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Génin NEJ, Weinzierl ROJ. Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations. Biomolecules 2020; 10:biom10091289. [PMID: 32906795 PMCID: PMC7565877 DOI: 10.3390/biom10091289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 01/01/2023] Open
Abstract
Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed.
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Affiliation(s)
- Nicolas E. J. Génin
- Institut de Chimie Organique et Analytique, Université d’Orléans, 45100 Orléans, France;
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2
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Ramezanpour M, Lee J, Taneva SG, Tieleman DP, Cornell RB. An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair. J Biol Chem 2018. [PMID: 29519816 DOI: 10.1074/jbc.ra118.002053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122 The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface.
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Affiliation(s)
- Mohsen Ramezanpour
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Jaeyong Lee
- the Departments of Molecular Biology and Biochemistry and
| | | | - D Peter Tieleman
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Rosemary B Cornell
- the Departments of Molecular Biology and Biochemistry and .,Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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3
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Cheng KJ, Demir Ö, Amaro RE. A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases. Genes (Basel) 2017. [PMID: 28632168 PMCID: PMC5485530 DOI: 10.3390/genes8060166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3’ end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites. Two additional TUTases called TbMEAT1 and TbTUT4 have also been reported to share similar function. TbRET1 and TbRET2 are essential enzymes for the parasite viability making them potential drug targets. For this study, we clustered molecular dynamics (MD) trajectories of four TUTases based on active site shape measured by Pocket Volume Measurer (POVME) program. Among the four TUTases, TbRET1 exhibited the largest average pocket volume, while TbMEAT1’s and TbTUT4’s active sites displayed the most flexibility. A side pocket was also identified within the active site in all TUTases with TbRET1 having the most pronounced. Our results indicate that TbRET1’s larger side pocket can be exploited to achieve selective inhibitor design as FTMap identifies it as a druggable pocket.
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Affiliation(s)
- Kevin J Cheng
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Özlem Demir
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
- National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA.
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Rajappa-Titu L, Suematsu T, Munoz-Tello P, Long M, Demir Ö, Cheng KJ, Stagno JR, Luecke H, Amaro RE, Aphasizheva I, Aphasizhev R, Thore S. RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting. Nucleic Acids Res 2016; 44:10862-10878. [PMID: 27744351 PMCID: PMC5159558 DOI: 10.1093/nar/gkw917] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/27/2016] [Accepted: 10/04/2016] [Indexed: 11/13/2022] Open
Abstract
Terminal uridyltransferases (TUTases) execute 3′ RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei. In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3′ processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3′ processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets.
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Affiliation(s)
- Lional Rajappa-Titu
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Paola Munoz-Tello
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Marius Long
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Özlem Demir
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin J Cheng
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason R Stagno
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Hartmut Luecke
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA .,Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland .,INSERM, U1212, ARNA Laboratory, Bordeaux 33000, France.,CNRS UMR5320, ARNA Laboratory, Bordeaux 33000, France.,University of Bordeaux, ARNA Laboratory, Bordeaux 33000, France
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5
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Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G. The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes. Drug Discov Today 2015; 20:686-702. [PMID: 25615716 DOI: 10.1016/j.drudis.2015.01.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 12/08/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Among all tools available to design new drugs, molecular dynamics (MD) simulations have become an essential technique. Initially developed to investigate molecular models with a limited number of atoms, computers now enable investigations of large macromolecular systems with a simulation time reaching the microsecond range. The reviewed articles cover four years of research to give an overview on the actual impact of MD on the current medicinal chemistry landscape with a particular emphasis on studies of ligand-protein interactions. With a special focus on studies combining computational approaches with data gained from other techniques, this review shows how deeply embedded MD simulations are in drug design strategies and articulates what the future of this technique could be.
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Affiliation(s)
- Jérémie Mortier
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
| | - Christin Rakers
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Manuela S Murgueitio
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany.
