1
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [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: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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2
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Guo W, Ale TA, Sun S, Sanchez JE, Li L. A Comprehensive Study on the Electrostatic Properties of Tubulin-Tubulin Complexes in Microtubules. Cells 2023; 12:cells12020238. [PMID: 36672172 PMCID: PMC9857020 DOI: 10.3390/cells12020238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/08/2023] Open
Abstract
Microtubules are key players in several stages of the cell cycle and are also involved in the transportation of cellular organelles. Microtubules are polymerized by α/β tubulin dimers with a highly dynamic feature, especially at the plus ends of the microtubules. Therefore, understanding the interactions among tubulins is crucial for characterizing microtubule dynamics. Studying microtubule dynamics can help researchers make advances in the treatment of neurodegenerative diseases and cancer. In this study, we utilize a series of computational approaches to study the electrostatic interactions at the binding interfaces of tubulin monomers. Our study revealed that among all the four types of tubulin-tubulin binding modes, the electrostatic attractive interactions in the α/β tubulin binding are the strongest while the interactions of α/α tubulin binding in the longitudinal direction are the weakest. Our calculations explained that due to the electrostatic interactions, the tubulins always preferred to form α/β tubulin dimers. The interactions between two protofilaments are the weakest. Thus, the protofilaments are easily separated from each other. Furthermore, the important residues involved in the salt bridges at the binding interfaces of the tubulins are identified, which illustrates the details of the interactions in the microtubule. This study elucidates some mechanistic details of microtubule dynamics and also identifies important residues at the binding interfaces as potential drug targets for the inhibition of cancer cells.
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Affiliation(s)
- Wenhan Guo
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Tolulope Ayodeji Ale
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Shengjie Sun
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Jason E. Sanchez
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
- Department of Physics, University of Texas at El Paso, El Paso, TX 79902, USA
- Correspondence:
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3
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Wilson L, Krasny R, Luchko T. Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs. J Comput Chem 2022; 43:1251-1270. [PMID: 35567580 DOI: 10.1002/jcc.26889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/07/2022]
Abstract
The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D-RISM to calculate the solvation thermodynamics and density distribution of 7-ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms.
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Affiliation(s)
- Leighton Wilson
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert Krasny
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Los Angeles, California, USA
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4
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Wang J, Miller DD, Li W. Molecular interactions at the colchicine binding site in tubulin: An X-ray crystallography perspective. Drug Discov Today 2022; 27:759-776. [PMID: 34890803 PMCID: PMC8901563 DOI: 10.1016/j.drudis.2021.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/02/2023]
Abstract
Tubulin is an important cancer drug target. Compounds that bind at the colchicine site in tubulin have attracted significant interest as they are generally less affected by multidrug resistance than other potential drugs. Modeling is useful in understanding the interactions between tubulin and colchicine binding site inhibitors (CBSIs), but because the colchicine binding site contains two flexible loops whose conformations are highly ligand-dependent, modeling has its limitations. X-ray crystallography provides experimental pictures of tubulin-ligand interactions at this challenging colchicine site. Since 2004, when the first X-ray structure of tubulin in complex with N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) was published, many X-ray crystal structures have been reported for tubulin complexes involving the colchicine binding site. In this review, we summarize the crystal structures of tubulin in complexes with various CBSIs, aiming to facilitate the discovery of new generations of tubulin inhibitors.
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Affiliation(s)
- Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Duane D Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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5
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Nasedkin A, Ermilova I, Swenson J. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:927-940. [PMID: 34215900 PMCID: PMC8448678 DOI: 10.1007/s00249-021-01553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
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6
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Huang M, Wang Y. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:215-235. [PMID: 32519381 PMCID: PMC7725852 DOI: 10.1002/mas.21637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 05/05/2023]
Abstract
GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
- Correspondence author: Yinsheng Wang. Telephone: (951)827-2700;
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7
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Ayukawa R, Iwata S, Imai H, Kamimura S, Hayashi M, Ngo KX, Minoura I, Uchimura S, Makino T, Shirouzu M, Shigematsu H, Sekimoto K, Gigant B, Muto E. GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation. J Cell Biol 2021; 220:211760. [PMID: 33544140 PMCID: PMC7871348 DOI: 10.1083/jcb.202007033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleation of microtubules (MTs) is essential for cellular activities, but its mechanism is unknown because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. Here, combining rapid flush negative stain electron microscopy (EM) and kinetic analysis, we demonstrate that the formation of straight oligomers of critical size is essential for nucleation. Both GDP and GTP tubulin form single-stranded oligomers with a broad range of curvatures, but upon nucleation, the curvature distribution of GTP oligomers is shifted to produce a minor population of straight oligomers. With tubulin having the Y222F mutation in the β subunit, the proportion of straight oligomers increases and nucleation accelerates. Our results support a model in which GTP binding generates a minor population of straight oligomers compatible with lateral association and further growth to MTs. This study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.
