Zhang J, Shen X, Guo J, Liu XM. Vector Analysis of Cytoskeletal Structural Tension and the Mechanisms that Underpin Spectrin-Related Forces in Pyroptosis. Antioxid Redox Signal 2019; 30:1503-1520. [PMID: 29669427 DOI: 10.1089/ars.2017.7366] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Aims: Pyroptotic cells are characterized by plasma swelling, membrane blebbing, and disintegration of the cell membrane mediated by spectrin-based membrane skeleton and intercellular competitive tension activities. The spectrin-based membrane skeleton is involved in membrane organization through the regulation of intercellular tension. Using genetically encoded tension sensors to attain noninvasive force measurements in structural proteins, we investigated how cytoskeletal structural tension influences changes in plasma morphology during pyroptosis and the regulatory mechanism of cytoskeletal structural tension that underpins pyroptosis. Results: The results indicate that increasing spectrin tension is caused by osmotic swelling. Hightened tension of spectrin was closely associated with the shrink tension transmitted synergistically by microfilaments (MFs) and microtubules (MTs). However, the increment of spectrin tension in pyroptotic cells was controlled antagonistically by MF and MT forces. Different from MF tension, outward MT forces participated in the formation of membrane blebs. Spectrin tension caused by inward MF forces resisted pyroptosis swelling. Stabilization of MF and MT structure had little influence on intracellular tension and pyroptosis deformation. Pyroptosis-induced cytoskeletal structural tension was highly dependent on calcium signaling and reactive oxygen species generation. Blocking of membrane pores, nonselective ion flux, or elimination of caspase-1 cleavage resulted in the remission of structural forces associated with pyroptosis failure. Innovation and Conclusions: The data suggest that subcellular tension, in terms of magnitude and vector, is integral to pyroptosis through the mediation of swelling and blebbing and the elimination of structural tension, especially MT forces, may result in pyroptosis inhibition.
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Affiliation(s)
- Tingting Chen
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, People's Republic of China.,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Yichen Guo
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), Birmingham, Alabama
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Jiarui Zhang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Xu Shen
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Jun Guo
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, People's Republic of China.,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), Birmingham, Alabama
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24
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 PMCID: PMC6495662 DOI: 10.1107/s1600576718018046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 DOI: 10.26434/chemrxiv.7012622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 05/23/2023] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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Shemesh A, Ginsburg A, Levi-Kalisman Y, Ringel I, Raviv U. Structure, Assembly, and Disassembly of Tubulin Single Rings. Biochemistry 2018; 57:6153-6165. [PMID: 30247898 DOI: 10.1021/acs.biochem.8b00560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single and double tubulin rings were studied under a range of conditions and during microtubule (MT) assembly and disassembly. Here, tubulin was purified from porcine brain and used without any further modifications or additives that promote ring assembly. The structure of single GDP-rich tubulin rings was determined by cryo-transmission electron microscopy and synchrotron solution X-ray scattering. The scattering curves were fitted to atomic models, using our state-of-the-art analysis software, D+ . We found that there is a critical concentration for ring formation, which increased with GTP concentration with temperature. MT assembly or disassembly, induced by changes in temperature, was analyzed by time-resolved small-angle X-ray scattering. During MT assembly, the fraction of rings and unassembled dimers simultaneously decreased. During MT disassembly, the mass fraction of dimers increased. The increase in the concentration of rings was delayed until the fraction of dimers was sufficiently high. We verified that pure dimers, eluted via size-exclusion chromatography, could also form rings. Interestingly, X-ray radiation triggered tubulin ring disassembly. The concentration of disassembled rings versus exposure time followed a first-order kinetics. The disassembly rate constant and initial concentration were determined. X-ray radiation-triggered disassembly was used to determine the concentration of rings. We confirmed that following a temperature jump, the mass fraction of rings decreased and then stabilized at a constant value during the first stage of the MT assembly kinetics. This study sheds light on the most basic assembly and disassembly conditions for in vitro single GDP-rich tubulin rings and their relation to MT kinetics.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