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Durrant JD, Votapka L, Sørensen J, Amaro RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput 2014; 10:5047-5056. [PMID: 25400521 PMCID: PMC4230373 DOI: 10.1021/ct500381c] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 02/08/2023]
Abstract
![]()
Analysis of macromolecular/small-molecule
binding pockets can provide
important insights into molecular recognition and receptor dynamics.
Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm
has been widely adopted as a simple-to-use tool for measuring and
characterizing pocket volumes and shapes. We here present POVME 2.0,
which is an order of magnitude faster, has improved accuracy, includes
a graphical user interface, and can produce volumetric density maps
for improved pocket analysis. To demonstrate the utility of the algorithm,
we use it to analyze the binding pocket of RNA editing ligase 1 from
the unicellular parasite Trypanosoma brucei, the
etiological agent of African sleeping sickness. The POVME analysis
characterizes the full dynamics of a potentially druggable transient
binding pocket and so may guide future antitrypanosomal drug-discovery
efforts. We are hopeful that this new version will be a useful tool
for the computational- and medicinal-chemist community.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
| | - Lane Votapka
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Jesper Sørensen
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
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Demir O, Labaied M, Merritt C, Stuart K, Amaro RE. Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des 2014; 84:131-9. [PMID: 24903413 DOI: 10.1111/cbdd.12302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/12/2013] [Accepted: 02/07/2014] [Indexed: 11/27/2022]
Abstract
Human African trypanosomiasis (HAT) is a major health problem in sub-Saharan Africa caused by Trypanosoma brucei infection. Current HAT drugs are difficult to administer and not effective against all parasite species at different stages of the disease which indicates an unmet pharmaceutical need. TbRET2 is an indispensable enzyme for the parasite and is targeted here using a computational approach that combines molecular dynamics simulations and virtual screening. The compounds prioritized are then tested in T. brucei via Alamar blue cell viability assays. This work identified 20 drug-like compounds which are candidates for further testing in the drug discovery process.
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Affiliation(s)
- Ozlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
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Park YJ, Hol WGJ. Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds. J Struct Biol 2012; 180:362-73. [PMID: 22902563 PMCID: PMC3483419 DOI: 10.1016/j.jsb.2012.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sleeping sickness. These organisms have many highly unusual features including a unique U-insertion/deletion RNA editing process in the single mitochondrion. A key multi-protein complex, called the ∼20S editosome, or editosome, carries out a cascade of essential RNA-modifying reactions and contains a core of 12 different proteins of which six are the interaction proteins A1 to A6. Each of these interaction proteins comprises a C-terminal OB-fold and the smallest interaction protein A6 has been shown to interact with four other editosome OB-folds. Here we report the results of a "linked OB-fold" approach to obtain a view of how multiple OB-folds might interact in the core of the editosome. Constructs with variants of linked domains in 25 expression and co-expression experiments resulted in 13 soluble multi-OB-fold complexes. In several instances, these complexes were more homogeneous in size than those obtained from corresponding unlinked OB-folds. The crystal structure of A3(OB) linked to A6 could be elucidated and confirmed the tight interaction between these two OB domains as seen also in our recent complex of A3(OB) and A6 with nanobodies. In the current crystal structure of A3(OB) linked to A6, hydrophobic side chains reside in well-defined pockets of neighboring OB-fold domains. When analyzing the available crystal structures of editosome OB-folds, it appears that in five instances "Pocket 1" of A1(OB), A3(OB) and A6 is occupied by a hydrophobic side chain from a neighboring protein. In these three different OB-folds, Pocket 1 is formed by two conserved sequence motifs and an invariant arginine. These pockets might play a key role in the assembly or mechanism of the editosome by interacting with hydrophobic side chains from other proteins.
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Affiliation(s)
- Young-Jun Park
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Wim G. J. Hol
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA,To whom correspondence should be addressed. Telephone: +1 (206) 685 7044; Fax: +1 (206) 685 7002;
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