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Affiliation(s)
- Rie Ayukawa
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seigo Iwata
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Hiroshi Imai
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Masahito Hayashi
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kien Xuan Ngo
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seiichi Uchimura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Tsukasa Makino
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Hideki Shigematsu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Ken Sekimoto
- Matière et Systèmes Complexes (MSC), CNRS UMR 7057, Université de Paris, Paris, France.,Gulliver, CNRS UMR 7083, ESPCI Paris and Université Paris Sciences et Lettres, Paris, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Etsuko Muto
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
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8
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Atomistic Basis of Microtubule Dynamic Instability Assessed Via Multiscale Modeling. Ann Biomed Eng 2021; 49:1716-1734. [PMID: 33537926 PMCID: PMC8302526 DOI: 10.1007/s10439-020-02715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]
Abstract
Microtubule “dynamic instability,” the abrupt switching from assembly to disassembly caused by the hydrolysis of GTP to GDP within the β subunit of the αβ-tubulin heterodimer, is necessary for vital cellular processes such as mitosis and migration. Despite existing high-resolution structural data, the key mechanochemical differences between the GTP and GDP states that mediate dynamic instability behavior remain unclear. Starting with a published atomic-level structure as an input, we used multiscale modeling to find that GTP hydrolysis results in both longitudinal bond weakening (~ 4 kBT) and an outward bending preference (~ 1.5 kBT) to both drive dynamic instability and give rise to the microtubule tip structures previously observed by light and electron microscopy. More generally, our study provides an example where atomic level structural information is used as the sole input to predict cellular level dynamics without parameter adjustment.
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9
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Tong D, Voth GA. Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability. Biophys J 2020; 118:2938-2951. [PMID: 32413312 DOI: 10.1016/j.bpj.2020.04.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
The dynamic instability of microtubules (MTs), which refers to their ability to switch between polymerization and depolymerization states, is crucial for their function. It has been proposed that the growing MT ends are protected by a "GTP cap" that consists of GTP-bound tubulin dimers. When the speed of GTP hydrolysis is faster than dimer recruitment, the loss of this GTP cap will lead the MT to undergo rapid disassembly. However, the underlying atomistic mechanistic details of the dynamic instability remains unclear. In this study, we have performed long-time atomistic molecular dynamics simulations (1 μs for each system) for MT patches as well as a short segment of a closed MT in both GTP- and GDP-bound states. Our results confirmed that MTs in the GDP state generally have weaker lateral interactions between neighboring protofilaments (PFs) and less cooperative outward bending conformational change, where the difference between bending angles of neighboring PFs tends to be larger compared with GTP ones. As a result, when the GDP state tubulin dimer is exposed at the growing MT end, these factors will be more likely to cause the MT to undergo rapid disassembly. We also compared simulation results between the special MT seam region and the remaining material and found that the lateral interactions between MT PFs at the seam region were comparatively much weaker. This finding is consistent with the experimental suggestion that the seam region tends to separate during the disassembly process of an MT.
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Affiliation(s)
- Dudu Tong
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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10
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Fedorov VA, Orekhov PS, Kholina EG, Zhmurov AA, Ataullakhanov FI, Kovalenko IB, Gudimchuk NB. Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability. PLoS Comput Biol 2019; 15:e1007327. [PMID: 31469822 PMCID: PMC6742422 DOI: 10.1371/journal.pcbi.1007327] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 09/12/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022] Open
Abstract
Thirteen tubulin protofilaments, made of αβ-tubulin heterodimers, interact laterally to produce cytoskeletal microtubules. Microtubules exhibit the striking property of dynamic instability, manifested in their intermittent growth and shrinkage at both ends. This behavior is key to many cellular processes, such as cell division, migration, maintenance of cell shape, etc. Although assembly and disassembly of microtubules is known to be linked to hydrolysis of a guanosine triphosphate molecule in the pocket of β-tubulin, detailed mechanistic understanding of corresponding conformational changes is still lacking. Here we take advantage of the recent generation of in-microtubule structures of tubulin to examine the properties of protofilaments, which serve as important microtubule assembly and disassembly intermediates. We find that initially straight tubulin protofilaments, relax to similar non-radially curved and slightly twisted conformations. Our analysis further suggests that guanosine triphosphate hydrolysis primarily affects the flexibility and conformation of the inter-dimer interface, without a strong impact on the shape or flexibility of αβ-heterodimer. Inter-dimer interfaces are significantly more flexible compared to intra-dimer interfaces. We argue that such a difference in flexibility could be key for distinct stability of the plus and minus microtubule ends. The higher flexibility of the inter-dimer interface may have implications for development of pulling force by curving tubulin protofilaments during microtubule disassembly, a process of major importance for chromosome motions in mitosis.
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Affiliation(s)
| | - Philipp S. Orekhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | | | - Artem A. Zhmurov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | - Fazoil I. Ataullakhanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya B. Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Sechenov University, Moscow, Russia
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow, Russia
- Astrakhan State University, Astrakhan, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
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11
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Kelley AR, Bach SB, Perry G. Analysis of post-translational modifications in Alzheimer's disease by mass spectrometry. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2040-2047. [DOI: 10.1016/j.bbadis.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/19/2018] [Accepted: 11/04/2018] [Indexed: 01/09/2023]
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12
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Igaev M, Grubmüller H. Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit. eLife 2018; 7:34353. [PMID: 29652248 PMCID: PMC5945277 DOI: 10.7554/elife.34353] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/12/2018] [Indexed: 11/24/2022] Open
Abstract
Microtubules (MTs) are key components of the cytoskeleton and play a central role in cell division and development. MT assembly is known to be associated with a structural change in αβ-tubulin dimers from kinked to straight conformations. How GTP binding renders individual dimers polymerization-competent, however, is still unclear. Here, we have characterized the conformational dynamics and energetics of unassembled tubulin using atomistic molecular dynamics and free energy calculations. Contrary to existing allosteric and lattice models, we find that GTP-tubulin favors a broad range of almost isoenergetic curvatures, whereas GDP-tubulin has a much lower bending flexibility. Moreover, irrespective of the bound nucleotide and curvature, two conformational states exist differing in location of the anchor point connecting the monomers that affects tubulin bending, with one state being strongly favored in solution. Our findings suggest a new combined model in which MTs incorporate and stabilize flexible GTP-dimers with a specific anchor point state.
