1
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Kurnikov IV, Pereyaslavets L, Kamath G, Sakipov SN, Voronina E, Butin O, Illarionov A, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Ivahnenko I, Chen Y, Lock CB, Levitt M, Kornberg RD, Fain B. Neural Network Corrections to Intermolecular Interaction Terms of a Molecular Force Field Capture Nuclear Quantum Effects in Calculations of Liquid Thermodynamic Properties. J Chem Theory Comput 2024; 20:1347-1357. [PMID: 38240485 PMCID: PMC11042917 DOI: 10.1021/acs.jctc.3c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We incorporate nuclear quantum effects (NQE) in condensed matter simulations by introducing short-range neural network (NN) corrections to the ab initio fitted molecular force field ARROW. Force field NN corrections are fitted to average interaction energies and forces of molecular dimers, which are simulated using the Path Integral Molecular Dynamics (PIMD) technique with restrained centroid positions. The NN-corrected force field allows reproduction of the NQE for computed liquid water and methane properties such as density, radial distribution function (RDF), heat of evaporation (HVAP), and solvation free energy. Accounting for NQE through molecular force field corrections circumvents the need for explicit computationally expensive PIMD simulations in accurate calculations of the properties of chemical and biological systems. The accuracy and locality of pairwise NN NQE corrections indicate that this approach could be applicable to complex heterogeneous systems, such as proteins.
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Affiliation(s)
- Igor V Kurnikov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ganesh Kamath
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan N Sakipov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Alexey Illarionov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ilya Ivahnenko
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - YuChun Chen
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher B Lock
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Boris Fain
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
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2
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Kamath G, Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, Chen Y, Kornberg RD, Levitt M, Fain B. Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions. J Phys Chem A 2024; 128:807-812. [PMID: 38232765 PMCID: PMC11008955 DOI: 10.1021/acs.jpca.3c07598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
We present a formalism of a neural network encoding bonded interactions in molecules. This intramolecular encoding is consistent with the models of intermolecular interactions previously designed by this group. Variants of the encoding fed into a corresponding neural network may be used to economically improve the representation of torsional degrees of freedom in any force field. We test the accuracy of the reproduction of the ab initio potential energy surface on a set of conformations of two dipeptides, methyl-capped ALA and ASP, in several scenarios. The encoding, either alone or in conjunction with an analytical potential, improves agreement with ab initio energies that are on par with those of other neural network-based potentials. Using the encoding and neural nets in tandem with an analytical model places the agreements firmly within "chemical accuracy" of ±0.5 kcal/mol.
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Affiliation(s)
- Ganesh Kamath
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Alexey Illarionov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan Sakipov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor V Kurnikov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov MSU, Skobeltsyn Institute of Nuclear Physics, Moscow 119991, Russia
| | - Ilya Ivahnenko
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Department of Physics, Lomonosov MSU, Moscow 119991, Russia
| | - Yevhen K Cherniavskyi
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher Lock
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Sean Greenslade
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - YuChun Chen
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Boris Fain
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
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3
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Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Kamath G, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, Sankaranarayanan SKRS, Kurnikova MG, Potoff J, Kornberg RD, Levitt M, Fain B. Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions. J Am Chem Soc 2023; 145:23620-23629. [PMID: 37856313 PMCID: PMC10623557 DOI: 10.1021/jacs.3c07628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 10/21/2023]
Abstract
A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.
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Affiliation(s)
- Alexey Illarionov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan Sakipov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor V. Kurnikov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ganesh Kamath
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Skobeltsyn Institute of Nuclear Physics, Moscow, 119991, Russia
| | - Ilya Ivahnenko
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Dept. of Physics, Moscow, 119991, Russia
| | - Yevhen K. Cherniavskyi
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher Lock
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Department
of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Sean Greenslade
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Subramanian KRS Sankaranarayanan
- Center
for Nanoscale Materials, Argonne National
Lab, Argonne, Illinois 604391, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States
| | - Maria G. Kurnikova
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jeffrey Potoff
- Department
of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Roger D. Kornberg
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Michael Levitt
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Boris Fain
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
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4
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Stepanov AV, Xie J, Zhu Q, Shen Z, Su W, Kuai L, Soll R, Rader C, Shaver G, Douthit L, Zhang D, Kalinin R, Fu X, Zhao Y, Qin T, Baran PS, Gabibov AG, Bushnell D, Neri D, Kornberg RD, Lerner RA. Control of the antitumour activity and specificity of CAR T cells via organic adapters covalently tethering the CAR to tumour cells. Nat Biomed Eng 2023:10.1038/s41551-023-01102-5. [PMID: 37798444 DOI: 10.1038/s41551-023-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/25/2023] [Indexed: 10/07/2023]
Abstract
On-target off-tumour toxicity limits the anticancer applicability of chimaeric antigen receptor (CAR) T cells. Here we show that the tumour-targeting specificity and activity of T cells with a CAR consisting of an antibody with a lysine residue that catalytically forms a reversible covalent bond with a 1,3-diketone hapten can be regulated by the concentration of a small-molecule adapter. This adapter selectively binds to the hapten and to a chosen tumour antigen via a small-molecule binder identified via a DNA-encoded library. The adapter therefore controls the formation of a covalent bond between the catalytic antibody and the hapten, as well as the tethering of the CAR T cells to the tumour cells, and hence the cytotoxicity and specificity of the cytotoxic T cells, as we show in vitro and in mice with prostate cancer xenografts. Such small-molecule switches of T-cell cytotoxicity and specificity via an antigen-independent 'universal' CAR may enhance the control and safety profile of CAR-based cellular immunotherapies.