| | - Avi Ginsburg
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Institute for Drug Research, School of Pharmacy , The Hebrew University of Jerusalem , Jerusalem 9112102 , Israel
| | - Yael Levi-Kalisman
- Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Institute of Life Sciences , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy , The Hebrew University of Jerusalem , Jerusalem 9112102 , Israel
| | - Uri Raviv
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
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Asor R, Ben-Nun-Shaul O, Oppenheim A, Raviv U. Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles. ACS NANO 2017; 11:9814-9824. [PMID: 28956913 PMCID: PMC6545118 DOI: 10.1021/acsnano.7b03131] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Crystallization is a fundamental and ubiquitous process that is well understood in the case of atoms or small molecules, but its outcome is still hard to predict in the case of nanoparticles or macromolecular complexes. Controlling the organization of virus nanoparticles into a variety of 3D supramolecular architectures is often done by multivalent ions and is of great interest for biomedical applications such as drug or gene delivery and biosensing, as well as for bionanomaterials and catalysis. In this paper, we show that slow dialysis, over several hours, of wild-type Simian Virus 40 (wt SV40) nanoparticle solution against salt solutions containing MgCl2, with or without added NaCl, results in wt SV40 nanoparticles arranged in a body cubic center crystal structure with Im3m space group, as a thermodynamic product, in coexistence with soluble wt SV40 nanoparticles. The nanoparticle crystals formed above a critical MgCl2 concentrations. Reentrant melting and resolubilization of the virus nanoparticles took place when the MgCl2 concentrations passed a second threshold. Using synchrotron solution X-ray scattering we determined the structures and the mass fraction of the soluble and crystal phases as a function of MgCl2 and NaCl concentrations. A thermodynamic model, which balances the chemical potentials of the Mg2+ ions in each of the possible states, explains our observations. The model reveals the mechanism of both the crystallization and the reentrant melting and resolubilization and shows that counterion entropy is the main driving force for both processes.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Orly Ben-Nun-Shaul
- Department of Haematology, Hebrew University Faculty of Medicine and Hadassah Medical Organization , Ein Karem, Jerusalem, 91120, Israel
| | - Ariella Oppenheim
- Department of Haematology, Hebrew University Faculty of Medicine and Hadassah Medical Organization , Ein Karem, Jerusalem, 91120, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
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28
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Synchrotron small-angle X-ray scattering and electron microscopy characterization of structures and forces in microtubule/Tau mixtures. Methods Cell Biol 2017; 141:155-178. [PMID: 28882300 DOI: 10.1016/bs.mcb.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Tau, a neuronal protein known to bind to microtubules and thereby regulate microtubule dynamic instability, has been shown recently to not only undergo conformational transitions on the microtubule surface as a function of increasing microtubule coverage density (i.e., with increasing molar ratio of Tau to tubulin dimers) but also to mediate higher-order microtubule architectures, mimicking fascicles of microtubules found in the axon initial segment. These discoveries would not have been possible without fine structure characterization of microtubules, with and without applied osmotic pressure through the use of depletants. Herein, we discuss the two primary techniques used to elucidate the structure, phase behavior, and interactions in microtubule/Tau mixtures: transmission electron microscopy and synchrotron small-angle X-ray scattering. While the former is able to provide striking qualitative images of bundle morphologies and vacancies, the latter provides angstrom-level resolution of bundle structures and allows measurements in the presence of in situ probes, such as osmotic depletants. The presented structural characterization methods have been applied both to equilibrium mixtures, where paclitaxel is used to stabilize microtubules, and also to dissipative nonequilibrium mixtures at 37°C in the presence of GTP and lacking paclitaxel.
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29
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Wei S, Huang W, Su F, Tang X, Huang N, Li L. Lyotropic meso-phase behavior of supra-molecular nanotubes with helical charge distribution. SOFT MATTER 2017; 13:3475-3479. [PMID: 28440381 DOI: 10.1039/c7sm00603a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report diverse meso-phase arrangements of supra-molecular nanotubes assembled by ionic benzene-1,3,5-tricarboxamide (BTA) molecules in water; their transition pathway and equilibrium structure are controlled by the helical structure. Besides, the different sensitivity to the condition of initial solutions is revealed for the final rectangular phase and the intermediate phase.