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Affiliation(s)
- Maxim Igaev
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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13
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Natarajan K, Mohan J, Senapati S. Relating nucleotide-dependent conformational changes in free tubulin dimers to tubulin assembly. Biopolymers 2016; 99:282-91. [PMID: 23426572 DOI: 10.1002/bip.22153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/29/2012] [Indexed: 11/07/2022]
Abstract
The complex dynamic behavior of microtubules (MTs) is believed to be primarily due to the αβ-tubulin dimer architecture and its intrinsic GTPase activity. Hence, a detailed knowledge of the conformational variations of isolated α-GTP-β-GTP- and α-GTP-β-GDP-tubulin dimers in solution and their implications to interdimer interactions and stability is directly relevant to understand the MT dynamics. An attempt has been made here by combining molecular dynamics (MD) simulations and protein-protein docking studies that unravels key structural features of tubulin dimer in different nucleotide states and correlates their association to tubulin assembly. Results from simulations suggest that tubulin dimers and oligomers attain curved conformations in both GTP and GDP states. Results also indicate that the tubulin C-terminal domain and the nucleotide state are closely linked. Protein-protein docking in combination with MD simulations suggest that the GTP-tubulin dimers engage in relatively stronger interdimer interactions even though the interdimer interfaces are bent in both GTP and GDP tubulin complexes, providing valuable insights on in vitro finding that GTP-tubulin is a better assembly candidate than GDP-tubulin during the MT nucleation and elongation processes.
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Affiliation(s)
- Kathiresan Natarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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14
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Churchill CDM, Klobukowski M, Tuszynski JA. Elucidating the mechanism of action of the clinically approved taxanes: a comprehensive comparison of local and allosteric effects. Chem Biol Drug Des 2015; 86:1253-66. [PMID: 26032329 DOI: 10.1111/cbdd.12595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/26/2022]
Abstract
The clinically approved taxanes (paclitaxel, docetaxel and cabazitaxel) target the tubulin protein in microtubules. Despite the clinical success of these agents, the mechanism of action of this class of drugs remains elusive, making rational design of taxanes difficult. Molecular dynamics simulations of these three taxanes with the αβ-tubulin heterodimer examine the similarities and differences in the effects of the drugs on tubulin, probing both local and allosteric effects. Despite their structural similarity, the drugs adopt different conformations in the binding site on β-tubulin. The taxanes similarly increase the helical character of α- and β-tubulins. No correlations are found between microtubule assembly and (i) binding affinity or (ii) the role of the M-loop in enhancing lateral contacts. Instead, changes in intra- and interdimer longitudinal contacts are indicative of the mechanism of action of the taxanes. We find β:H1-S1', and more importantly β:H9 and β:H10, play a role translating the effect of local drug binding in β-tubulin to an allosteric effect in α-tubulin and propose that the displacement of these secondary structures towards α-tubulin may be used as a predictor of the effect of taxanes on the tubulin heterodimers in rational drug design approaches.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.,Department of Physics, University of Alberta, 4-181 CCIS, Edmonton, AB, T6G 2E1, Canada
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15
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Designing and Testing of Novel Taxanes to Probe the Highly Complex Mechanisms by Which Taxanes Bind to Microtubules and Cause Cytotoxicity to Cancer Cells. PLoS One 2015; 10:e0129168. [PMID: 26052950 PMCID: PMC4460180 DOI: 10.1371/journal.pone.0129168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022] Open
Abstract
Our previous work identified an intermediate binding site for taxanes in the microtubule nanopore. The goal of this study was to test derivatives of paclitaxel designed to bind to this intermediate site differentially depending on the isotype of β-tubulin. Since β-tubulin isotypes have tissue-dependent expression--specifically, the βIII isotype is very abundant in aggressive tumors and much less common in normal tissues--this is expected to lead to tubulin targeted drugs that are more efficacious and have less side effects. Seven derivatives of paclitaxel were designed and four of these were amenable for synthesis in sufficient purity and yield for further testing in breast cancer model cell lines. None of the derivatives studied were superior to currently used taxanes, however computer simulations provided insights into the activity of the derivatives. Our results suggest that neither binding to the intermediate binding site nor the final binding site is sufficient to explain the activities of the derivative taxanes studied. These findings highlight the need to iteratively improve on the design of taxanes based on their activity in model systems. Knowledge gained on the ability of the engineered drugs to bind to targets and bring about activity in a predictable manner is a step towards personalizing therapies.
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16
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Burns KM, Sarpe V, Wagenbach M, Wordeman L, Schriemer DC. HX-MS2 for high performance conformational analysis of complex protein states. Protein Sci 2015; 24:1313-24. [PMID: 26009873 DOI: 10.1002/pro.2707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/05/2015] [Accepted: 05/14/2015] [Indexed: 01/15/2023]
Abstract
Water-mediated hydrogen exchange (HX) processes involving the protein main chain are sensitive to structural dynamics and molecular interactions. Measuring deuterium uptake in amide bonds provides information on conformational states, structural transitions and binding events. Increasingly, deuterium levels are measured by mass spectrometry (MS) from proteolytically generated peptide fragments of large molecular systems. However, this bottom-up method has limited spectral capacity and requires a burdensome manual validation exercise, both of which restrict analysis of protein systems to generally less than 150 kDa. In this study, we present a bottom-up HX-MS(2) method that improves peptide identification rates, localizes high-quality HX data and simplifies validation. The method combines a new peptide scoring algorithm (WUF, weighted unique fragment) with data-independent acquisition of peptide fragmentation data. Scoring incorporates the validation process and emphasizes identification accuracy. The HX-MS(2) method is illustrated using data from a conformational analysis of microtubules treated with dimeric kinesin MCAK. When compared to a conventional Mascot-driven HX-MS method, HX-MS(2) produces two-fold higher α/β-tubulin sequence depth at a peptide utilization rate of 74%. A Mascot approach delivers a utilization rate of 44%. The WUF score can be constrained by false utilization rate (FUR) calculations to return utilization values exceeding 90% without serious data loss, indicating that automated validation should be possible. The HX-MS(2) data confirm that N-terminal MCAK domains anchor kinesin force generation in kinesin-mediated depolymerization, while the C-terminal tails regulate MCAK-tubulin interactions.