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Affiliation(s)
- Alexey V Stepanov
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - Wenji Su
- WuXi AppTec Co., Ltd, Shanghai, China
| | | | | | - Christoph Rader
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Geramie Shaver
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Lacey Douthit
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ding Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Roman Kalinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Xiang Fu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yingying Zhao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Tian Qin
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - David Bushnell
- Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Roger D Kornberg
- Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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5
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Wang X, Wang Y, Liu S, Zhang Y, Xu K, Ji L, Kornberg RD, Zhang H. Class I histone deacetylase complex: Structure and functional correlates. Proc Natl Acad Sci U S A 2023; 120:e2307598120. [PMID: 37459529 PMCID: PMC10374167 DOI: 10.1073/pnas.2307598120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
The Schizosaccharomyces pombe Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of Clr6S alone and a cryo-EM map of Clr6S in complex with a nucleosome. The active center, revealed at near-atomic resolution, includes features important for catalysis-A water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail and is likely important for the function of the deacetylase, which acts at multiple sites in other histone tails.
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Affiliation(s)
- Xiao Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yannan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Simiao Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Ke Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Liting Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Roger D Kornberg
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Heqiao Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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6
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Lorch Y, Kornberg RD, Maier-Davis B. Role of the histone tails in histone octamer transfer. Nucleic Acids Res 2023; 51:3671-3678. [PMID: 36772826 PMCID: PMC10164550 DOI: 10.1093/nar/gkad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 02/12/2023] Open
Abstract
The exceptionally high positive charge of the histones, concentrated in the N- and C-terminal tails, is believed to contribute to the stability of the nucleosome by neutralizing the negative charge of the nucleosomal DNA. We find, on the contrary, that the high positive charge contributes to instability, performing an essential function in chromatin remodeling. We show that the tails are required for removal of the histone octamer by the RSC chromatin remodeling complex, and this function is not due to direct RSC-tail interaction. We also show that the tails are required for histone octamer transfer from nucleosomes to DNA, and this activity of the tails is a consequence of their positive charge. Thus, the histone tails, intrinsically disordered protein regions, perform a critical role in chromatin structure and transcription, unrelated to their well-known role in regulation through posttranscriptional modification.
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Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barbara Maier-Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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7
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Nawrocki G, Leontyev I, Sakipov S, Darkhovskiy M, Kurnikov I, Pereyaslavets L, Kamath G, Voronina E, Butin O, Illarionov A, Olevanov M, Kostikov A, Ivahnenko I, Patel DS, Sankaranarayanan SKRS, Kurnikova MG, Lock C, Crooks GE, Levitt M, Kornberg RD, Fain B. Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field. J Chem Theory Comput 2022; 18:7751-7763. [PMID: 36459593 PMCID: PMC9753910 DOI: 10.1021/acs.jctc.2c00930] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 12/03/2022]
Abstract
Protein-ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)─a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein-ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ∼0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.
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Affiliation(s)
- Grzegorz Nawrocki
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Igor Leontyev
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Serzhan Sakipov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | | | - Igor Kurnikov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | | | - Ganesh Kamath
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Ekaterina Voronina
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
- Faculty
of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Oleg Butin
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Alexey Illarionov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Michael Olevanov
- Faculty
of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | | | - Ilya Ivahnenko
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Dhilon S. Patel
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Subramanian K. R. S. Sankaranarayanan
- Center
for Nanoscale Materials, Argonne National
Lab, Lemont, Illinois 60439, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States
| | - Maria G. Kurnikova
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Christopher Lock
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
- Department
of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Gavin E. Crooks
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Michael Levitt
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Boris Fain
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
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8
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Wang L, Zhao L, Li Y, Ma P, Kornberg RD, Nie Y. Harnessing coronavirus spike proteins' binding affinity to ACE2 receptor through a novel baculovirus surface display system. Biochem Biophys Res Commun 2022; 606:23-28. [PMID: 35338855 PMCID: PMC8920473 DOI: 10.1016/j.bbrc.2022.03.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/28/2022] [Accepted: 03/13/2022] [Indexed: 11/22/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerging infectious disease currently spreading across the world. The spike (S) protein plays a key role in the receptor recognition and cell membrane fusion, making it an important target for developing vaccines, therapeutic antibodies and diagnosis. In this study, we constructed a baculovirus surface display system that efficiently presents both SARS-CoV and SARS-CoV-2 S proteins (including ectodomain, S1 subunit and receptor-binding-domain, RBD) on the surface of recombinant baculoviruses, utilizing transmembrane anchors from gp64 (signal peptide) and vesicular stomatitis virus (VSV). These recombinant baculoviruses were capable of transducing engineered HEK 293T cells overexpressing ACE2 receptors with significantly higher transduction efficiencies, indicating that S proteins displayed on baculovirus surface have antigenicity and can recognize and bind ACE2 receptors. Additionally, the transduction of SARS-CoV-2 S proteins can be inhibited by an antibody against the SARS-CoV-2 RBD. These results demonstrate that this baculovirus surface display system is a promising tool for developing antibodies, vaccines and recombinant protein production.