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Affiliation(s)
- Shenghui Wei
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China.
| | - Weiheng Huang
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China.
| | - Fengmei Su
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China.
| | - Xiaoliang Tang
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China.
| | - Ningdong Huang
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China.
| | - Liangbin Li
- National Synchrotron Radiation Lab, University of Science and Technology of China, Hefei, China. and Department of Polymer Science and Engineering, CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei, China
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30
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Narayanan T, Wacklin H, Konovalov O, Lund R. Recent applications of synchrotron radiation and neutrons in the study of soft matter. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2016.1277212] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Hanna Wacklin
- European Spallation Source ERIC, Lund, Sweden
- Physical Chemistry, Lund University, Lund, Sweden
| | | | - Reidar Lund
- Department of Chemistry, University of Oslo, Blindern, Oslo, Norway
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31
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Munch K, Nam K, Schierup MH, Mailund T. Selective Sweeps across Twenty Millions Years of Primate Evolution. Mol Biol Evol 2016; 33:3065-3074. [DOI: 10.1093/molbev/msw199] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Kim K, Sikora A, Nakazawa H, Umetsu M, Hwang W, Teizer W. Isomorphic coalescence of aster cores formed in vitro from microtubules and kinesin motors. Phys Biol 2016; 13:056002. [PMID: 27652512 DOI: 10.1088/1478-3975/13/5/056002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report fluorescence microscopy studies of the formation of aster-like structures emerging from a cellular element-based active system and a novel analysis of the aster condensation. The system consists of rhodamine labeled microtubules which are dynamically coupled by functionalized kinesin motor proteins cross-linked via streptavidin-coated quantum dots (QDs). The aster-shaped objects contain core structures. The cores are aggregates of the QD-motor protein complexes, and result from the dynamic condensation of sub-clusters that are connected to each other randomly. The structural specificity of the aster core reflects a configuration of the initial connectivity between sub-clusters. Detailed image analysis allows us to extract a novel correlation between the condensation speed and the sub-cluster separation. The size of the core is scaled down during the condensation process, following a power law dependence on the distance between sub-clusters. The exponent of the power law is close to two, as expected from a geometric model. This single exponent common to all the contractile lines implies that there exists a time regime during which an isomorphic contraction of the aster core continues during the condensation process. We analyze the observed contraction by using a model system with potential applicability in a wide range of emergent phenomena in randomly coupled active networks, which are prevalent in the cellular environment.
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Affiliation(s)
- K Kim
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Japan
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33
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Choi MC, Chung PJ, Song C, Miller HP, Kiris E, Li Y, Wilson L, Feinstein SC, Safinya CR. Paclitaxel suppresses Tau-mediated microtubule bundling in a concentration-dependent manner. Biochim Biophys Acta Gen Subj 2016; 1861:3456-3463. [PMID: 27632200 DOI: 10.1016/j.bbagen.2016.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 08/31/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Microtubules (MTs) are protein nanotubes comprised of straight protofilaments (PFs), head to tail assemblies of αβ-tubulin heterodimers. Previously, it was shown that Tau, a microtubule-associated protein (MAP) localized to neuronal axons, regulates the average number of PFs in microtubules with increasing inner radius <RinMT> observed for increasing Tau/tubulin-dimer molar ratio ΦTau at paclitaxel/tubulin-dimer molar ratio ΛPtxl=1/1. METHODS We report a synchrotron SAXS and TEM study of the phase behavior of microtubules as a function of varying concentrations of paclitaxel (1/32≤ΛPtxl≤1/4) and Tau (human isoform 3RS, 0≤Φ3RS≤1/2) at room temperature. RESULTS Tau and paclitaxel have opposing regulatory effects on microtubule bundling architectures and microtubule diameter. Surprisingly and in contrast to previous results at ΛPtxl=1/1 where microtubule bundles are absent, in the lower paclitaxel concentration regime (ΛPtxl≤1/4), we observe both microtubule doublets and triplets with increasing Tau. Furthermore, increasing paclitaxel concentration (up to ΛPtxl=1/1) slightly decreased the average microtubule diameter (by ~1 PF) while increasing Tau concentration (up to Φ3RS=1/2) significantly increased the diameter (by ~2-3 PFs). CONCLUSIONS The suppression of Tau-mediated microtubule bundling with increasing paclitaxel is consistent with paclitaxel seeding more, but shorter, microtubules by rapidly exhausting tubulin available for polymerization. Microtubule bundles require the aggregate Tau-Tau attractions along the microtubule length to overcome individual microtubule thermal energies disrupting bundles. GENERAL SIGNIFICANCE Investigating MAP-mediated interactions between microtubules (as it relates to in vivo behavior) requires the elimination or minimization of paclitaxel.
