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Santiago Á, Razo-Hernández RS, Pastor N. Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. J Chem Inf Model 2020; 60:866-879. [PMID: 31917925 DOI: 10.1021/acs.jcim.9b00824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The TATA-box binding protein (TBP) is an important element of the transcription machinery in archaea and eukaryotic organisms. TBP is expressed in organisms adapted to different temperatures, indicating a robust structure, and experimental studies have shown that the mid-unfolding temperature (Tm) of TBP is directly correlated with the optimal growth temperature (OGT) of the organism. To understand which are the relevant structural requirements for its stability, we present the first structural and dynamic computational study of TBPs, combining molecular dynamics (MD) simulations and a quantitative structure-property relationship (QSPR) over a set of TBPs of organisms adapted to different temperatures. We found that the main structural properties of TBP used to adapt to high temperatures are an increase in the ease of desolvation of charged residues at the surface, an increase in the local resiliency, the presence of Leu clusters in the protein core, and an increase in the loss of hydrophobic packing in the N-terminal subdomain. In view of our results, we consider that TBP is a good model to study thermal adaptation, and our analysis opens the possibility of performing protein engineering on TBPs to study transcription at high or low temperatures.
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Affiliation(s)
- Ángel Santiago
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Nina Pastor
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología , Universidad Nacional Autónoma de México , Av. Universidad 2001, Col. Chamilpa , Cuernavaca , Morelos 62210 , México
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Santiago Á, Razo-Hernández RS, Pastor N. The TATA-binding Protein DNA-binding domain of eukaryotic parasites is a potentially druggable target. Chem Biol Drug Des 2019; 95:130-149. [PMID: 31569300 DOI: 10.1111/cbdd.13630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/14/2019] [Accepted: 09/21/2019] [Indexed: 12/17/2022]
Abstract
The TATA-binding protein (TBP) is a central transcription factor in eukaryotes that interacts with a large number of different transcription factors; thus, affecting these interactions will be lethal for any living being. In this work, we present the first structural and dynamic computational study of the surface properties of the TBP DNA-binding domain for a set of parasites involved in diseases of worldwide interest. The sequence and structural differences of these TBPs, as compared with human TBP, were proposed to select representative ensembles generated from molecular dynamics simulations and to evaluate their druggability by molecular ensemble-based docking of drug-like molecules. We found that potential druggable sites correspond to the NC2-binding site, N-terminal tail, H2 helix, and the interdomain region, with good selectivity for Plasmodium falciparum, Necator americanus, Entamoeba histolytica, Candida albicans, and Taenia solium TBPs. The best hit compounds share structural similarity among themselves and have predicted dissociation constants ranging from nM to μM. These can be proposed as initial scaffolds for experimental testing and further optimization. In light of the obtained results, we propose TBP as an attractive therapeutic target for treatment of parasitic diseases.
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Affiliation(s)
- Ángel Santiago
- Centro de Investigación en Dinámica Celular - IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.,Doctorado en Ciencias, CIDC-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular - IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular - IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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Nickels PC, Wünsch B, Holzmeister P, Bae W, Kneer LM, Grohmann D, Tinnefeld P, Liedl T. Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp. Science 2017; 354:305-307. [PMID: 27846560 DOI: 10.1126/science.aah5974] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/06/2016] [Indexed: 11/02/2022]
Abstract
Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer. We used the conformer switching of a Holliday junction as a benchmark and studied the TATA-binding protein-induced bending of a DNA duplex under tension. The observed suppression of bending above 10 piconewtons provides further evidence of mechanosensitivity in gene regulation.
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Affiliation(s)
- Philipp C Nickels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Bettina Wünsch
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Phil Holzmeister
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Luisa M Kneer
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Dina Grohmann
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany.
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Abstract
The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.
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Uncovering ancient transcription systems with a novel evolutionary indicator. Sci Rep 2016; 6:27922. [PMID: 27307191 PMCID: PMC4910066 DOI: 10.1038/srep27922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
TBP and TFIIB are evolutionarily conserved transcription initiation factors in archaea and eukaryotes. Information about their ancestral genes would be expected to provide insight into the origin of the RNA polymerase II-type transcription apparatus. In obtaining such information, the nucleotide sequences of current genes of both archaea and eukaryotes should be included in the analysis. However, the present methods of evolutionary analysis require that a subset of the genes should be excluded as an outer group. To overcome this limitation, we propose an innovative concept for evolutionary analysis that does not require an outer group. This approach utilizes the similarity in intramolecular direct repeats present in TBP and TFIIB as an evolutionary measure revealing the degree of similarity between the present offspring genes and their ancestors. Information on the properties of the ancestors and the order of emergence of TBP and TFIIB was also revealed. These findings imply that, for evolutionarily early transcription systems billions of years ago, interaction of RNA polymerase II with transcription initiation factors and the regulation of its enzymatic activity was required prior to the accurate positioning of the enzyme. Our approach provides a new way to discuss mechanistic and system evolution in a quantitative manner.
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Gietl A, Holzmeister P, Blombach F, Schulz S, von Voithenberg LV, Lamb DC, Werner F, Tinnefeld P, Grohmann D. Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways. Nucleic Acids Res 2014; 42:6219-31. [PMID: 24744242 PMCID: PMC4041446 DOI: 10.1093/nar/gku273] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 02/01/2023] Open
Abstract
During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP-DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are highly conserved in structure and function among the eukaryotic-archaeal domain but intriguingly have to operate under vastly different conditions. Employing single-pair fluorescence resonance energy transfer, we monitored DNA bending by eukaryotic and archaeal TBPs in the absence and presence of TFB in real-time. We observed that the lifetime of the TBP-DNA interaction differs significantly between the archaeal and eukaryotic system. We show that the eukaryotic DNA-TBP interaction is characterized by a linear, stepwise bending mechanism with an intermediate state distinguished by a distinct bending angle. TF(II)B specifically stabilizes the fully bent TBP-promoter DNA complex and we identify this step as a regulatory checkpoint. In contrast, the archaeal TBP-DNA interaction is extremely dynamic and TBP from the archaeal organism Sulfolobus acidocaldarius strictly requires TFB for DNA bending. Thus, we demonstrate that transcription initiation follows diverse pathways on the way to the formation of the pre-initiation complex.
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Affiliation(s)
- Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
| | - Fabian Blombach
- RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St., London WC1E 6BT, UK
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
| | - Lena Voith von Voithenberg
- Department of Chemistry, Center for Nanoscience (CeNS) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University, Butenandtstraße 11, 81377 Munich, Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University, Butenandtstraße 11, 81377 Munich, Germany
| | - Finn Werner
- RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St., London WC1E 6BT, UK
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
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