103 results on '"J Weinzierl"'
Search Results
2. Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations
- Author
-
Nicolas E. J. Génin and Robert O. J. Weinzierl
- Subjects
RNA polymerase ,nucleoside triphosphate ,main channel ,secondary channel ,tertiary channel ,downstream bubble ,Microbiology ,QR1-502 - 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.
- Published
- 2020
- Full Text
- View/download PDF
3. Multivalent and Bidirectional Binding of Transcriptional Transactivation Domains to the MED25 Coactivator
- Author
-
Heather M. Jeffery and Robert O. J. Weinzierl
- Subjects
transactivation domain ,coactivator ,mediator ,MED25 ,VP16 ,ETV5 ,Microbiology ,QR1-502 - Abstract
The human mediator subunit MED25 acts as a coactivator that binds the transcriptional activation domains (TADs) present in various cellular and viral gene-specific transcription factors. Previous studies, including on NMR measurements and site-directed mutagenesis, have only yielded low-resolution models that are difficult to refine further by experimental means. Here, we apply computational molecular dynamics simulations to study the interactions of two different TADs from the human transcription factor ETV5 (ERM) and herpes virus VP16-H1 with MED25. Like other well-studied coactivator-TAD complexes, the interactions of these intrinsically disordered domains with the coactivator surface are temporary and highly dynamic (‘fuzzy’). Due to the fact that the MED25 TAD-binding region is organized as an elongated cleft, we specifically asked whether these TADs are capable of binding in either orientation and how this could be achieved structurally and energetically. The binding of both the ETV5 and VP16-TADs in either orientation appears to be possible but occurs in a conformationally distinct manner and utilizes different sets of hydrophobic residues present in the TADs to drive the interactions. We propose that MED25 and at least a subset of human TADs specifically evolved a redundant set of molecular interaction patterns to allow binding to particular coactivators without major prior spatial constraints.
- Published
- 2020
- Full Text
- View/download PDF
4. Robotic Affinity Purification of Soluble and Insoluble Recombinant Glutathione-S-Transferase Fusion Proteins
- Author
-
Robert O J, Weinzierl
- Subjects
Robotic Surgical Procedures ,Recombinant Fusion Proteins ,Escherichia coli ,Glutathione ,Chromatography, Affinity ,Glutathione Transferase - Abstract
A completely automated purification of glutathione-S-transferase (GST) fusion proteins, either in soluble form or after renaturation of insoluble inclusion bodies, is described. Depending on the expression levels and the amount of glutathione affinity matrix employed, the protocol yields approximately 30-100 μg of purified GST-fusion protein from 2 mL microplate cultures. The high yield is facilitated by employing an efficient chemical/enzymatic lysis procedure for preparing bacterial cell lysates. Insoluble GST-fusion proteins are automatically refolded by a high-throughput robotic microdialysis procedure that also assesses the degree of successful refolding by integrated GST enzymatic assays and quantitation of soluble protein successfully recovered after affinity purification. For soluble GST-fusion proteins the purification procedure is normally completed within 60 min, whereas urea-based denaturation-renaturation strategies typically require an additional 18 h. The integration of quantitation of cell growth and affinity-purified GST-fusion protein yield allows direct comparisons of different expression constructs and the yield of soluble GST-fusion proteins to be optimized in a systematic manner.
- Published
- 2022
5. Molecular Dynamics of 'Fuzzy' Transcriptional Activator-Coactivator Interactions.
- Author
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Natalie S. Scholes and Robert O. J. Weinzierl
- Published
- 2016
- Full Text
- View/download PDF
6. Robotic Affinity Purification of Soluble and Insoluble Recombinant Glutathione-S-Transferase Fusion Proteins
- Author
-
Robert O. J. Weinzierl
- Published
- 2022
7. The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions.
- Author
-
Simone C. Wiesler and Robert O. J. Weinzierl
- Published
- 2011
- Full Text
- View/download PDF
8. Untersuchung der Regelwerke für den passiven Schallschutz unter Berücksichtigung aktueller Verkehrslärmspektren – Teil 1
- Author
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J. Weinzierl and W. Wieland
- Subjects
Acoustics and Ultrasonics ,Public Health, Environmental and Occupational Health ,Pollution - Abstract
In den Regelwerken zum passiven Schallschutz von Umfassungsbauteilen wird das erforderliche Schalldämm-Maß der Fassade als Einzahlwert entsprechend dem Bewertungsverfahren nach DIN EN ISO 717-1 [1] ermittelt. Um die spektrale Zusammensetzung verschiedener Lärmquellen und die frequenzabhängige Schalldämmung von Fassadenbauteilen zu berücksichtigen, werden in den einschlägigen Regelwerken Korrektursummanden bzw. Spektrum-Anpassungswerte verwendet. Im folgenden Beitrag wird der Einfluss verschiedener Außenlärmspektren und frequenz- abhängiger Schalldämm-Maße auf den Innenpegel diskutiert. Insbesondere werden die Unterschiede zwischen Holz- und Massivbauweise bezüglich des Schutzziels bzw. des Innenpegels betrachtet. Die Untersuchungen zeigen, dass keine generelle Differenzierung zwischen Leicht- und Massivbauweise erforderlich ist. Für hochschalldämmende Leichtbaukonstruktionen mit einem Ctr,50–5000 < –8 dB wird jedoch ein Korrekturterm für das erforderliche Fassaden-Schalldämm-Maß zur Sicherstellung des Schutzziels vorgeschlagen. Summary In the regulations for passive noise protection of surrounding components, the required sound reduction index of the facade is determined as a single value according to the assessment procedure according to DIN EN ISO 717-1 [1]. In order to take into account the spectral composition of different noise sources and the frequency-dependent sound insulation of facade components, correction summands or spectrum adaptation values are used in the relevant regulations. The following article discusses the influence of various outside noise spectra and frequency-dependent sound insulation measures on the inside level. In particular, the differences between wood and solid construction were considered with regard to the protection goal and the internal level. The investigations show that no general differentiation between lightweight and solid construction is necessary. For highly sound-insulating lightweight constructions with a Ctr, 50–5000  