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Affiliation(s)
- Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixia Zhao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Roger D Kornberg
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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9
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Pereyaslavets L, Kamath G, Butin O, Illarionov A, Olevanov M, Kurnikov I, Sakipov S, Leontyev I, Voronina E, Gannon T, Nawrocki G, Darkhovskiy M, Ivahnenko I, Kostikov A, Scaranto J, Kurnikova MG, Banik S, Chan H, Sternberg MG, Sankaranarayanan SKRS, Crawford B, Potoff J, Levitt M, Kornberg RD, Fain B. Accurate determination of solvation free energies of neutral organic compounds from first principles. Nat Commun 2022; 13:414. [PMID: 35058472 PMCID: PMC8776904 DOI: 10.1038/s41467-022-28041-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/03/2022] [Indexed: 12/28/2022] Open
Abstract
The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools' computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.
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Affiliation(s)
| | - Ganesh Kamath
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | - Oleg Butin
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | - Michael Olevanov
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
- Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Igor Kurnikov
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | - Igor Leontyev
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | - Ekaterina Voronina
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
- Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tyler Gannon
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | | | | | | | - Jessica Scaranto
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Maria G Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Suvo Banik
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Henry Chan
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Michael G Sternberg
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
| | - Subramanian K R S Sankaranarayanan
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Brad Crawford
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffrey Potoff
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI, 48202, USA
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Boris Fain
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA.
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10
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Abstract
Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers.
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Affiliation(s)
- Andrew J Beel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Maia Azubel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
| | - Pierre-Jean Matteï
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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11
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Jagota M, Townshend RJL, Kang LW, Bushnell DA, Dror RO, Kornberg RD, Azubel M. Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy. Ultramicroscopy 2021; 227:113302. [PMID: 34062386 DOI: 10.1016/j.ultramic.2021.113302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/24/2023]
Abstract
A computational method was developed to recover the three-dimensional coordinates of gold nanoparticles specifically attached to a protein complex from tilt-pair images collected by electron microscopy. The program was tested on a simulated dataset and applied to a real dataset comprising tilt-pair images recorded by cryo electron microscopy of RNA polymerase II in a complex with four gold-labeled single-chain antibody fragments. The positions of the gold nanoparticles were determined, and comparison of the coordinates among the tetrameric particles revealed the range of motion within the protein complexes.
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Affiliation(s)
- Milind Jagota
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, Korea
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 2021; 372:984-989. [PMID: 34045355 PMCID: PMC8172041 DOI: 10.1126/science.abe2218] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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Affiliation(s)
- Claire Hoencamp
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - SP, 15054-000, Brazil
| | - Roy G H P van Heesbeen
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bram van den Broek
- BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Aditya N Mhaskar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhenzhen Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Namita Mitra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weijie Yao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leonid L Moroz
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Andrea Kohn
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Judy St Leger
- Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | | | | | | | - Fabian Lim
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma Farley
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Alexander Haddad
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Chauss
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayse Sena Mutlu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evin Hildebrandt
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | - Hans H Cheng
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | | | - Theresa L U Burnham
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Kevin A Hovel
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Andrew J Beel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre-Jean Mattei
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gregory Cary
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Federica Di Palma
- Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Asha S Multani
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sen Pathak
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liesl Nel-Themaat
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - René H Medema
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
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13
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Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD. Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. eLife 2021; 10:68068. [PMID: 33904398 PMCID: PMC8137143 DOI: 10.7554/elife.68068] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/25/2021] [Indexed: 01/07/2023] Open
Abstract
Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology. Cells adapt and respond to changes by regulating the activity of their genes. To turn genes on or off, they use a family of proteins called transcription factors. Transcription factors influence specific but overlapping groups of genes, so that each gene is controlled by several transcription factors that act together like a dimmer switch to regulate gene activity. The presence of transcription factors attracts proteins such as the Mediator complex, which activates genes by gathering the protein machines that read the genes. The more transcription factors are found near a specific gene, the more strongly they attract Mediator and the more active the gene is. A specific region on the transcription factor called the activation domain is necessary for this process. The biochemical sequences of these domains vary greatly between species, yet activation domains from, for example, yeast and human proteins are often interchangeable. To understand why this is the case, Sanborn et al. analyzed the genome of baker’s yeast and identified 150 activation domains, each very different in sequence. Three-quarters of them bound to a subunit of the Mediator complex called Med15. Sanborn et al. then developed a machine learning algorithm to predict activation domains in both yeast and humans. This algorithm also showed that negatively charged and greasy regions on the activation domains were essential to be activated by the Mediator complex. Further analyses revealed that activation domains used different poses to bind multiple sites on Med15, a behavior known as ‘fuzzy’ binding. This creates a high overall affinity even though the binding strength at each individual site is low, enabling the protein complexes to remain dynamic. These weak interactions together permit fine control over the activity of several genes, allowing cells to respond quickly and precisely to many changes. The computer algorithm used here provides a new way to identify activation domains across species and could improve our understanding of how living things grow, adapt and evolve. It could also give new insights into mechanisms of disease, particularly cancer, where transcription factors are often faulty.
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Affiliation(s)
- Adrian L Sanborn
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.,Department of Computer Science, Stanford University, Stanford, United States
| | - Benjamin T Yeh
- Department of Computer Science, Stanford University, Stanford, United States
| | - Jordan T Feigerle
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Cynthia V Hao
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | | | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, United States.,Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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14
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Zhang H, Chen DH, Mattoo RUH, Bushnell DA, Wang Y, Yuan C, Wang L, Wang C, Davis RE, Nie Y, Kornberg RD. Mediator structure and conformation change. Mol Cell 2021; 81:1781-1788.e4. [PMID: 33571424 DOI: 10.1016/j.molcel.2021.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 01/22/2023]
Abstract
Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions.