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Affiliation(s)
- Kyle M Burns
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Mike Wagenbach
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, 98195-7290
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, 98195-7290
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
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17
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Statistical mechanics provides novel insights into microtubule stability and mechanism of shrinkage. PLoS Comput Biol 2015; 11:e1004099. [PMID: 25692909 PMCID: PMC4333834 DOI: 10.1371/journal.pcbi.1004099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/21/2014] [Indexed: 01/11/2023] Open
Abstract
Microtubules are nano-machines that grow and shrink stochastically, making use of the coupling between chemical kinetics and mechanics of its constituent protofilaments (PFs). We investigate the stability and shrinkage of microtubules taking into account inter-protofilament interactions and bending interactions of intrinsically curved PFs. Computing the free energy as a function of PF tip position, we show that the competition between curvature energy, inter-PF interaction energy and entropy leads to a rich landscape with a series of minima that repeat over a length-scale determined by the intrinsic curvature. Computing Langevin dynamics of the tip through the landscape and accounting for depolymerization, we calculate the average unzippering and shrinkage velocities of GDP protofilaments and compare them with the experimentally known results. Our analysis predicts that the strength of the inter-PF interaction (E(s)(m)) has to be comparable to the strength of the curvature energy (E(b)(m)) such that E(s)(m) - E(b)(m) ≈ 1kBT, and questions the prevalent notion that unzippering results from the domination of bending energy of curved GDP PFs. Our work demonstrates how the shape of the free energy landscape is crucial in explaining the mechanism of MT shrinkage where the unzippered PFs will fluctuate in a set of partially peeled off states and subunit dissociation will reduce the length.
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18
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Negi AS, Gautam Y, Alam S, Chanda D, Luqman S, Sarkar J, Khan F, Konwar R. Natural antitubulin agents: importance of 3,4,5-trimethoxyphenyl fragment. Bioorg Med Chem 2014; 23:373-89. [PMID: 25564377 DOI: 10.1016/j.bmc.2014.12.027] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 01/29/2023]
Abstract
Microtubules are polar cytoskeletal filaments assembled from head-to-tail and comprised of lateral associations of α/β-tubulin heterodimers that play key role in various cellular processes. Because of their vital role in mitosis and various other cellular processes, microtubules have been attractive targets for several disease conditions and especially for cancer. Antitubulin is the most successful class of antimitotic agents in cancer chemotherapeutics. The target recognition of antimitotic agents as a ligand is not much explored so far. However, 3,4,5-trimethoxyphenyl fragment has been much highlighted and discussed in such type of interactions. In this review, some of the most important naturally occurring antimitotic agents and their interactions with microtubules are discussed with a special emphasis on the role of 3,4,5-trimethoxyphenyl unit. At last, some emerging naturally occurring antimitotic agents have also been tabulated.
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Affiliation(s)
- Arvind S Negi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India.
| | - Yashveer Gautam
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India
| | - Sarfaraz Alam
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India
| | - Debabrata Chanda
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India
| | - Suaib Luqman
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India
| | - Jayanta Sarkar
- CSIR-Central Drug Research Institute (CSIR-CDRI), B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Feroz Khan
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Kukrail Picnic Spot Road, PO CIMAP, Lucknow 226015, India
| | - Rituraj Konwar
- CSIR-Central Drug Research Institute (CSIR-CDRI), B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
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19
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Nucleotide exchange in dimeric MCAK induces longitudinal and lateral stress at microtubule ends to support depolymerization. Structure 2014; 22:1173-1183. [PMID: 25066134 DOI: 10.1016/j.str.2014.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Members of the kinesin-13 subfamily use motor domains in an unconventional fashion to initiate microtubule (MT) depolymerization at MT ends, suggesting unique conformational transitions for lattice engagement, end adaptation, or both. Using hydrogen-deuterium exchange and electron microscopy, we explored conformational changes in free dimeric mitotic centromere-associated kinesin (MCAK) and when bound to a depolymerization intermediate. ATP hydrolysis relaxes the conformation of the dimer, notably in the neck and N-terminal domain. Exchanging ADP in dimeric MCAK with ATP at the MT plus end induces outward curvature in α/β-tubulin, accompanied by a restructuring of the MCAK neck and N terminus, as it returns to a closed state. Reestablishing a closed dimer induces lateral separation of paired tubulin dimers, which may assist in depolymerization. Thus, full-length ADP-MCAK transitions from an open diffusion-competent configuration to a closed state upon plus end-mediated nucleotide exchange, which is mediated by conformational changes in the N-terminal domains of the dimer.