- Published
- 2020
9. Untersuchung der Regelwerke für den passiven Schallschutz unter Berücksichtigung aktueller Verkehrslärmspektren – Teil 2
- Author
-
W. Wieland and J. Weinzierl
- Subjects
Acoustics and Ultrasonics ,Public Health, Environmental and Occupational Health ,Pollution - Abstract
Die DIN 4109-2:2018 [2] sieht aufgrund der Frequenzzusammensetzung von Schienenverkehrsgeräuschen in Verbindung mit dem Frequenzspektrum der Schalldämm-Maße von Außenbauteilen eine pauschale Minderung des Beurteilungspegels von 5 dB vor. Inwieweit dieser Pauschalansatz, nachfolgend als Schienenkorrekturterm bezeichnet, ohne Differenzierung nach Zuggattungen und Fahrgeschwindigkeit Bestand haben wird, ist aktuell auch Thema im Schiedsverfahren zur DIN 4109 [2]. Die vorliegende Untersuchung, welche für eine Lochfassade mit geringem Fensterflächenanteil durchgeführt wurde, nimmt eine vergleichende Betrachtung der für innerstädtischen Schienenverkehrslärm und Straßenverkehrslärm ermittelten Korrektursummanden vor. Die Differenzen aus den Korrektursummanden für Schienenverkehr und Straßenverkehr werden mit dem bisherigen Ansatz zum Schienenkorrekturterm von 5 dB verglichen. Summary DIN 4109-2: 2018 [2] provides for a general reduction in the assessment level of 5 dB due to the frequency composition of rail traffic noise in connection with the frequency spectrum of the sound insulation dimensions of external components. The extent to which this flat-rate approach, hereinafter referred to as the rail correction term, will persist without differentiation according to the type of train and the speed of travel is currently also an issue in the arbitration proceedings to DIN 4109 [2]. The present investigation, which was carried out for a perforated facade with a small proportion of windows, takes a comparative look at the correction summaries determined for inner-city rail traffic noise and road traffic noise. The differences from the correction summands for rail traffic and road traffic are compared with the previous approach to the rail correction term of 5 dB.
- Published
- 2020
10. An approach towards understanding an open-structure frequency-doubler.
- Author
-
M. Shaalan, M. Bozzi, J. Weinzierl, and H. L. Hartnagel
- Published
- 1998
- Full Text
- View/download PDF
11. Clinical significance of substantially elevated von Willebrand factor antigen levels in patients with advanced chronic liver disease
- Author
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M. Trauner, Mattias Mandorfer, Lorenz Balcar, Peter Quehenberger, AF Stättermayer, Bernhard Scheiner, RJ Nussbaumer, Rafael Paternostro, Matthias Pinter, Georg Semmler, Benedikt Simbrunner, Lukas Hartl, Thomas Reiberger, Douglas C. Bauer, Katharina Pomej, Mathias Jachs, and J Weinzierl
- Subjects
medicine.medical_specialty ,business.industry ,Internal medicine ,medicine ,In patient ,Clinical significance ,business ,Chronic liver disease ,medicine.disease ,Gastroenterology ,Von Willebrand factor Antigen - Published
- 2021
12. Factor VIII/protein C ratio independently predicts liver-related events but does not reflect the hypercoagulable state in patients with advanced-chronic liver disease
- Author
-
M. Trauner, RJ Nussbaumer, Mathias Jachs, Lorenz Balcar, Ton Lisman, Georg Semmler, Bernhard Scheiner, AF Stättermayer, Benedikt Simbrunner, Matthias Pinter, J Weinzierl, Peter Quehenberger, Douglas C. Bauer, Rafael Paternostro, Thomas Reiberger, Mattias Mandorfer, and Lukas Hartl
- Subjects
medicine.medical_specialty ,business.industry ,Internal medicine ,medicine ,In patient ,Chronic liver disease ,medicine.disease ,business ,Gastroenterology ,Protein C ,medicine.drug - Published
- 2021
13. Analysis of quasi-optical power combiners by vector field measurements at 150 GHz
- Author
-
R. Judaschke and J. Weinzierl
- Subjects
Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
A Two-dimensional quasi-optical power dividing/combining circuit has been experimentally investigated at 150 GHz. It consists of a rectangular horn antenna array as receiving/transmitting unit and a dual offset reflector setup to match the radiated field(s) to the pattern of the receiving antenna(s). To verify both design and adjustment of the quasi-optical circuit, electric field scans have been performed in selected planes and volumes of the setup. To measure the spatial electric field distribution, a vector field measurement system has been developed which operates in the frequency range between 148 GHz and 152 GHz. Excellent agreement between calculated and measured results for a horn antenna array approve the predicted results calculated under the physical optics approximation. Measured power dividing/combining efficiency of the passive structure of 63% for an inter-element spacing of 10$ lambda$ indicates that the power combining principle is a suitable method up to submillimeter wavelengths.