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Affiliation(s)
- Heqiao Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rayees U H Mattoo
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yannan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Chunnian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China
| | - Ralph E Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Nie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China.
| | - Roger D Kornberg
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Xavier PL, Ayyer K, Yefanov O, Gelisio L, Bielecki J, Samanta AK, Bajt S, Sha R, Bushnell DA, Kornberg RD, Ovcharenko Y, Kuepper J, Meyer M, Seeman NC, Chapman HN. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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16
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He P, Wang C, Wang Y, Wang C, Zhou C, Cao D, Li J, Bushnell DA, Li Q, Kornberg RD, Xie W, Wang Z. A Novel AKR1C3 Specific Prodrug TH3424 With Potent Antitumor Activity in Liver Cancer. Clin Pharmacol Ther 2021; 110:229-237. [PMID: 33483974 DOI: 10.1002/cpt.2171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 12/24/2022]
Abstract
Overexpression of AKR1C3, an aldo-keto reductase, was recently discovered in liver cancers. In this study, an inverse correlation between AKR1C3 expression and survival of patients with liver cancer was observed. AKR1C3 inhibitors, however, failed to suppress liver cancer cell growth. The prodrug TH3424, which releases a DNA alkylating reagent upon reduction by AKR1C3, was developed to target tumors with overexpression of AKR1C3. TH3424 showed specific killing of liver cancer cells with AKR1C3 overexpression both in vitro and in vivo. In patient-derived mouse xenograft models, TH3424 at doses as low as 1.5 mg/kg eliminated liver tumors with no apparent toxicity. Therefore, TH3424 is a promising drug candidate for liver cancer and other types of cancers overexpressing AKR1C3.
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Affiliation(s)
- Ping He
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China
| | - Chunnian Wang
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
| | - Yanlan Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China
| | - Caiyan Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Changhua Zhou
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong No. 2 Provincial People's Hospital, Guangzhou, China
| | - Jiang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University, Guangzhou, China
| | - David A Bushnell
- Department of Structural Biology, Stanford University, Stanford, California, USA
| | - Qing Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China
| | - Roger D Kornberg
- Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China.,Department of Structural Biology, Stanford University, Stanford, California, USA
| | - Wei Xie
- Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China.,MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhong Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Centre for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, China
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17
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Abstract
Whereas the core nucleosome is thought to serve as a packaging device for the coiling and contraction in length of genomic DNA, we suggest that it serves primarily in the regulation of transcription. A nucleosome on a promoter prevents the initiation of transcription. The association of nucleosomes with most genomic DNA prevents initiation from cryptic promoters. The nucleosome thus serves not only as a general gene repressor, but also as a repressor of all transcription (genic, intragenic, and intergenic). The core nucleosome performs a fundamental regulatory role, apart from the histone "tails," which modulate gene activity.
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Affiliation(s)
- Roger D Kornberg
- Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Yahli Lorch
- Department of Structural Biology, Stanford School of Medicine, Stanford, CA 94305, USA.
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18
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Feigerle JT, Kornberg RD. IID in 3D: Improved Resolution of Transcription Factor Structure by Cryo-Electron Microscopy. Biochemistry 2019; 58:2653-2654. [PMID: 31150224 DOI: 10.1021/acs.biochem.9b00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jordan T Feigerle
- Department of Structural Biology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Roger D Kornberg
- Department of Structural Biology , Stanford University School of Medicine , Stanford , California 94305 , United States
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19
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Azubel M, Carter SD, Weiszmann J, Zhang J, Jensen GJ, Li Y, Kornberg RD. FGF21 trafficking in intact human cells revealed by cryo-electron tomography with gold nanoparticles. eLife 2019; 8:43146. [PMID: 30688648 PMCID: PMC6349402 DOI: 10.7554/elife.43146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
The fibroblast growth factor FGF21 was labeled with molecularly defined gold nanoparticles (AuNPs), applied to human adipocytes, and imaged by cryo-electron tomography (cryo-ET). Most AuNPs were in pairs about 80 Å apart, on the outer cell surface. Pairs of AuNPs were also abundant inside the cells in clathrin-coated vesicles and endosomes. AuNPs were present but no longer paired in multivesicular bodies. FGF21 could thus be tracked along the endocytotic pathway. The methods developed here to visualize signaling coupled to endocytosis can be applied to a wide variety of cargo and may be extended to studies of other intracellular transactions.
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Affiliation(s)
- Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Stephen D Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Jennifer Weiszmann
- Cardiometabolic Disorders, Amgen Inc. Discovery Research, South San Francisco, United states
| | - Jun Zhang
- Cardiometabolic Disorders, Amgen Inc. Discovery Research, South San Francisco, United states
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United states
| | - Yang Li
- Cardiometabolic Disorders, Amgen Inc. Discovery Research, South San Francisco, United states.,Surrozen Inc, South San Francisco, United states
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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20
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Lorch Y, Maier-Davis B, Kornberg RD. Histone Acetylation Inhibits RSC and Stabilizes the +1 Nucleosome. Mol Cell 2018; 72:594-600.e2. [PMID: 30401433 DOI: 10.1016/j.molcel.2018.09.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022]
Abstract
The +1 nucleosome of yeast genes, within which reside transcription start sites, is characterized by histone acetylation, by the displacement of an H2A-H2B dimer, and by a persistent association with the RSC chromatin-remodeling complex. Here we demonstrate the interrelationship of these characteristics and the conversion of a nucleosome to the +1 state in vitro. Contrary to expectation, acetylation performs an inhibitory role, preventing the removal of a nucleosome by RSC. Inhibition is due to both enhanced RSC-histone interaction and diminished histone-chaperone interaction. Acetylation does not prevent all RSC activity, because stably bound RSC removes an H2A-H2B dimer on a timescale of seconds in an irreversible manner.