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Affiliation(s)
- Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Peter J Chung
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Chaeyeon Song
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Herbert P Miller
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - E Kiris
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Leslie Wilson
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Stuart C Feinstein
- Neuroscience Research Institute and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Cyrus R Safinya
- Materials Department, Physics Department, Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA.
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34
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Ringel I, Raviv U. Reciprocal Grids: A Hierarchical Algorithm for Computing Solution X-ray Scattering Curves from Supramolecular Complexes at High Resolution. J Chem Inf Model 2016; 56:1518-27. [DOI: 10.1021/acs.jcim.6b00159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Israel Ringel
- Azrieli College of Engineering, Jerusalem 9103501, Israel
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35
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Tau mediates microtubule bundle architectures mimicking fascicles of microtubules found in the axon initial segment. Nat Commun 2016; 7:12278. [PMID: 27452526 PMCID: PMC4962469 DOI: 10.1038/ncomms12278] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/17/2016] [Indexed: 11/24/2022] Open
Abstract
Tau, an intrinsically disordered protein confined to neuronal axons, binds to and regulates microtubule dynamics. Although there have been observations of string-like microtubule fascicles in the axon initial segment (AIS) and hexagonal bundles in neurite-like processes in non-neuronal cells overexpressing Tau, cell-free reconstitutions have not replicated either geometry. Here we map out the energy landscape of Tau-mediated, GTP-dependent ‘active' microtubule bundles at 37 °C, as revealed by synchrotron SAXS and TEM. Widely spaced bundles (wall-to-wall distance Dw–w≈25–41 nm) with hexagonal and string-like symmetry are observed, the latter mimicking bundles found in the AIS. A second energy minimum (Dw–w≈16–23 nm) is revealed under osmotic pressure. The wide spacing results from a balance between repulsive forces, due to Tau's projection domain (PD), and a stabilizing sum of transient sub-kBT cationic/anionic charge–charge attractions mediated by weakly penetrating opposing PDs. This landscape would be significantly affected by charge-altering modifications of Tau associated with neurodegeneration. Tau, an intrinsically disordered axonal protein, binds to and regulates microtubule dynamics. Here, the authors use SAXS and electron microscopy to examine the architectures of microtubule bundles, including those mimicking microtubule fascicles in the axon initial segment.
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36
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Abstract
The content of spermidine and spermine in mammalian cells has important roles in protein and nucleic acid synthesis and structure, protection from oxidative damage, activity of ion channels, cell proliferation, differentiation, and apoptosis. Spermidine is essential for viability and acts as the precursor of hypusine, a post-translational addition to eIF5A allowing the translation of mRNAs encoding proteins containing polyproline tracts. Studies with Gy mice and human patients with the very rare X-linked genetic condition Snyder-Robinson syndrome that both lack spermine synthase show clearly that the correct spermine:spermidine ratio is critical for normal growth and development.