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20
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Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP. The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery. PLoS Comput Biol 2014; 10:e1003464. [PMID: 24516374 PMCID: PMC3916224 DOI: 10.1371/journal.pcbi.1003464] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
αβ-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αβ-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol) and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αβ-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αβ-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.
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Affiliation(s)
- Lili X. Peng
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Monica T. Hsu
- Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Massimiliano Bonomi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - David A. Agard
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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21
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Risinger AL, Li J, Bennett MJ, Rohena CC, Peng J, Schriemer DC, Mooberry SL. Taccalonolide binding to tubulin imparts microtubule stability and potent in vivo activity. Cancer Res 2013; 73:6780-92. [PMID: 24048820 DOI: 10.1158/0008-5472.can-13-1346] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The taccalonolides are highly acetylated steroids that stabilize cellular microtubules and overcome multiple mechanisms of taxane resistance. Recently, two potent taccalonolides, AF and AJ, were identified that bind to tubulin directly and enhance microtubule polymerization. Extensive studies were conducted to characterize these new taccalonolides. AF and AJ caused aberrant mitotic spindles and bundling of interphase microtubules that differed from the effects of either paclitaxel or laulimalide. AJ also distinctly affected microtubule polymerization in that it enhanced the rate and extent of polymerization in the absence of any noticeable effect on microtubule nucleation. In addition, the resulting microtubules were found to be profoundly cold stable. These data, along with studies showing synergistic antiproliferative effects between AJ and either paclitaxel or laulimalide, suggest a distinct binding site. Direct binding studies demonstrated that AJ could not be displaced from microtubules by paclitaxel, laulimalide, or denaturing conditions, suggesting irreversible binding of AJ to microtubules. Mass spectrometry confirmed a covalent interaction of AJ with a peptide of β-tubulin containing the cyclostreptin-binding sites. Importantly, AJ imparts strong inter-protofilament stability in a manner different from other microtubule stabilizers that covalently bind to tubulin, consistent with the distinct effects of the taccalonolides as compared with other stabilizers. AF was found to be a potent and effective antitumor agent that caused tumor regression in the MDA-MB-231 breast cancer xenograft model. The antitumor efficacy of some taccalonolides, which stabilize microtubules in a manner different from other microtubule stabilizers, provides the impetus to explore the therapeutic potential of this site.
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Affiliation(s)
- A L Risinger
- Authors' Affiliations: Departments of Pharmacology, Medicine, and Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas; and Department of Biochemistry & Molecular Biology, University of Calgary, Alberta, Canada
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22
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Quiniou E, Guichard P, Perahia D, Marco S, Mouawad L. An atomistic view of microtubule stabilization by GTP. Structure 2013; 21:833-43. [PMID: 23623730 DOI: 10.1016/j.str.2013.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/08/2013] [Accepted: 03/08/2013] [Indexed: 11/27/2022]
Abstract
A microtubule is a dynamic system formed of αβ-tubulins. The presence of nonhydrolyzable guanosine-5'-triphosphate (GTP)/guanosine diphosphate (GDP) on the β-tubulins provokes microtubule polymerization/depolymerization. Despite the large number of experimental studies of this dynamical process, its mechanism is still unclear. To provide insights into this mechanism we studied the first depolymerization steps of GDP/GTP-bound microtubules by normal-mode analysis with the all-atom model. We also constructed a depolymerizing microtubule and compared it to cryo-electron microscopy tomograms (cyro-ET). The results show that during depolymerization, the protofilaments not only curve but twist to weaken their lateral interactions. These interactions are stabilized by GTP, but not evenly. Not all of the interface residues are of equal importance: five of them, belonging to the H2-S3 loop, play a special role; acting as a lock whose key is the γ-phosphate of GTP. Sequence alignments of several tubulins confirm the importance of these residues.
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Affiliation(s)
- Eric Quiniou
- Institut Curie, Centre de Recherche, U759, Bât. 112, Centre Universitaire, 91405 Orsay Cedex, France
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23
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Ludueña RF. A Hypothesis on the Origin and Evolution of Tubulin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:41-185. [DOI: 10.1016/b978-0-12-407699-0.00002-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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24
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Burns KM, Rey M, Baker CAH, Schriemer DC. Platform dependencies in bottom-up hydrogen/deuterium exchange mass spectrometry. Mol Cell Proteomics 2012. [PMID: 23197788 DOI: 10.1074/mcp.m112.023770] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS) platforms that consisted of a FT-MS and a high-resolution QTOF mass spectrometer, each with matched front-end fluidic systems. Digests of proteins spanning a 20-110 kDa range were deuterated to equilibrium, and figures-of-merit for a typical bottom-up (HDX-MS) experiment were compared for each platform. The Orbitrap Velos identified 64% more peptides than the 5600 QTOF, with a 42% overlap between the two systems, independent of protein size. Precision in deuterium measurements using the Orbitrap marginally exceeded that of the QTOF, depending on the Orbitrap resolution setting. However, the unique nature of FT-MS data generates situations where deuteration measurements can be inaccurate, because of destructive interference arising from mismatches in elemental mass defects. This is shown through the analysis of the peptides common to both platforms, where deuteration values can be as low as 35% of the expected values, depending on FT-MS resolution, peptide length and charge state. These findings are supported by simulations of Orbitrap transients, and highlight that caution should be exercised in deriving centroid mass values from FT transients that do not support baseline separation of the full isotopic composition.