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Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Barbara Maier-Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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21
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Pereyaslavets L, Kurnikov I, Kamath G, Butin O, Illarionov A, Leontyev I, Olevanov M, Levitt M, Kornberg RD, Fain B. On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations. Proc Natl Acad Sci U S A 2018; 115:8878-8882. [PMID: 30127031 PMCID: PMC6130346 DOI: 10.1073/pnas.1806064115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In many important processes in chemistry, physics, and biology the nuclear degrees of freedom cannot be described using the laws of classical mechanics. At the same time, the vast majority of molecular simulations that employ wide-coverage force fields treat atomic motion classically. In light of the increasing desire for and accelerated development of quantum mechanics (QM)-parameterized interaction models, we reexamine whether the classical treatment is sufficient for a simple but crucial chemical species: alkanes. We show that when using an interaction model or force field in excellent agreement with the "gold standard" QM data, even very basic simulated properties of liquid alkanes, such as densities and heats of vaporization, deviate significantly from experimental values. Inclusion of nuclear quantum effects via techniques that treat nuclear degrees of freedom using the laws of classical mechanics brings the simulated properties much closer to reality.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
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22
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23
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Azubel M, Koh AL, Koyasu K, Tsukuda T, Kornberg RD. Structure Determination of a Water-Soluble 144-Gold Atom Particle at Atomic Resolution by Aberration-Corrected Electron Microscopy. ACS Nano 2017; 11:11866-11871. [PMID: 29136369 DOI: 10.1021/acsnano.7b06051] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Structure determination by transmission electron microscopy has revealed the long sought 144-gold atom particle. The structure exhibits deviations from face-centered cubic packing of the gold atoms, similar to the solution structure of another gold nanoparticle, and in contrast to a previous X-ray crystal structure. Evidence from analytical methods points to a low number of 3-mercaptobenzoic acid ligands covering the surface of the particle.
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Affiliation(s)
- Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Ai Leen Koh
- Stanford Nano Shared Facilities, Stanford University , Stanford, California 94305, United States
| | - Kiichirou Koyasu
- Department of Chemistry, School of Science, The University of Tokyo , Tokyo 113-0033, Japan
| | - Tatsuya Tsukuda
- Department of Chemistry, School of Science, The University of Tokyo , Tokyo 113-0033, Japan
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
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24
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Nie Y, Zhang F, Yuan C, Li L, Sun Y, Wang Y, Zhao L, Robinson PJ, Berger I, Kornberg RD. Streamlining protein complex production using multiprotein expression technologies. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317082997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD. Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex. Cell 2016; 166:1411-1422.e16. [PMID: 27610567 DOI: 10.1016/j.cell.2016.08.050] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/14/2016] [Accepted: 08/19/2016] [Indexed: 12/23/2022]
Abstract
A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.
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Affiliation(s)
- Philip J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ralph E Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre-Jean Mattei
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Abstract
By a modification of the method of Brust et al., water-soluble, thiolate-protected gold nanoparticles that are uniform in size were synthesized with no requirement for purification. The modification of the method was equilibration in the first step, which proved crucial for achieving size homogeneity. The thiol-to-gold ratio controlled the size of the particles, and the choice of thiol controlled the reactivity of the particles toward thiol exchange.
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Affiliation(s)
- Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
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27
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Eagen KP, Hartl TA, Kornberg RD. Stable Chromosome Condensation Revealed by Chromosome Conformation Capture. Cell 2016; 163:934-46. [PMID: 26544940 DOI: 10.1016/j.cell.2015.10.026] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 07/01/2015] [Accepted: 10/07/2015] [Indexed: 11/27/2022]
Abstract
Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to 10-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes.