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Affiliation(s)
- Anthony E Pegg
- From the Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
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Safinya CR, Chung PJ, Song C, Li Y, Ewert KK, Choi MC. The effect of multivalent cations and Tau on paclitaxel-stabilized microtubule assembly, disassembly, and structure. Adv Colloid Interface Sci 2016; 232:9-16. [PMID: 26684364 PMCID: PMC4864139 DOI: 10.1016/j.cis.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 01/22/2023]
Abstract
In this review we describe recent studies directed at understanding the formation of novel nanoscale assemblies in biological materials systems. In particular, we focus on the effects of multivalent cations, and separately, of microtubule-associated protein (MAP) Tau, on microtubule (MT) ordering (bundling), MT disassembly, and MT structure. Counter-ion directed bundling of paclitaxel-stabilized MTs is a model electrostatic system, which parallels efforts to understand MT bundling by intrinsically disordered proteins (typically biological polyampholytes) expressed in neurons. We describe studies, which reveal an unexpected transition from tightly spaced MT bundles to loose bundles consisting of strings of MTs as the valence of the cationic counter-ion decreases from Z=3 to Z=2. This transition is not predicted by any current theories of polyelectrolytes. Notably, studies of a larger series of divalent counter-ions reveal strong ion specific effects. Divalent counter-ions may either bundle or depolymerize paclitaxel-stabilized MTs. The ion concentration required for depolymerization decreases with increasing atomic number. In a more biologically related system we review synchrotron small angle x-ray scattering (SAXS) studies on the effect of the Tau on the structure of paclitaxel-stabilized MTs. The electrostatic binding of MAP Tau isoforms leads to an increase in the average radius of microtubules with increasing Tau coverage (i.e. a re-distribution of protofilament numbers in MTs). Finally, inspired by MTs as model nanotubes, we briefly describe other more robust lipid-based cylindrical nanostructures, which may have technological applications, for example, in drug encapsulation and delivery.
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Affiliation(s)
- Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA.
| | - Peter J Chung
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Chaeyeon Song
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA
| | - Kai K Ewert
- Materials Department, University of California, Santa Barbara, CA 93106, USA; Physics Department, University of California, Santa Barbara, CA 93106, USA; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
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Regulation of Microtubule Assembly by Tau and not by Pin1. J Mol Biol 2016; 428:1742-59. [PMID: 26996940 DOI: 10.1016/j.jmb.2016.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
Abstract
The molecular mechanism by which the microtubule-associated protein (MAP) tau regulates the formation of microtubules (MTs) is poorly understood. The activity of tau is controlled via phosphorylation at specific Ser/Thr sites. Of those phosphorylation sites, 17 precede a proline, making them potential recognition sites for the peptidyl-prolyl isomerase Pin1. Pin1 binding and catalysis of phosphorylated tau at the AT180 epitope, which was implicated in Alzheimer's disease, has been reported to be crucial for restoring tau's ability to promote MT polymerization in vitro and in vivo [1]. Surprisingly, we discover that Pin1 does not promote phosphorylated tau-induced MT formation in vitro, refuting the commonly accepted model in which Pin1 binding and catalysis on the A180 epitope restores the function of the Alzheimer's associated phosphorylated tau in tubulin assembly [1, 2]. Using turbidity assays, time-resolved small angle X-ray scattering (SAXS), and time-resolved negative stain electron microscopy (EM), we investigate the mechanism of tau-mediated MT assembly and the role of the Thr231 and Ser235 phosphorylation on this process. We discover novel GTP-tubulin ring-shaped species, which are detectable in the earliest stage of tau-induced polymerization and may play a crucial role in the early nucleation phase of MT assembly. Finally, by NMR and SAXS experiments, we show that the tau molecules must be located on the surface of MTs and tubulin rings during the polymerization reaction. The interaction between tau and tubulin is multipartite, with a high affinity interaction of the four tubulin-binding repeats, and a weaker interaction with the proline-rich sequence and the termini of tau.
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Abstract
The protection and sustainable utilization of natural resources are among the most pressing global problems of the 21st century.