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Affiliation(s)
- Kyle M Burns
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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25
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Steric and allosteric factors prevent simultaneous binding of transferrin-binding proteins A and B to transferrin. Biochem J 2012; 444:189-97. [DOI: 10.1042/bj20112133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to acquire iron directly from host Tf (transferrin) is an adaptation common to important bacterial pathogens belonging to the Pasteurellaceae, Moraxellaceae and Neisseriaceae families. A surface receptor comprising an integral outer membrane protein, TbpA (Tf-binding protein A), and a surface-exposed lipoprotein, TbpB (Tf-binding protein B), mediates the iron acquisition process. TbpB is thought to extend from the cell surface for capture of Tf to initiate the process and deliver Tf to TbpA. TbpA functions as a gated channel for the passage of iron into the periplasm. In the present study we have mapped the effect of TbpA from Actinobacillus pleuropneumoniae on pTf (porcine Tf) using H/DX-MS (hydrogen/deuterium exchange coupled to MS) and compare it with a previously determined binding site for TbpB. The proposed TbpA footprint is adjacent to and potentially overlapping the TbpB-binding site, and induces a structural instability in the TbpB site. This suggests that simultaneous binding to pTf by both receptors would be hindered. We demonstrate that a recombinant TbpB lacking a portion of its anchor peptide is unable to form a stable ternary TbpA–pTf–TbpB complex. This truncated TbpB does not bind to a preformed Tf–TbpA complex, and TbpA removes pTf from a preformed Tf–TbpB complex. Thus the results of the present study support a model whereby TbpB ‘hands-off’ pTf to TbpA, which completes the iron removal and transport process.
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26
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André JR, Clément MJ, Adjadj E, Toma F, Curmi PA, Manivet P. The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament. J Comput Aided Mol Des 2012; 26:397-407. [PMID: 22527959 DOI: 10.1007/s10822-012-9566-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/20/2012] [Indexed: 12/20/2022]
Abstract
The dynamics of microtubules is essential for many microtubule-dependent cellular functions such as the mitosis. It has been recognized for a long time that GTP hydrolysis in αβ-tubulin polymers plays a critical role in this dynamics. However, the effects of the changes in the nature of the guanosine nucleotide at the E-site in β-tubulin on microtubule structure and stability are still not well understood. In the present work, we performed all-atom molecular dynamics simulations of a αβα-tubulin heterotrimer harboring a guanosine nucleotide in three different states at the E-site: GTP, GDP-Pi and GDP. We found that changes in the nucleotide state is associated with significant conformational variations at the α-tubulin N- and β-tubulin M-loops which impact the interactions between tubulin protofilaments. The results also show that GTP hydrolysis reduces αβ-tubulin interdimer contacts in favor of intradimer interface. From an atomistic point view, we propose a role for α-tubulin glutamate residue 254 in catalytic magnesium coordination and identified a water molecule in the nucleotide binding pocket which is most probably required for nucleotide hydrolysis. Finally, the results are discussed with reference to the role of taxol in microtubule stability and the recent tubulin-sT2R crystal structures.
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Affiliation(s)
- Joseph R André
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 829, Evry, France
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27
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Percy AJ, Rey M, Burns KM, Schriemer DC. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal Chim Acta 2012; 721:7-21. [PMID: 22405295 DOI: 10.1016/j.aca.2012.01.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure-function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure-function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in "dynamic topography" and thus represents a powerful means of monitoring protein structure-function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.
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Affiliation(s)
- Andrew J Percy
- Department of Chemistry, University of Calgary, Alberta, Canada
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28
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Freedman H, Luchko T, Luduena RF, Tuszynski JA. Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface. Proteins 2011; 79:2968-82. [PMID: 21905119 DOI: 10.1002/prot.23155] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/27/2011] [Accepted: 07/17/2011] [Indexed: 11/10/2022]
Abstract
Tubulin, an α/β heterodimer, has had most of its 3D structure analyzed; however, the carboxy (C)-termini remain elusive. Importantly, the C-termini play critical roles in regulating microtubule structure and function. They are sites of most of the post-translational modifications of tubulin and interaction sites with molecular motors and microtubule-associated proteins. Simulated annealing was used in our molecular dynamics modeling to predict the interactions of the C-terminal tails with the tubulin dimer. We examined differences in their flexibility, interactions with the body of tubulin, and the existence of structural motifs. We found that the α-tubulin tail interacts with the H11 helix of β-tubulin, and the β-tubulin tail interacts with the H11 helix of α-tubulin. Tail domains and H10/B9 loops interact with each other and compete for interactions with positively-charged residues of the H11 helix on the neighboring monomer. In a simulation in which α-tubulin's H10/B9 loop switches on sub-nanosecond intervals between interactions with the C-terminal tail of α-tubulin and the H11 helix of β-tubulin, the intermediate domain of α-tubulin showed more fluctuations compared to those in the other simulations, indicating that tail domains may cause shifts in the position of this domain. This suggests that C-termini may affect the conformation of the tubulin dimer which may explain their essential function in microtubule formation and effects on ligand binding to microtubules. Our modeling also provides evidence for a disordered-helical/helical double-state system of the T3/H3 region of the microtubule, which could be linked to depolymerization following GTP hydrolysis.