- Published
- 2007
14. Molecular Dynamics Simulations of Human FOXO3 Reveal Intrinsically Disordered Regions Spread Spatially by Intramolecular Electrostatic Repulsion
- Author
-
Robert O. J. Weinzierl
- Subjects
0301 basic medicine ,Implicit solvation ,Static Electricity ,Structural diversity ,0601 Biochemistry and Cell Biology ,01 natural sciences ,Biochemistry ,Microbiology ,Article ,03 medical and health sciences ,Molecular dynamics ,DNA-binding ,computational biology ,Protein Domains ,longevity ,0103 physical sciences ,Humans ,cancer ,Molecular Biology ,Transcription factor ,transcription factor ,Physics ,010304 chemical physics ,Forkhead Box Protein O3 ,apoptosis ,FOXO3 ,local compaction tool ,Electrostatics ,intrinsically disordered protein ,QR1-502 ,Intrinsically Disordered Proteins ,Folding (chemistry) ,030104 developmental biology ,molecular dynamics simulation ,Chemical physics ,Intramolecular force ,Linker - Abstract
The human transcription factor FOXO3 (a member of the ‘forkhead’ family of transcription factors) controls a variety of cellular functions that make it a highly relevant target for intervention in anti-cancer and anti-aging therapies. FOXO3 is a mostly intrinsically disordered protein (IDP). Absence of knowledge of its structural properties outside the DNA-binding domain constitutes a considerable obstacle to a better understanding of structure/function relationships. Here, I present extensive molecular dynamics (MD) simulation data based on implicit solvation models of the entire FOXO3/DNA complex, and accelerated MD simulations under explicit solvent conditions of a central region of particular structural interest (FOXO3120–530). A new graphical tool for studying and visualizing the structural diversity of IDPs, the Local Compaction Plot (LCP), is introduced. The simulations confirm the highly disordered nature of FOXO3 and distinguish various degrees of folding propensity. Unexpectedly, two ‘linker’ regions immediately adjacent to the DNA-binding domain are present in a highly extended conformation. This extended conformation is not due to their amino acid composition, but rather is caused by electrostatic repulsion of the domains connected by the linkers. FOXO3 is thus an IDP present in an unusually extended conformation to facilitate interaction with molecular interaction partners.
- Published
- 2021
15. Nucleotide loading modes of human RNA polymerase II as deciphered by molecular simulations
- Author
-
Robert O. J. Weinzierl, Nicolas E. J. Génin, and Medical Research Council (MRC)
- Subjects
Models, Molecular ,0301 basic medicine ,Transcription, Genetic ,Protein Conformation ,Molecular Conformation ,lcsh:QR1-502 ,secondary channel ,RNA polymerase II ,Molecular Dynamics Simulation ,0601 Biochemistry and Cell Biology ,01 natural sciences ,Biochemistry ,Article ,lcsh:Microbiology ,downstream bubble ,Transcription Factors, TFII ,03 medical and health sciences ,Molecular dynamics ,chemistry.chemical_compound ,Catalytic Domain ,RNA polymerase ,0103 physical sciences ,Humans ,nucleoside triphosphate ,Nucleotide ,tertiary channel ,Molecular Biology ,chemistry.chemical_classification ,010304 chemical physics ,biology ,Nucleotides ,TFIIF ,diffusion ,Active site ,DNA ,main channel ,loading ,030104 developmental biology ,chemistry ,biology.protein ,Nucleoside triphosphate ,Biophysics ,Nucleic Acid Conformation ,RNA ,entry ,Transcription factor II F ,RNA Polymerase II - 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.
- Published
- 2020
16. Multivalent and bidirectional binding of transcriptional transactivation domains to the MED25 coactivator
- Author
-
Heather Jeffery and Robert O. J. Weinzierl
- Subjects
Transcriptional Activation ,Protein subunit ,lcsh:QR1-502 ,Mutagenesis (molecular biology technique) ,computational prediction ,Computational biology ,intrinsically disordered ,transactivation domain ,0601 Biochemistry and Cell Biology ,01 natural sciences ,Biochemistry ,MED25 ,‘fuzzy’ complex ,Article ,lcsh:Microbiology ,bidirectional binding ,03 medical and health sciences ,Molecular dynamics ,Transactivation ,Mediator ,VP16 ,Protein Domains ,0103 physical sciences ,Coactivator ,Humans ,Molecular Biology ,Transcription factor ,030304 developmental biology ,0303 health sciences ,Mediator Complex ,010304 chemical physics ,Chemistry ,ETV5 ,coactivator ,molecular dynamics simulation ,ERM ,mediator ,Transcriptional transactivation ,Protein Binding ,Transcription Factors - Abstract
The human mediator subunit MED25 acts as a coactivator that binds the transcriptional activation domains (TADs) present in various cellular and viral gene-specific transcription factors. Previous studies, including on NMR measurements and site-directed mutagenesis, have only yielded low-resolution models that are difficult to refine further by experimental means. Here, we apply computational molecular dynamics simulations to study the interactions of two different TADs from the human transcription factor ETV5 (ERM) and herpes virus VP16-H1 with MED25. Like other well-studied coactivator-TAD complexes, the interactions of these intrinsically disordered domains with the coactivator surface are temporary and highly dynamic (&lsquo, fuzzy&rsquo, ). Due to the fact that the MED25 TAD-binding region is organized as an elongated cleft, we specifically asked whether these TADs are capable of binding in either orientation and how this could be achieved structurally and energetically. The binding of both the ETV5 and VP16-TADs in either orientation appears to be possible but occurs in a conformationally distinct manner and utilizes different sets of hydrophobic residues present in the TADs to drive the interactions. We propose that MED25 and at least a subset of human TADs specifically evolved a redundant set of molecular interaction patterns to allow binding to particular coactivators without major prior spatial constraints.
- Published
- 2020
17. Optimization of Molecular Dynamics Simulations of c-MYC1-88—An Intrinsically Disordered System
- Author
-
Sandra S. Sullivan and Robert O. J. Weinzierl
- Subjects
0301 basic medicine ,Implicit solvation ,Intrinsically disordered proteins ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Molecular dynamics ,oncoproteins ,0103 physical sciences ,Water model ,lcsh:Science ,Protein secondary structure ,Ecology, Evolution, Behavior and Systematics ,Physics ,010304 chemical physics ,Paleontology ,molecular dynamics simulations ,Range (mathematics) ,030104 developmental biology ,c-MYC ,Space and Planetary Science ,Trajectory analysis ,lcsh:Q ,Biological system ,Primary sequence - Abstract
Many of the proteins involved in key cellular regulatory events contain extensive intrinsically disordered regions that are not readily amenable to conventional structure/function dissection. The oncoprotein c-MYC plays a key role in controlling cell proliferation and apoptosis and more than 70% of the primary sequence is disordered. Computational approaches that shed light on the range of secondary and tertiary structural conformations therefore provide the only realistic chance to study such proteins. Here, we describe the results of several tests of force fields and water models employed in molecular dynamics simulations for the N-terminal 88 amino acids of c-MYC. Comparisons of the simulation data with experimental secondary structure assignments obtained by NMR establish a particular implicit solvation approach as highly congruent. The results provide insights into the structural dynamics of c-MYC1-88, which will be useful for guiding future experimental approaches. The protocols for trajectory analysis described here will be applicable for the analysis of a variety of computational simulations of intrinsically disordered proteins.