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Affiliation(s)
- Kyle P Eagen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tom A Hartl
- Departments of Developmental Biology, Genetics, and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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28
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Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. eLife 2015; 4. [PMID: 26402457 PMCID: PMC4631838 DOI: 10.7554/elife.08719] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/23/2015] [Indexed: 12/18/2022] Open
Abstract
The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI:http://dx.doi.org/10.7554/eLife.08719.001 Inside a cell, proteins are made from instructions encoded by DNA. To produce a particular protein, a section of DNA within a gene is copied into a molecule of messenger ribonucleic acid (or mRNA). This process is called transcription and is carried out by an enzyme known as RNA polymerase. Transcription begins in a region of DNA called a promoter, which is found at the start of the gene. RNA polymerase is brought to the DNA by many proteins, including the so-called Mediator complex. Mediator receives signals from within the cell and from the environment, processes the information, and instructs RNA polymerase whether to transcribe the gene or not. Mediator performs this important role in all organisms from yeast to humans, but it is not clear how it works. A crucial step towards the solution of this problem is to understand the three-dimensional structure of the complex. Previous research using a technique called ‘electron microscopy’ showed that Mediator is composed of three modules, referred to as Head, Middle and Tail. The images from electron microscopy were not sufficiently detailed to reveal the organization of the proteins within these modules. An open-source Integrative Modeling Platform (IMP for short) was recently developed to arrive at structural models of large protein complexes from a combination of experimental data and computer models. Now, Robinson, Trnka, Pellarin et al. have used this platform to study the Mediator complex. First, Robinson, Trnka, Pellarin et al. collected experimental data on the structure of the Mediator complex using two approaches called ‘chemical cross-linking’ and ‘mass spectrometry’. This data was combined with biochemical and structural information from previous studies to generate a three-dimensional model of the structure of the entire Mediator using IMP. The model is detailed enough to show the location and orientation of all the proteins in the complex. For example, a protein called Med17 connects the Head and Middle modules, while another subunit—known as Med14—spans the entire complex and makes extensive contacts with other proteins in all three modules. DOI:http://dx.doi.org/10.7554/eLife.08719.002
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Affiliation(s)
- Philip J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States.,Structural Bioinformatics Unit, Paris, France
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Ralph Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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29
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Fazal FM, Meng CA, Murakami K, Kornberg RD, Block SM. Real-time observation of the initiation of RNA polymerase II transcription. Nature 2015; 525:274-7. [PMID: 26331540 PMCID: PMC4624315 DOI: 10.1038/nature14882] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/03/2015] [Indexed: 01/22/2023]
Abstract
Biochemical and structural studies have shown that the initiation of RNA polymerase II (pol II) transcription proceeds in the following stages: assembly of pol II with general transcription factors (GTFs) and promoter DNA in a “closed” preinitiation complex (PIC)1,2; unwinding about 15 bp of the promoter DNA to form an “open” complex3,4; scanning downstream to a transcription start site; synthesis of a short transcript, believed to be about 10 nucleotides; and promoter escape. We have assembled a 32-protein, 1.5 megadalton PIC5 derived from Saccharomyces cerevisiae and observed subsequent initiation processes in real time with optical tweezers6. Contrary to expectation, scanning driven by transcription factor IIH (TFIIH)7-12 entailed the rapid opening of an extended bubble, averaging 85 bp, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.
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Affiliation(s)
- Furqan M Fazal
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Cong A Meng
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
| | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA.,Department of Biology, Stanford University, Stanford, California 94305, USA
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30
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Abstract
AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. Lorch et al. find that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. These sequences instead facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. AT-rich DNA is concentrated in the nucleosome-free regions (NFRs) associated with transcription start sites of most genes. We tested the hypothesis that AT-rich DNA engenders NFR formation by virtue of its rigidity and consequent exclusion of nucleosomes. We found that the AT-rich sequences present in many NFRs have little effect on the stability of nucleosomes. Rather, these sequences facilitate the removal of nucleosomes by the RSC chromatin remodeling complex. RSC activity is stimulated by AT-rich sequences in nucleosomes and inhibited by competition with AT-rich DNA. RSC may remove NFR nucleosomes without effect on adjacent ORF nucleosomes. Our findings suggest that many NFRs are formed and maintained by an active mechanism involving the ATP-dependent removal of nucleosomes rather than a passive mechanism due to the intrinsic instability of nucleosomes on AT-rich DNA sequences.
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Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Barbara Maier-Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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31
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Azubel M, Koivisto J, Malola S, Bushnell D, Hura GL, Koh AL, Tsunoyama H, Tsukuda T, Pettersson M, Häkkinen H, Kornberg RD. Nanoparticle imaging. Electron microscopy of gold nanoparticles at atomic resolution. Science 2014; 345:909-12. [PMID: 25146285 DOI: 10.1126/science.1251959] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, but only one AuNP larger than 1 nanometer in diameter [a 102-gold atom NP (Au102NP)] has been solved to atomic resolution. Whereas the Au102NP structure was determined by x-ray crystallography, other large AuNPs have proved refractory to this approach. Here, we report the structure determination of a Au68NP at atomic resolution by aberration-corrected transmission electron microscopy, performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small-angle x-ray scattering and by comparison of observed infrared absorption spectra with calculations by density functional theory.
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Affiliation(s)
- Maia Azubel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jaakko Koivisto
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Sami Malola
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - David Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Greg L Hura
- Physical Bioscience Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Ai Leen Koh
- Stanford Nanocharacterization Laboratory, Stanford University, Stanford, CA 94305, USA
| | | | - Tatsuya Tsukuda
- Catalysis Research Center, Hokkaido University, Sapporo, Japan
| | - Mika Pettersson
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Hannu Häkkinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland. Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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32
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Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Levitt M, Kornberg RD, Gibbons BJ. Architecture of an RNA polymerase II transcription pre-initiation complex. Science 2013; 342:1238724. [PMID: 24072820 PMCID: PMC4039082 DOI: 10.1126/science.1238724] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The protein density and arrangement of subunits of a complete, 32-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by means of cryogenic electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs) and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft.