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Affiliation(s)
- Holly Freedman
- CCMAR, FCT, University of Algarve, Campus de Gambelas, Faro, Portugal
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29
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Hinow P, Rezania V, Lopus M, Jordan MA, Tuszyński JA. Modeling the effects of drug binding on the dynamic instability of microtubules. Phys Biol 2011; 8:056004. [PMID: 21836336 DOI: 10.1088/1478-3975/8/5/056004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We propose a stochastic model that accounts for the growth, catastrophe and rescue processes of steady-state microtubules assembled from MAP-free tubulin in the possible presence of a microtubule-associated drug. As an example of the latter, we both experimentally and theoretically study the perturbation of microtubule dynamic instability by S-methyl-D-DM1, a synthetic derivative of the microtubule-targeted agent maytansine and a potential anticancer agent. Our model predicts that among the drugs that act locally at the microtubule tip, primary inhibition of the loss of GDP tubulin results in stronger damping of microtubule dynamics than inhibition of GTP tubulin addition. On the other hand, drugs whose action occurs in the interior of the microtubule need to be present in much higher concentrations to have visible effects.
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Affiliation(s)
- Peter Hinow
- Department of Mathematical Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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Grafmüller A, Voth GA. Intrinsic bending of microtubule protofilaments. Structure 2011; 19:409-17. [PMID: 21397191 DOI: 10.1016/j.str.2010.12.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 01/05/2023]
Abstract
The complex polymerization dynamics of the microtubule (MT) plus end are closely linked to the hydrolysis of the GTP nucleotide bound to the β-tubulin. The destabilization is thought to be associated with the conformational change of the tubulin dimers from the straight conformation in the MT lattice to a curved conformation. It remains under debate whether this transformation is directly related to the nucleotide state, or a consequence of the longitudinal or lateral contacts in the MT lattice. Here, we present large-scale atomistic simulations of short tubulin protofilaments with both nucleotide states, starting from both extreme conformations. Our simulations indicate that both interdimer and intradimer contacts in both GDP and GTP-bound tubulin dimers and protofilaments in solution bend. There are no observable differences between the mesoscopic properties of the contacts in GTP and GDP-bound tubulin or the intradime and interdimer interfaces.
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Affiliation(s)
- Andrea Grafmüller
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA
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31
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Sperry JB, Smith CL, Caparon MG, Ellenberger T, Gross ML. Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes. Biochemistry 2011; 50:4038-45. [PMID: 21466233 PMCID: PMC3096607 DOI: 10.1021/bi200244k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein--protein interactions are ubiquitous and essential for most biological processes. Although new proteomic technologies have generated large catalogs of interacting proteins, considerably less is known about these interactions at the molecular level, information that would aid in predicting protein interactions, designing therapeutics to alter these interactions, and understanding the effects of disease-producing mutations. Here we describe mapping the interacting surfaces of the bacterial toxin SPN (Streptococcus pyogenes NAD(+) hydrolase) in complex with its antitoxin IFS (immunity factor for SPN) by using hydrogen-deuterium amide exchange and electrospray ionization mass spectrometry. This approach affords data in a relatively short time for small amounts of protein, typically 5-7 pmol per analysis. The results show a good correspondence with a recently determined crystal structure of the IFS--SPN complex but additionally provide strong evidence for a folding transition of the IFS protein that accompanies its binding to SPN. The outcome shows that mass-based chemical footprinting of protein interaction surfaces can provide information about protein dynamics that is not easily obtained by other methods and can potentially be applied to large, multiprotein complexes that are out of range for most solution-based methods of biophysical analysis.
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Affiliation(s)
- Justin B. Sperry
- Analytical Research and Development, Pfizer Inc., Chesterfield, MO 63017
| | - Craig L. Smith
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Michael G. Caparon
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO 63110
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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Khrapunovich-Baine M, Menon V, Yang CPH, Northcote PT, Miller JH, Angeletti RH, Fiser A, Horwitz SB, Xiao H. Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation. J Biol Chem 2011; 286:11765-78. [PMID: 21245138 DOI: 10.1074/jbc.m110.162214] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.
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Affiliation(s)
- Marina Khrapunovich-Baine
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Barbier P, Dorléans A, Devred F, Sanz L, Allegro D, Alfonso C, Knossow M, Peyrot V, Andreu JM. Stathmin and interfacial microtubule inhibitors recognize a naturally curved conformation of tubulin dimers. J Biol Chem 2010; 285:31672-81. [PMID: 20675373 PMCID: PMC2951239 DOI: 10.1074/jbc.m110.141929] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Tubulin is able to switch between a straight microtubule-like structure and a curved structure in complex with the stathmin-like domain of the RB3 protein (T(2)RB3). GTP hydrolysis following microtubule assembly induces protofilament curvature and disassembly. The conformation of the labile tubulin heterodimers is unknown. One important question is whether free GDP-tubulin dimers are straightened by GTP binding or if GTP-tubulin is also curved and switches into a straight conformation upon assembly. We have obtained insight into the bending flexibility of tubulin by analyzing the interplay of tubulin-stathmin association with the binding of several small molecule inhibitors to the colchicine domain at the tubulin intradimer interface, combining structural and biochemical approaches. The crystal structures of T(2)RB3 complexes with the chiral R and S isomers of ethyl-5-amino-2-methyl-1,2-dihydro-3-phenylpyrido[3,4-b]pyrazin-7-yl-carbamate, show that their binding site overlaps with colchicine ring A and that both complexes have the same curvature as unliganded T(2)RB3. The binding of these ligands is incompatible with a straight tubulin structure in microtubules. Analytical ultracentrifugation and binding measurements show that tubulin-stathmin associations (T(2)RB3, T(2)Stath) and binding of ligands (R, S, TN-16, or the colchicine analogue MTC) are thermodynamically independent from one another, irrespective of tubulin being bound to GTP or GDP. The fact that the interfacial ligands bind equally well to tubulin dimers or stathmin complexes supports a bent conformation of the free tubulin dimers. It is tempting to speculate that stathmin evolved to recognize curved structures in unassembled and disassembling tubulin, thus regulating microtubule assembly.