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Affiliation(s)
- W. C. Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
| | - T. Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
| | - P. Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
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40
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Chung PJ, Choi MC, Miller HP, Feinstein HE, Raviv U, Li Y, Wilson L, Feinstein SC, Safinya CR. Direct force measurements reveal that protein Tau confers short-range attractions and isoform-dependent steric stabilization to microtubules. Proc Natl Acad Sci U S A 2015; 112:E6416-25. [PMID: 26542680 PMCID: PMC4664379 DOI: 10.1073/pnas.1513172112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Microtubules (MTs) are hollow cytoskeletal filaments assembled from αβ-tubulin heterodimers. Tau, an unstructured protein found in neuronal axons, binds to MTs and regulates their dynamics. Aberrant Tau behavior is associated with neurodegenerative dementias, including Alzheimer's. Here, we report on a direct force measurement between paclitaxel-stabilized MTs coated with distinct Tau isoforms by synchrotron small-angle X-ray scattering (SAXS) of MT-Tau mixtures under osmotic pressure (P). In going from bare MTs to MTs with Tau coverage near the physiological submonolayer regime (Tau/tubulin-dimer molar ratio; ΦTau = 1/10), isoforms with longer N-terminal tails (NTTs) sterically stabilized MTs, preventing bundling up to PB ∼ 10,000-20,000 Pa, an order of magnitude larger than bare MTs. Tau with short NTTs showed little additional effect in suppressing the bundling pressure (PB ∼ 1,000-2,000 Pa) over the same range. Remarkably, the abrupt increase in PB observed for longer isoforms suggests a mushroom to brush transition occurring at 1/13 < ΦTau < 1/10, which corresponds to MT-bound Tau with NTTs that are considerably more extended than SAXS data for Tau in solution indicate. Modeling of Tau-mediated MT-MT interactions supports the hypothesis that longer NTTs transition to a polyelectrolyte brush at higher coverages. Higher pressures resulted in isoform-independent irreversible bundling because the polyampholytic nature of Tau leads to short-range attractions. These findings suggest an isoform-dependent biological role for regulation by Tau, with longer isoforms conferring MT steric stabilization against aggregation either with other biomacromolecules or into tight bundles, preventing loss of function in the crowded axon environment.
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Affiliation(s)
- Peter J Chung
- Materials Department, University of California, Santa Barbara, CA 93106; Physics Department, University of California, Santa Barbara, CA 93106; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106
| | - Myung Chul Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Herbert P Miller
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106
| | - H Eric Feinstein
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106
| | - Uri Raviv
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, CA 93106
| | - Leslie Wilson
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106
| | - Stuart C Feinstein
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106; Neuroscience Research Institute, University of California, Santa Barbara, CA 93106
| | - Cyrus R Safinya
- Materials Department, University of California, Santa Barbara, CA 93106; Physics Department, University of California, Santa Barbara, CA 93106; Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA 93106;
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41
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Mayzlish-Gati E, Laufer D, Grivas CF, Shaknof J, Sananes A, Bier A, Ben-Harosh S, Belausov E, Johnson MD, Artuso E, Levi O, Genin O, Prandi C, Khalaila I, Pines M, Yarden RI, Kapulnik Y, Koltai H. Strigolactone analogs act as new anti-cancer agents in inhibition of breast cancer in xenograft model. Cancer Biol Ther 2015; 16:1682-8. [PMID: 26192476 DOI: 10.1080/15384047.2015.1070982] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Strigolactones (SLs) are a novel class of plant hormones. Previously, we found that analogs of SLs induce growth arrest and apoptosis in breast cancer cell lines. These compounds also inhibited the growth of breast cancer stem cell enriched-mammospheres with increased potency. Furthermore, strigolactone analogs inhibited growth and survival of colon, lung, prostate, melanoma, osteosarcoma and leukemia cancer cell lines. To further examine the anti-cancer activity of SLs in vivo, we have examined their effects on growth and viability of MDA-MB-231 tumor xenografts model either alone or in combination with paclitaxel. We show that strigolactone act as new anti-cancer agents in inhibition of breast cancer in xenograft model. In addition we show that SLs affect the integrity of the microtubule network and therefore may inhibit the migratory phenotype of the highly invasive breast cancer cell lines that were examined.