- Published
- 2020
18. The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement
- Author
-
Robert O. J. Weinzierl
- Subjects
Microbiology ,QR1-502 - Abstract
The availability of in vitro assembly systems to produce recombinant archaeal RNA polymerases (RNAPs) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying RNAP function. Over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. The Bridge Helix domain, which appears in numerous X-ray structures as a 35-amino-acid-long alpha helix, coordinates the concerted movement of several other domains during catalysis through kinking of two discrete molecular hinges. Mutations affecting these kinking mechanisms have a direct effect on the specific catalytic activity of RNAP and can in some instances more than double it. Molecular dynamics simulations have established themselves as exceptionally useful for providing additional insights and detailed models to explain the underlying structural motions.
- Published
- 2011
- Full Text
- View/download PDF
19. High-Throughput Simulations of Protein Dynamics in Molecular Machines: The ‘Link’ Domain of RNA Polymerase
- Author
-
J. Weinzierl, Robert O., primary
- Published
- 2012
- Full Text
- View/download PDF
20. An Amino Acid Substitution in RNA Polymerase That Inhibits the Utilization of an Alternative Sigma Factor
- Author
-
Ann Hochschild, Robert O. J. Weinzierl, Richard Losick, Cinthia P. Garcia, Anna F. Wang Erickson, and Padraig Deighan
- Subjects
0301 basic medicine ,Models, Molecular ,Protein Conformation ,Protein subunit ,Mutant ,Sigma Factor ,Biology ,Microbiology ,Gene Expression Regulation, Enzymologic ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Transcription (biology) ,Sigma factor ,RNA polymerase ,Gene expression ,Escherichia coli ,Molecular Biology ,Gene ,Conserved Sequence ,Coiled coil ,DNA-Directed RNA Polymerases ,Gene Expression Regulation, Bacterial ,030104 developmental biology ,chemistry ,Biochemistry ,Amino Acid Substitution ,bacteria ,Bacillus subtilis ,Research Article - Abstract
Sigma (σ) factors direct gene transcription by binding to and determining the promoter recognition specificity of RNA polymerase (RNAP) in bacteria. Genes transcribed under the control of alternative sigma factors allow cells to respond to stress and undergo developmental processes, such as sporulation in Bacillus subtilis , in which gene expression is controlled by a cascade of alternative sigma factors. Binding of sigma factors to RNA polymerase depends on the coiled-coil (or clamp helices) motif of the β′ subunit. We have identified an amino acid substitution (L257P) in the coiled coil that markedly inhibits the function of σ H , the earliest-acting alternative sigma factor in the sporulation cascade. Cells with this mutant RNAP exhibited an early and severe block in sporulation but not in growth. The mutant was strongly impaired in σ H -directed gene expression but not in the activity of the stress-response sigma factor σ B . Pulldown experiments showed that the mutant RNAP was defective in associating with σ H but could still associate with σ A and σ B . The differential effects of the L257P substitution on sigma factor binding to RNAP are likely due to a conformational change in the β′ coiled coil that is specifically detrimental for interaction with σ H . This is the first example, to our knowledge, of an amino acid substitution in RNAP that exhibits a strong differential effect on a particular alternative sigma factor. IMPORTANCE In bacteria, all transcription is mediated by a single multisubunit RNA polymerase (RNAP) enzyme. However, promoter-specific transcription initiation necessitates that RNAP associates with a σ factor. Bacteria contain a primary σ factor that directs transcription of housekeeping genes and alternative σ factors that direct transcription in response to environmental or developmental cues. We identified an amino acid substitution (L257P) in the B. subtilis β′ subunit whereby RNAP L257P associates with some σ factors (σ A and σ B ) and enables vegetative cell growth but is defective in utilization of σ H and is consequently blocked for sporulation. To our knowledge, this is the first identification of an amino acid substitution within the core enzyme that affects utilization of a specific sigma factor.
- Published
- 2017
21. The RNA Polymerase Factory and Archaeal Transcription
- Author
-
Robert O. J. Weinzierl
- Subjects
Transcription factories ,Protein Denaturation ,Protein Folding ,Transcription, Genetic ,biology ,Archaeal Proteins ,RNA-dependent RNA polymerase ,RNA polymerase II ,DNA-Directed RNA Polymerases ,General Chemistry ,Archaea ,Recombinant Proteins ,Protein Structure, Tertiary ,chemistry.chemical_compound ,chemistry ,Biochemistry ,RNA polymerase ,Mutagenesis, Site-Directed ,biology.protein ,RNA polymerase I ,Transcription factor II D ,RNA polymerase II holoenzyme ,Polymerase - Published
- 2013
22. Revealing the functions of TFIIB
- Author
-
Simone C. Wiesler and Robert O. J. Weinzierl
- Subjects
Models, Molecular ,Sequence Homology, Amino Acid ,Transcription, Genetic ,Chemistry ,Archaeal Proteins ,Methanococcales ,Mutant ,DNA-Directed RNA Polymerases ,Crystallography, X-Ray ,Bioinformatics ,Biochemistry ,Protein Structure, Tertiary ,Transcription initiation ,enzymes and coenzymes (carbohydrates) ,Mutation ,Transcription Factor TFIIB ,Genetics ,Biophysics ,Amino Acid Sequence ,Point of View ,Linker ,Transcription factor II B ,Protein Binding ,Biotechnology - Abstract
The TFIIB linker domain stimulates the catalytic activity of archaeal RNAP. By characterising a range of super-stimulating mutants we identified a novel rate-limiting step in transcription initiation. Our results help to interpret structural findings and pave the way towards higher-resolution structures of the RNAP-TFIIB linker interface.