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Affiliation(s)
- Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Hans Elmlund
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Nir Kalisman
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - David A. Bushnell
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Christopher M. Adams
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA 94305, U.S.A
| | - Maia Azubel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Dominika Elmlund
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Yael Levi-Kalisman
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Xin Liu
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Michael Levitt
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Brian J. Gibbons
- Department of Structural Biology, Stanford University, Stanford, CA 94305, U.S.A
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33
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Murakami K, Calero G, Brown CR, Liu X, Davis RE, Boeger H, Kornberg RD. Formation and fate of a complete 31-protein RNA polymerase II transcription preinitiation complex. J Biol Chem 2013; 288:6325-32. [PMID: 23303183 DOI: 10.1074/jbc.m112.433623] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Whereas individual RNA polymerase II (pol II)-general transcription factor (GTF) complexes are unstable, an assembly of pol II with six GTFs and promoter DNA could be isolated in abundant homogeneous form. The resulting complete pol II transcription preinitiation complex (PIC) contained equimolar amounts of all 31 protein components. An intermediate in assembly, consisting of four GTFs and promoter DNA, could be isolated and supplemented with the remaining components for formation of the PIC. Nuclease digestion and psoralen cross-linking mapped the PIC between positions -70 and -9, centered on the TATA box. Addition of ATP to the PIC resulted in quantitative conversion to an open complex, which retained all 31 proteins, contrary to expectation from previous studies. Addition of the remaining NTPs resulted in run-off transcription, with an efficiency that was promoter-dependent and was as great as 17.5% with the promoters tested.
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Affiliation(s)
- Kenji Murakami
- Department of Structural Biology, Stanford University, Stanford, California 94305, USA
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34
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Liu X, Bushnell DA, Kornberg RD. RNA polymerase II transcription: structure and mechanism. Biochim Biophys Acta 2012; 1829:2-8. [PMID: 23000482 DOI: 10.1016/j.bbagrm.2012.09.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/07/2012] [Indexed: 01/25/2023]
Abstract
A minimal RNA polymerase II (pol II) transcription system comprises the polymerase and five general transcription factors (GTFs) TFIIB, -D, -E, -F, and -H. The addition of Mediator enables a response to regulatory factors. The GTFs are required for promoter recognition and the initiation of transcription. Following initiation, pol II alone is capable of RNA transcript elongation and of proofreading. Structural studies reviewed here reveal roles of GTFs in the initiation process and shed light on the transcription elongation mechanism. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
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Affiliation(s)
- Xin Liu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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35
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Larson MH, Zhou J, Kaplan CD, Palangat M, Kornberg RD, Landick R, Block SM. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci U S A 2012; 109:6555-60. [PMID: 22493230 PMCID: PMC3340090 DOI: 10.1073/pnas.1200939109] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During transcription, RNA polymerase II (RNAPII) must select the correct nucleotide, catalyze its addition to the growing RNA transcript, and move stepwise along the DNA until a gene is fully transcribed. In all kingdoms of life, transcription must be finely tuned to ensure an appropriate balance between fidelity and speed. Here, we used an optical-trapping assay with high spatiotemporal resolution to probe directly the motion of individual RNAPII molecules as they pass through each of the enzymatic steps of transcript elongation. We report direct evidence that the RNAPII trigger loop, an evolutionarily conserved protein subdomain, serves as a master regulator of transcription, affecting each of the three main phases of elongation, namely: substrate selection, translocation, and catalysis. Global fits to the force-velocity relationships of RNAPII and its trigger loop mutants support a Brownian ratchet model for elongation, where the incoming NTP is able to bind in either the pre- or posttranslocated state, and movement between these two states is governed by the trigger loop. Comparison of the kinetics of pausing by WT and mutant RNAPII under conditions that promote base misincorporation indicate that the trigger loop governs fidelity in substrate selection and mismatch recognition, and thereby controls aspects of both transcriptional accuracy and rate.
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Affiliation(s)
| | | | - Craig D. Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843; and
| | - Murali Palangat
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Steven M. Block
- Biophysics Program
- Department of Applied Physics
- Department of Biology, Stanford University, Stanford, CA 94305
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36
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Abstract
How does RNA polymerase recognize a promoter in duplex DNA? How are the DNA strands pried apart to enable RNA synthesis? A crystal structure by Feklistov and Darst unexpectedly reveals that these two processes are interconnected.
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Affiliation(s)
- Xin Liu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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37
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Zhou J, Larson MH, Kaplan C, Palangat M, Kornberg RD, Landick R, Block SM. RNA Polymerase II Translocation and Fidelity are Governed by Trigger Loop Dynamics: A Single-Molecule Study. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Abstract
The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.
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Affiliation(s)
- Xin Liu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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39
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Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature 2011; 475:240-3. [PMID: 21725323 DOI: 10.1038/nature10162] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/28/2011] [Indexed: 01/14/2023]
Abstract
Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 ångströms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.
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Affiliation(s)
- Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
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40
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Lorch Y, Griesenbeck J, Boeger H, Maier-Davis B, Kornberg RD. Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex. Nat Struct Mol Biol 2011; 18:881-5. [PMID: 21725295 PMCID: PMC3150231 DOI: 10.1038/nsmb.2072] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 04/22/2011] [Indexed: 01/24/2023]
Abstract
Purified chromatin rings, excised from the PHO5 locus of Saccharomyces cerevisiae in transcriptionally repressed and activated states, were remodeled with RSC and ATP. Nucleosomes were translocated, and those originating on the promoter of repressed rings were removed, whereas those originating on the open reading frame (ORF) were retained. Treatment of the repressed rings with histone deacetylase diminished the removal of promoter nucleosomes. These findings point to a principle of promoter chromatin remodeling for transcription, namely that promoter specificity resides primarily in the nucleosomes rather than in the remodeling complex that acts upon them.