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Affiliation(s)
| | - Dana Laufer
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel.,b Faculty of Engineering Sciences; The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Christopher F Grivas
- c Department of Human Science ; SNHS; Georgetown University ; Washington, DC USA
| | - Julia Shaknof
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel
| | - Amiram Sananes
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel.,b Faculty of Engineering Sciences; The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Ariel Bier
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel
| | - Shani Ben-Harosh
- b Faculty of Engineering Sciences; The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Eduard Belausov
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel
| | - Michael D Johnson
- d Department of Oncology ; Georgetown University Medical Center ; Washington, DC USA.,e The Lombardi Comprehensive Cancer Center; Georgetown University Medical Center ; Washington, DC USA
| | - Emma Artuso
- f Department of Chemistry ; University of Turin ; Torino , Italy
| | - Oshrat Levi
- g Institute of Animal Sciences; Volcani Center ; Bet Dagan , Israel
| | - Ola Genin
- g Institute of Animal Sciences; Volcani Center ; Bet Dagan , Israel
| | - Cristina Prandi
- f Department of Chemistry ; University of Turin ; Torino , Italy
| | - Isam Khalaila
- b Faculty of Engineering Sciences; The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering ; Ben-Gurion University of the Negev ; Beer-Sheva , Israel
| | - Mark Pines
- g Institute of Animal Sciences; Volcani Center ; Bet Dagan , Israel
| | - Ronit I Yarden
- c Department of Human Science ; SNHS; Georgetown University ; Washington, DC USA.,e The Lombardi Comprehensive Cancer Center; Georgetown University Medical Center ; Washington, DC USA
| | - Yoram Kapulnik
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel
| | - Hinanit Koltai
- a Institute of Plant Sciences; ARO; Volcani Center ; Bet Dagan , Israel
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42
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Yao Y, Metwalli E, Su B, Körstgens V, Moseguí González D, Miasnikova A, Laschewsky A, Opel M, Santoro G, Roth SV, Müller-Buschbaum P. Arrangement of Maghemite Nanoparticles via Wet Chemical Self-Assembly in PS-b-PNIPAM Diblock Copolymer Films. ACS APPLIED MATERIALS & INTERFACES 2015; 7:13080-13091. [PMID: 26001128 DOI: 10.1021/acsami.5b03308] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The structure and magnetic behavior of hybrid films composed of maghemite (γ-Fe2O3) nanoparticles (NPs) and an asymmetric diblock copolymer (DBC) polystyrene61-block-polyN-isopropylacrylamide115 are investigated. The NPs are coated with PS chains, which allow for a selective incorporation inside the PS domains at different NP concentrations. Upon incorporation of low amounts of NPs into the DBC thin films, the initial parallel (to film surface) cylinder morphology changes to a well ordered, perpendicularly oriented one. The characteristic domain distance of the DBC is increased due to the swelling of the PS domains with NPs. At higher NP concentrations, the excess NPs which can no longer be embedded in the PS domains, are accumulated at the film surface, and NP aggregates form. Irrespective of NP concentration, a superparamagnetic behavior of the metal oxide-DBC hybrid films is found. Such superparamagnetic properties make the established hybrid films interesting for high density magnetic storage media and thermoresponsive magnetic sensors.