- Published
- 2011
23. Activity Map of the Escherichia coli RNA Polymerase Bridge Helix*
- Author
-
Beatriz Cámara, Milija Jovanovic, Martin Buck, Sivaramesh Wigneshweraraj, Simone C. Wiesler, Patricia C. Burrows, Daniel Bose, Robert O. J. Weinzierl, and Xiaodong Zhang
- Subjects
genetic processes ,Molecular Sequence Data ,Gene Expression ,Biochemistry ,Microbiology ,RNA Synthesis ,Gene Expression Regulation, Enzymologic ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein structure ,Transcription Initiation Factors ,Transcription (biology) ,RNA polymerase ,Escherichia coli ,A-DNA ,Amino Acid Sequence ,Molecular Biology ,Polymerase ,030304 developmental biology ,RNA Cleavage ,0303 health sciences ,Alanine ,Binding Sites ,biology ,Sequence Homology, Amino Acid ,Lysine ,RNA Polymerase ,Genetic Complementation Test ,RNA ,Cell Biology ,DNA-Directed RNA Polymerases ,Gene Expression Regulation, Bacterial ,Alanine scanning ,Protein Structure, Tertiary ,enzymes and coenzymes (carbohydrates) ,chemistry ,Mutation ,biology.protein ,health occupations ,bacteria ,Transcription ,030217 neurology & neurosurgery ,DNA ,Protein Binding ,Sinorhizobium meliloti - Abstract
Transcription, the synthesis of RNA from a DNA template, is performed by multisubunit RNA polymerases (RNAPs) in all cellular organisms. The bridge helix (BH) is a distinct feature of all multisubunit RNAPs and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and RNA and DNA binding. Because the BH has been captured in both kinked and straight conformations in different crystals structures of RNAP, recently supported by molecular dynamics studies, it has been proposed that cycling between these conformations is an integral part of the nucleotide addition cycle. To further evaluate the role of the BH, we conducted systematic alanine scanning mutagenesis of the Escherichia coli RNAP BH to determine its contributions to activities required for transcription. Combining our data with an atomic model of E. coli RNAP, we suggest that alterations in the interactions between the BH and (i) the trigger loop, (ii) fork loop 2, and (iii) switch 2 can help explain the observed changes in RNAP functionality associated with some of the BH variants. Additionally, we show that extensive defects in E. coli RNAP functionality depend upon a single previously not studied lysine residue (Lys-781) that is strictly conserved in all bacteria. It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality.
- Published
- 2011
24. The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions
- Author
-
Simone C. Wiesler and Robert O. J. Weinzierl
- Subjects
Transcriptional Activation ,Archaeal Proteins ,RNA polymerase II ,Gene Regulation, Chromatin and Epigenetics ,Abortive initiation ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Genetics ,Transcription factor ,030304 developmental biology ,Sequence Deletion ,0303 health sciences ,biology ,General transcription factor ,Methanococcales ,Promoter ,Protein Structure, Tertiary ,enzymes and coenzymes (carbohydrates) ,Phenotype ,Amino Acid Substitution ,Mutation ,biology.protein ,Transcription Factor TFIIB ,RNA Polymerase II ,Transcription factor II B ,030217 neurology & neurosurgery ,Transcription factor II A - Abstract
RNA polymerases (RNAPs) require basal transcription factors to assist them during transcription initiation. One of these factors, TFIIB, combines promoter recognition, recruitment of RNAP, promoter melting, start site selection and various post-initiation functions. The ability of 381 site-directed mutants in the TFIIB 'linker domain' to stimulate abortive transcription was systematically quantitated using promoter-independent dinucleotide extension assays. The results revealed two distinct clusters (mjTFIIB E78-R80 and mjTFIIB R90-G94, respectively) that were particularly sensitive to substitutions. In contrast, a short sequence (mjTFIIB A81-K89) between these two clusters tolerated radical single amino acid substitutions; short deletions in that region even caused a marked increase in the ability of TFIIB to stimulate abortive transcription ('superstimulation'). The superstimulating activity did, however, not correlate with increased recruitment of the TFIIB/RNAP complex because substitutions in a particular residue (mjTFIIB K87) increased recruitment by more than 5-fold without affecting the rate of abortive transcript stimulation. Our work demonstrates that highly localized changes within the TFIIB linker have profound, yet surprisingly disconnected, effects on RNAP recruitment, TFIIB/RNAP complex stability and the rate of transcription initiation. The identification of superstimulating TFIIB variants reveals the existence of a previously unknown rate-limiting step acting on the earliest stages of gene expression.
- Published
- 2010
25. The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes
- Author
-
Hannah C. Carney, Dominika Trzaska, Lin Tan, Sven Nottebaum, and Robert O. J. Weinzierl
- Subjects
Archaeal Proteins ,Genetic Vectors ,Molecular Sequence Data ,Mutagenesis (molecular biology technique) ,Computational biology ,Biology ,Protein Engineering ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,law ,RNA polymerase ,Protein purification ,Genetics ,Amino Acid Sequence ,Saturated mutagenesis ,Polymerase ,030304 developmental biology ,0303 health sciences ,Base Sequence ,Nucleic Acid Enzymes ,030306 microbiology ,RNA ,DNA-Directed RNA Polymerases ,Robotics ,Protein engineering ,Archaea ,Recombinant Proteins ,Protein Subunits ,chemistry ,Mutagenesis ,Recombinant DNA ,biology.protein - Abstract
The in-depth structure/function analysis of large protein complexes, such as RNA polymerases (RNAPs), requires an experimental platform capable of assembling variants of such enzymes in large numbers in a reproducible manner under defined in vitro conditions. Here we describe a streamlined and integrated protocol for assembling recombinant archaeal RNAPs in a high-throughput 96-well format. All aspects of the procedure including construction of redesigned expression plasmids, development of automated protein extraction/in vitro assembly methods and activity assays were specifically adapted for implementation on robotic platforms. The optimized strategy allows the parallel assembly and activity assay of 96 recombinant RNAPs (including wild-type and mutant variants) with little or no human intervention within 24 h. We demonstrate the high-throughput potential of this system by evaluating the side-chain requirements of a single amino acid position of the RNAP Bridge Helix using saturation mutagenesis.