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Affiliation(s)
- Yahli Lorch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.
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41
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Hulkko E, Lopez-Acevedo O, Koivisto J, Levi-Kalisman Y, Kornberg RD, Pettersson M, Häkkinen H. Electronic and Vibrational Signatures of the Au102(p-MBA)44 Cluster. J Am Chem Soc 2011; 133:3752-5. [DOI: 10.1021/ja111077e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eero Hulkko
- Nanoscience Center, Department of Chemistry, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Olga Lopez-Acevedo
- Nanoscience Center, Department of Chemistry, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Jaakko Koivisto
- Nanoscience Center, Department of Chemistry, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Yael Levi-Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Mika Pettersson
- Nanoscience Center, Department of Chemistry, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Hannu Häkkinen
- Nanoscience Center, Department of Chemistry, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
- Nanoscience Center, Department of Physics, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
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42
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Levi-Kalisman Y, Jadzinsky PD, Kalisman N, Tsunoyama H, Tsukuda T, Bushnell DA, Kornberg RD. Synthesis and Characterization of Au102(p-MBA)44 Nanoparticles. J Am Chem Soc 2011; 133:2976-82. [DOI: 10.1021/ja109131w] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yael Levi-Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Pablo D. Jadzinsky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Nir Kalisman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Hironori Tsunoyama
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - Tatsuya Tsukuda
- Section of Catalytic Assemblies, Catalysis Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - David A. Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
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43
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Abstract
Chromatin prepared by a method involving limited nuclease digestion contains the same repeating structure as chromatin in the nucleus, whereas chromatin prepared by conventional methods involving shear does not.
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44
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Abstract
By adjustment of solvent conditions for synthesis, virtually monodisperse 4-mercaptobenzoic acid (p-MBA) monolayer-protected gold nanoparticles, 2 and 3 nm in diameter, were obtained. Large single crystals of the 2 nm particles could be grown from the reaction mixture. Uniformity was also demonstrated by the formation of two-dimensional arrays and by quantitative high-angle annular dark-field scanning transmission electron microscopy. The 2 and 3 nm particles were spontaneously reactive for conjugation with proteins and DNA, and further reaction could be prevented by repassivation with glutathione. Conjugates with antibody Fc fragment could be used to identify TAP-tagged proteins of interest in electron micrographs, through the binding of a pair of particles to the pair of protein A domains in the TAP tag.
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Affiliation(s)
- Christopher J Ackerson
- Department of Structural Biology, Stanford School of Medicine, 299 Campus Drive West, Stanford, California 94305, USA
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45
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Abstract
Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the "B finger," reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.
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Affiliation(s)
- Xin Liu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A. Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dong Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guillermo Calero
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D. Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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46
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Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 2009; 324:1203-6. [PMID: 19478184 DOI: 10.1126/science.1168729] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.
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Affiliation(s)
- Dong Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Abstract
A comprehensive survey of single amino-acid substitution mutations critical for RNA polymerase function published in Journal of Biology supports a proposed mechanism for polymerase action in which movement of the polymerase 'bridge helix' promotes transcriptional activity in cooperation with a critical substrate-interaction domain, the 'trigger loop'.
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Affiliation(s)
- Craig D Kaplan
- Department of Structural Biology, Stanford University, 299 Campus Dr, West, Stanford, CA 94305, USA
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48
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49
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Kaplan CD, Larsson KM, Kornberg RD. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell 2008; 30:547-56. [PMID: 18538653 DOI: 10.1016/j.molcel.2008.04.023] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/07/2008] [Accepted: 04/14/2008] [Indexed: 10/22/2022]
Abstract
Structural, biochemical, and genetic studies have led to proposals that a mobile element of multisubunit RNA polymerases, the Trigger Loop (TL), plays a critical role in catalysis and can be targeted by antibiotic inhibitors. Here we present evidence that the Saccharomyces cerevisiae RNA Polymerase II (Pol II) TL participates in substrate selection. Amino acid substitutions within the Pol II TL preferentially alter substrate usage and enzyme fidelity, as does inhibition of transcription by alpha-amanitin. Finally, substitution of His1085 in the TL specifically renders Pol II highly resistant to alpha-amanitin, indicating a functional interaction between His1085 and alpha-amanitin that is supported by rerefinement of an alpha-amanitin-Pol II crystal structure. We propose that alpha-amanitin-inhibited Pol II elongation, which is slow and exhibits reduced substrate selectivity, results from direct alpha-amanitin interference with the TL.
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Affiliation(s)
- Craig D Kaplan
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
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50
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Boeger H, Griesenbeck J, Kornberg RD. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 2008; 133:716-26. [PMID: 18485878 DOI: 10.1016/j.cell.2008.02.051] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 01/13/2008] [Accepted: 02/29/2008] [Indexed: 11/24/2022]
Abstract
The rate-limiting step of transcriptional activation in eukaryotes, and thus the critical point for gene regulation, is unknown. Combining biochemical analyses of the chromatin transition at the transcriptionally induced PHO5 promoter in yeast with modeling based on a small number of simple assumptions, we demonstrate that random removal and reformation of promoter nucleosomes can account for stochastic and kinetic properties of PHO5 expression. Our analysis suggests that the disassembly of promoter nucleosomes is rate limiting for PHO5 expression, and supports a model for the underlying mechanism of promoter chromatin remodeling, which appears to conserve a single nucleosome on the promoter at all times.
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Affiliation(s)
- Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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