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Affiliation(s)
- Yuan Yao
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
| | - Ezzeldin Metwalli
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
| | - Bo Su
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
| | - Volker Körstgens
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
| | - Daniel Moseguí González
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
| | - Anna Miasnikova
- ‡Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Andre Laschewsky
- ‡Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
- §Fraunhofer Institut für Angewandte Polymerforschung IAP, Geiselbergstrasse 69, 14476 Potsdam-Golm, Germany
| | - Matthias Opel
- ∥Walther-Meissner-Institut, Bayerische Akademie der Wissenschaften, Walther-Meissner-Strasse 8, 85748 Garching, Germany
| | - Gonzalo Santoro
- ⊥Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22603 Hamburg, Germany
- #Instituto de Ciencia de Materiales de Madrid, ICMM-CSIC, sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - Stephan V Roth
- ⊥Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Peter Müller-Buschbaum
- †Technische Universität München, Physik-Department, Lehrstuhl für Funktionelle Materialien, James-Franck-Str. 1, 85748 Garching, Germany
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43
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Mao Z, Xu B, Ji X, Zhou K, Zhang X, Chen M, Han X, Tang Q, Wang X, Xia Y. Titanium dioxide nanoparticles alter cellular morphology via disturbing the microtubule dynamics. NANOSCALE 2015; 7:8466-75. [PMID: 25891938 DOI: 10.1039/c5nr01448d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Titanium dioxide (TiO2) nanoparticles (NPs) have been widely used in our daily lives, for example, in the areas of sunscreens, cosmetics, toothpastes, food products, and nanomedical reagents. Recently, increasing concern has been raised about their neurotoxicity, but the mechanisms underlying such toxic effects are still unknown. In this work, we employed a human neuroblastoma cell line (SH-SY5Y) to study the effects of TiO2 NPs on neurological systems. Our results showed that TiO2 NPs did not affect cell viability but induced noticeable morphological changes until 100 μg ml(-1). Immunofluorescence detection showed disorder, disruption, retraction, and decreased intensity of the microtubules after TiO2 NPs treatment. Both α and β tubule expressions did not change in the TiO2 NP-treated group, but the percentage of soluble tubules was increased. A microtubule dynamic study in living cells indicated that TiO2 NPs caused a lower growth rate and a higher shortening rate of microtubules as well as shortened lifetimes of de novo microtubules. TiO2 NPs did not cause changes in the expression and phosphorylation state of tau proteins, but a tau-TiO2 NP interaction was observed. TiO2 NPs could interact with tubule heterodimers, microtubules and tau proteins, which led to the instability of microtubules, thus contributing to the neurotoxicity of TiO2 NPs.
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Affiliation(s)
- Zhilei Mao
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 211100, China
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44
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Zuckerman DM, Boucher LE, Xie K, Engelhardt H, Bosch J, Hoiczyk E. The bactofilin cytoskeleton protein BacM of Myxococcus xanthus forms an extended β-sheet structure likely mediated by hydrophobic interactions. PLoS One 2015; 10:e0121074. [PMID: 25803609 PMCID: PMC4372379 DOI: 10.1371/journal.pone.0121074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/29/2015] [Indexed: 11/18/2022] Open
Abstract
Bactofilins are novel cytoskeleton proteins that are widespread in Gram-negative bacteria. Myxococcus xanthus, an important predatory soil bacterium, possesses four bactofilins of which one, BacM (Mxan_7475) plays an important role in cell shape maintenance. Electron and fluorescence light microscopy, as well as studies using over-expressed, purified BacM, indicate that this protein polymerizes in vivo and in vitro into ~3 nm wide filaments that further associate into higher ordered fibers of about 10 nm. Here we use a multipronged approach combining secondary structure determination, molecular modeling, biochemistry, and genetics to identify and characterize critical molecular elements that enable BacM to polymerize. Our results indicate that the bactofilin-determining domain DUF583 folds into an extended β-sheet structure, and we hypothesize a left-handed β-helix with polymerization into 3 nm filaments primarily via patches of hydrophobic amino acid residues. These patches form the interface allowing head-to-tail polymerization during filament formation. Biochemical analyses of these processes show that folding and polymerization occur across a wide variety of conditions and even in the presence of chaotropic agents such as one molar urea. Together, these data suggest that bactofilins are comprised of a structure unique to cytoskeleton proteins, which enables robust polymerization.
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Affiliation(s)
- David M. Zuckerman
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Lauren E. Boucher
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Malaria Research Institute, Baltimore, Maryland, United States of America
| | - Kefang Xie
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Harald Engelhardt
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Malaria Research Institute, Baltimore, Maryland, United States of America
| | - Egbert Hoiczyk
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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45
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Stevens MJ. Materials science. How shape affects microtubule and nanoparticle assembly. Science 2014; 343:981-2. [PMID: 24578572 DOI: 10.1126/science.1250827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185-1315 USA
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