- Published
- 2007
26. Robotic high-throughput purification of affinity-tagged recombinant proteins
- Author
-
Simone C, Wiesler and Robert O J, Weinzierl
- Subjects
Bacteria ,Robotics ,Chromatography, Affinity ,Microspheres ,Recombinant Proteins ,Cell Proliferation - Abstract
Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories.
- Published
- 2015
27. Robotic High-Throughput Purification of Affinity-Tagged Recombinant Proteins
- Author
-
Simone C. Wiesler and Robert O. J. Weinzierl
- Subjects
Activity measurements ,Affinity chromatography ,law ,Chemistry ,Recombinant DNA ,Potential source ,Computational biology ,Throughput (business) ,law.invention - Abstract
Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories.
- Published
- 2015
28. Systematic mutational analysis of the LytTR DNA binding domain of Staphylococcus aureus virulence gene transcription factor AgrA
- Author
-
Sophie S, Nicod, Robert O J, Weinzierl, Lynn, Burchell, Andres, Escalera-Maurer, Ellen H, James, and Sivaramesh, Wigneshweraraj
- Subjects
Transcriptional Activation ,Staphylococcus aureus ,Structure-Activity Relationship ,Bacterial Proteins ,Mutagenesis ,Virulence Factors ,Mutation ,Gene regulation, Chromatin and Epigenetics ,Trans-Activators ,Protein Binding ,Protein Structure, Tertiary - Abstract
Most DNA-binding bacterial transcription factors contact DNA through a recognition α-helix in their DNA-binding domains. An emerging class of DNA-binding transcription factors, predominantly found in pathogenic bacteria interact with the DNA via a relatively novel type of DNA-binding domain, called the LytTR domain, which mainly comprises β strands. Even though the crystal structure of the LytTR domain of the virulence gene transcription factor AgrA from Staphylococcus aureus bound to its cognate DNA sequence is available, the contribution of specific amino acid residues in the LytTR domain of AgrA to transcription activation remains elusive. Here, for the first time, we have systematically investigated the role of amino acid residues in transcription activation in a LytTR domain-containing transcription factor. Our analysis, which involves in vivo and in vitro analyses and molecular dynamics simulations of S. aureus AgrA identifies a highly conserved tyrosine residue, Y229, as a major amino acid determinant for maximal activation of transcription by AgrA and provides novel insights into structure–function relationships in S. aureus AgrA.
- Published
- 2014
29. Genetics and development
- Author
-
M Rees, Rein Aasland, R. Mark Gardiner, Tracy Ferea, Robert O. J. Weinzierl, Sara E. Mole, Hannah M. Mitchison, Michael Tsang, Sibylle Mittnacht, Neil Hukriede, Richard Benton, and Mike Jones
- Subjects
Genetics ,Regulation of gene expression ,Computational biology ,Stem cell ,Biology ,Developmental Biology - Published
- 2002
30. Cell biology
- Author
-
Guy Servant, Julia Kaltschmidt, Micheal Tsang, Arshad Desai, Martin Pfaff, Paul A. Slesinger, Rein Aasland, Vas Ponnambalam, Elizabeth A. Holleran, Orion D. Weiner, Robert O. J. Weinzierl, Robert A. Sclafani, Peter van Roessel, Serge Roche, and Neil Huckriede
- Subjects
Cognitive science ,Physiology ,Computational biology ,Cell Biology ,Biology - Published
- 2002
31. Paper alert: Genetics and development
- Author
-
R. Mark Gardiner, Hannah M. Mitchison, Sibylle Mittnacht, Sara E. Mole, Neil Huckriede, Robert O. J. Weinzierl, Mike Jones, Michael Tsang, Tracy Ferea, M Rees, and Richard Benton
- Subjects
Genetics ,Engineering ethics ,Biology ,Developmental Biology - Published
- 2001
32. Paper alert: Cell biology
- Author
-
Elizabeth A. Holleran, Rein Aasland, Vas Ponnambalam, Neil Hukriede, Richard Benton, Michael Tsang, Robert O. J. Weinzierl, Michelle L. Matter, Orion D. Weiner, Arshad Desai, Paul A. Slesinger, Joe W. Ramos, and John P. Incardona
- Subjects
Zoology ,Cell Biology ,Computational biology ,Biology - Published
- 2001
33. Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12
- Author
-
Finn Werner, Jyrki J. Eloranta, and Robert O. J. Weinzierl
- Subjects
Methanococcus ,Saccharomyces cerevisiae Proteins ,Macromolecular Substances ,Archaeal Proteins ,Recombinant Fusion Proteins ,Protein subunit ,Molecular Sequence Data ,Sequence Homology ,RNA polymerase II ,Sequence alignment ,Article ,Substrate Specificity ,chemistry.chemical_compound ,Two-Hybrid System Techniques ,RNA polymerase ,Genetics ,Humans ,Amino Acid Sequence ,Peptide sequence ,Polymerase ,biology ,Thrombin ,RNA ,biology.organism_classification ,Protein Subunits ,Eukaryotic Cells ,chemistry ,biology.protein ,RNA Polymerase II ,Dimerization ,Sequence Alignment ,Protein Binding - Abstract
The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in archaeal RNA polymerases were only recently identified in a purified archaeal RNA polymerase preparation and, on the basis of localized sequence homologies, tentatively identified as archaeal versions of the eukaryotic RPB4 and RPB12 RNA polymerase subunits, respectively. We prepared recombinant versions of the F and P subunits from Methanococcus jannaschii and used them in in vitro and in vivo protein interaction assays to demonstrate that they interact with other archaeal subunits in a manner predicted from their eukaryotic counterparts. The overall structural conservation of the M. jannaschii F subunit, although not readily recognizable on the primary amino acid sequence level, is sufficiently high to allow the formation of an archaeal-human F-RPB7 hybrid complex.