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Affiliation(s)
- Pascale Barbier
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France, , To whom correspondence may be addressed. E-mail:
| | - Audrey Dorléans
- the Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, 91198 Gif sur Yvette, France, and
| | - Francois Devred
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Laura Sanz
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Diane Allegro
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Carlos Alfonso
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Marcel Knossow
- the Laboratoire d'Enzymologie et Biochimie Structurales, CNRS UPR3082, 91198 Gif sur Yvette, France, and
| | - Vincent Peyrot
- From INSERM UMR 911, Centre de Recherche en Oncologie Biologique et Oncopharmacologie, Aix-Marseille Université, Faculté de Pharmacie, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jose M. Andreu
- the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, To whom correspondence may be addressed. E-mail:
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Bennett MJ, Barakat K, Huzil JT, Tuszynski J, Schriemer DC. Discovery and Characterization of the Laulimalide-Microtubule Binding Mode by Mass Shift Perturbation Mapping. ACTA ACUST UNITED AC 2010; 17:725-34. [DOI: 10.1016/j.chembiol.2010.05.019] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 05/06/2010] [Accepted: 05/10/2010] [Indexed: 01/25/2023]
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Martín-Galiano AJ, Buey RM, Cabezas M, Andreu JM. Mapping flexibility and the assembly switch of cell division protein FtsZ by computational and mutational approaches. J Biol Chem 2010; 285:22554-65. [PMID: 20472561 DOI: 10.1074/jbc.m110.117127] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal beta-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723.
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Affiliation(s)
- Antonio J Martín-Galiano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
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Andreu JM, Schaffner-Barbero C, Huecas S, Alonso D, Lopez-Rodriguez ML, Ruiz-Avila LB, Núñez-Ramírez R, Llorca O, Martín-Galiano AJ. The antibacterial cell division inhibitor PC190723 is an FtsZ polymer-stabilizing agent that induces filament assembly and condensation. J Biol Chem 2010; 285:14239-46. [PMID: 20212044 DOI: 10.1074/jbc.m109.094722] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cell division protein FtsZ can form single-stranded filaments with a cooperative behavior by self-switching assembly. Subsequent condensation and bending of FtsZ filaments are important for the formation and constriction of the cytokinetic ring. PC190723 is an effective bactericidal cell division inhibitor that targets FtsZ in the pathogen Staphylococcus aureus and Bacillus subtilis and does not affect Escherichia coli cells, which apparently binds to a zone equivalent to the binding site of the antitumor drug taxol in tubulin (Haydon, D. J., Stokes, N. R., Ure, R., Galbraith, G., Bennett, J. M., Brown, D. R., Baker, P. J., Barynin, V. V., Rice, D. W., Sedelnikova, S. E., Heal, J. R., Sheridan, J. M., Aiwale, S. T., Chauhan, P. K., Srivastava, A., Taneja, A., Collins, I., Errington, J., and Czaplewski, L. G. (2008) Science 312, 1673-1675). We have found that the benzamide derivative PC190723 is an FtsZ polymer-stabilizing agent. PC190723 induced nucleated assembly of Bs-FtsZ into single-stranded coiled protofilaments and polymorphic condensates, including bundles, coils, and toroids, whose formation could be modulated with different solution conditions. Under conditions for reversible assembly of Bs-FtsZ, PC190723 binding reduced the GTPase activity and induced the formation of straight bundles and ribbons, which was also observed with Sa-FtsZ but not with nonsusceptible Ec-FtsZ. The fragment 2,6-difluoro-3-methoxybenzamide also induced Bs-FtsZ bundling. We propose that polymer stabilization by PC190723 suppresses in vivo FtsZ polymer dynamics and bacterial division. The biochemical action of PC190723 on FtsZ parallels that of the microtubule-stabilizing agent taxol on the eukaryotic structural homologue tubulin. Both taxol and PC190723 stabilize polymers against disassembly by preferential binding to each assembled protein. It is yet to be investigated whether both ligands target structurally related assembly switches.
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Affiliation(s)
- José M Andreu
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, Spain.
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Miller LM, Xiao H, Burd B, Horwitz SB, Angeletti RH, Verdier-Pinard P. Methods in tubulin proteomics. Methods Cell Biol 2010; 95:105-26. [PMID: 20466132 DOI: 10.1016/s0091-679x(10)95007-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
New analytical methods are needed for the successful outcome of experiments aimed at characterizing mechanisms of microtubule dynamics and at understanding the effects of drugs on microtubules. The identification of tubulin isotypes and of regions of the microtubule involved in drug interactions has been advanced by proteomic methodologies. The diversity of tubulin sequences and posttranslational modifications (PTMs) can generate a complex mixture of heterodimers with unique molecular dynamics driving specific functions. Mass spectrometry (MS)-based approaches have been developed, and in combination with chromatographic and/or electrophoretic separation of tubulin polypeptides or peptides, they have contributed to our understanding of tubulin proteomics. We present protocols that we have used for the analysis of tubulin isotypes and PTMs present in tubulin isolated from cells in culture or tissues and for the identification of tubulin regions altered by microtubule-stabilizing agents. Tubulin proteomics complements structural and computer modeling information for a high-resolution view of microtubule dynamics and its alteration by drugs. These methodologies will help in providing insights into tubulin isotype-specific functions and in the design of drugs targeting either all tubulin heterodimers indiscriminately or only those containing specific isotypes.
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Affiliation(s)
- Leah M Miller
- Laboratory of Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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