- Published
- 2000
34. Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target
- Author
-
Robert O. J. Weinzierl, Silvia Onesti, Peter Brick, and Flavia Todone
- Subjects
Genetics ,Multidisciplinary ,biology ,Eukaryotic Large Ribosomal Subunit ,Protein subunit ,Molecular Sequence Data ,RNA ,RNA polymerase II ,DNA-Directed RNA Polymerases ,Saccharomyces cerevisiae ,Biological Sciences ,Protein Structure, Secondary ,Cell biology ,chemistry.chemical_compound ,chemistry ,RNA polymerase ,biology.protein ,Eukaryotic Small Ribosomal Subunit ,Amino Acid Sequence ,Dimerization ,Transcription factor ,Polymerase - Abstract
Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12–18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae . The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP II basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed α-helical structures.
- Published
- 2000
35. Genetics and development
- Author
-
Serge Roche, Alison Schuldt, Mike Jones, Susan E. Douglas, Tracy Ferea, Robert O. J. Weinzierl, Tatjana Piotrowski, Rein Aasland, Elisabeth Dawson, and Sibylle Mittnacht
- Subjects
Engineering management ,Development (topology) ,Genetics ,Biology ,Developmental Biology - Published
- 2000
36. Cell biologyPaper alert
- Author
-
Arshad Desai, Rein Aasland, Martin Pfaff, Serge Roche, Neil Huckriede, Karl Matter, Robert O. J. Weinzierl, Paul A. Slesinger, Elizabeth A. Holleran, and E Izaurralde
- Subjects
medicine.anatomical_structure ,Cell ,medicine ,Cell Biology ,Biology ,Neuroscience - Published
- 1999
37. Eukaryotic RNA polymerase subunit RPB8 is a new relativeof the OB family
- Author
-
Geoff Kelly, Joachim Reischl, Robert O. J. Weinzierl, Stephen Matthews, and Stephan Krapp
- Subjects
Models, Molecular ,Recombinant Fusion Proteins ,Molecular Sequence Data ,5.8S ribosomal RNA ,RNA polymerase II ,Saccharomyces cerevisiae ,Biology ,Biochemistry ,Protein Structure, Secondary ,Evolution, Molecular ,chemistry.chemical_compound ,Structural Biology ,28S ribosomal RNA ,RNA polymerase ,Genetics ,Eukaryotic Small Ribosomal Subunit ,Amino Acid Sequence ,Nuclear Magnetic Resonance, Biomolecular ,Polymerase ,Eukaryotic Large Ribosomal Subunit ,RNA ,chemistry ,biology.protein ,RNA Polymerase II ,Sequence Alignment - Abstract
RNA polymerase II subunit RPB8 is an essential subunit that is highly conserved throughout eukaryotic evolution and is present in all three types of nuclear RNA polymerases. We report the first high resolution structural insight into eukaryotic RNA polymerase architecture with the solution structure of RPB8 from Saccharomyces cerevisiae. It consists of an eight stranded, antiparallel beta-barrel, four short helical regions and a large, unstructured omega-loop. The strands are connected in classic Greek-key fashion. The overall topology is unusual and contains a striking C2 rotational symmetry. Furthermore, it is most likely a novel associate of the oligonucleotide/oligosaccharide (OB) binding protein class.
- Published
- 1998
38. Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase
- Author
-
Simone C, Wiesler, Finn, Werner, and Robert O J, Weinzierl
- Subjects
Viral Proteins ,Transcription, Genetic ,Genes, Reporter ,Archaeal Proteins ,Escherichia coli Proteins ,Methanococcales ,Titrimetry ,Transcription Factor TFIIB ,DNA-Directed RNA Polymerases ,Luciferases ,Promoter Regions, Genetic ,Transcription Initiation, Genetic ,Protein Binding - Abstract
TFIIB-like general transcription factors are required for transcription initiation by all eukaryotic and archaeal RNA polymerases (RNAPs). TFIIB facilitates both recruitment and post-recruitment steps of initiation; in particular, TFIIB stimulates abortive initiation. X-ray crystallography of TFIIB-RNAP II complexes shows that the TFIIB linker region penetrates the RNAP active center, yet the impact of this arrangement on RNAP activity and underlying mechanisms remains elusive. Promoter-independent abortive initiation assays exploit the intrinsic ability of RNAP enzymes to initiate transcription from nicked DNA templates and record the formation of the first phosphodiester bonds. These assays can be used to measure the effect of transcription factors such as TFIIB and RNAP mutations on abortive transcription.
- Published
- 2013
39. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase
- Author
-
Simone C. Wiesler, Robert O. J. Weinzierl, and Finn Werner
- Subjects
Genetics ,General transcription factor ,genetic processes ,Biology ,Cell biology ,Abortive initiation ,enzymes and coenzymes (carbohydrates) ,chemistry.chemical_compound ,chemistry ,Transcription (biology) ,RNA polymerase ,health occupations ,bacteria ,Transcription factor II B ,Transcription factor ,DNA ,Transcription factor II A - Abstract
TFIIB-like general transcription factors are required for transcription initiation by all eukaryotic and archaeal RNA polymerases (RNAPs). TFIIB facilitates both recruitment and post-recruitment steps of initiation; in particular, TFIIB stimulates abortive initiation. X-ray crystallography of TFIIB-RNAP II complexes shows that the TFIIB linker region penetrates the RNAP active center, yet the impact of this arrangement on RNAP activity and underlying mechanisms remains elusive. Promoter-independent abortive initiation assays exploit the intrinsic ability of RNAP enzymes to initiate transcription from nicked DNA templates and record the formation of the first phosphodiester bonds. These assays can be used to measure the effect of transcription factors such as TFIIB and RNAP mutations on abortive transcription.
- Published
- 2013
40. A Fully Recombinant System for Activator-dependent Archaeal Transcription
- Author
-
Robert O. J. Weinzierl, E. Peter Geiduschek, Finn Werner, and Mohamed Ouhammouch
- Subjects
Models, Molecular ,Transcription, Genetic ,Archaeal Proteins ,Methanococcus ,Protein subunit ,RNA polymerase II ,Bioinformatics ,Biochemistry ,chemistry.chemical_compound ,Transcription (biology) ,RNA polymerase ,Molecular Biology ,Recombination, Genetic ,Base Sequence ,biology ,General transcription factor ,Activator (genetics) ,Methanocaldococcus jannaschii ,Cell Biology ,biology.organism_classification ,Recombinant Proteins ,Cell biology ,DNA-Binding Proteins ,Protein Subunits ,DNA, Archaeal ,chemistry ,biology.protein ,RNA Polymerase II ,DNA ,Transcription Factors - Abstract
The core components of the archaeal transcription apparatus closely resemble those of eukaryotic RNA polymerase II, while the DNA-binding transcriptional regulators are predominantly of bacterial type. Here we report the construction of an entirely recombinant system for positively regulated archaeal transcription. By omitting individual subunits, or sets of subunits, from the in vitro assembly of the 12-subunit RNA polymerase from the hyperthermophile Methanocaldococcus jannaschii, we describe a functional dissection of this RNA polymerase II-like enzyme, and its interactions with the general transcription factor TFE, as well as with the transcriptional activator Ptr2.
- Published
- 2004
41. High-throughput Purification of Affinity-tagged Recombinant Proteins
- Author
-
Simone C. Wiesler and Robert O. J. Weinzierl
- Subjects
Bioinformatics ,General Chemical Engineering ,Molecular Sequence Data ,Computational biology ,Biology ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein structure ,Transcription (biology) ,RNA polymerase ,Genetics ,Histidine ,Amino Acid Sequence ,Molecular Biology ,high-throughput ,030304 developmental biology ,automation ,Issue 66 ,Recombinant proteins ,0303 health sciences ,General transcription factor ,General Immunology and Microbiology ,Oligonucleotide ,General Neuroscience ,affinity purification ,High-Throughput Screening Assays ,chemistry ,Transcription preinitiation complex ,Transcription Factor TFIIB ,histidine tag ,Linker ,Transcription factor II B ,030217 neurology & neurosurgery - Abstract
X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity. In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates 1-5 . Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex 6-8 . TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase 9-11 . This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex 4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase 4 . Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results. This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.
- Published
- 2012
42. High-Throughput Simulations of Protein Dynamics in Molecular Machines: The ‘Link’ Domain of RNA Polymerase
- Author
-
Robert O. J. Weinzierl
- Subjects
Genetics ,0303 health sciences ,Chemistry ,Protein dynamics ,030302 biochemistry & molecular biology ,Allosteric regulation ,Computational biology ,Molecular machine ,03 medical and health sciences ,Molecular dynamics ,chemistry.chemical_compound ,Transcription (biology) ,RNA polymerase ,Nucleic acid ,030304 developmental biology ,Macromolecule - Abstract
Complex molecular machines are involved in all information-processing steps in cells. The handling of information-bearing macromolecules (predominantly nucleic acids and proteins) requires a range of catalytic capabilities, such as the sequence-specific synthesis of macromolecular entities from smaller precursors and further processing by breaking/joining of pre-existing molecular components. These catalytic activities have to be spatially and temporally precisely controlled to ensure accuracy and efficiency levels that are commensurate with the associated biological functions (Lyubimov et al., 2011). Unlike metabolic enzymes, which are often medium-sized enzymes with freely accessible active sites, the enzymes associated with replication, transcription, translation, recombination are typically large multi-subunit protein complexes capable of a complex conformational spectrum. This conformational spectrum manifests itself through the dynamic features of individual domains within these molecular machines: many of the domains act explicitly as nanomechanical elements by serving as allosteric sensors, molecular hinges and motor units (Bustamante et al., 2011; Heindl et al., 2011). A deeper understanding of the functions of molecular machines is currently a high-priority topic and ultimate success will strongly depend on a combination of ‘wet-lab’ experimental techniques (X-ray crystallography, NMR, spectroscopic methods, site-directed mutagenesis and chemical cross-linking) with sophisticated computational simulations. Fully atomistic molecular dynamics (MD) simulations offer the most comprehensive and detailed insights into the behavior of molecular entities and are therefore the method of choice for attempts to unravel the structural basis of molecular mechanisms (reviewed in Karplus & McCammon, 2002; Freddolino et al., 2010; McGeagh et al. 2011; Schlick et al., 2011).
- Published
- 2012
43. Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain
- Author
-
Hans Heindl, Tamas Kiss, Pamela Greenwell, Gabor Terstyanszky, Noam Weingarten, and Robert O. J. Weinzierl
- Subjects
Models, Molecular ,biology ,Mutagenesis ,RNA ,Methanocaldococcus jannaschii ,DNA-Directed RNA Polymerases ,Methanococcaceae ,Molecular Dynamics Simulation ,biology.organism_classification ,Biochemistry ,Molecular machine ,Protein Structure, Secondary ,Protein Structure, Tertiary ,chemistry.chemical_compound ,Crystallography ,Protein structure ,chemistry ,RNA polymerase ,Catalytic Domain ,Cations ,Helix ,Biophysics ,biology.protein ,Humans ,Polymerase - Abstract
RNAPs (RNA polymerases) are complex molecular machines that contain a highly conserved catalytic site surrounded by conformationally flexible domains. High-throughput mutagenesis in the archaeal model system Methanocaldococcus jannaschii has demonstrated that the nanomechanical properties of one of these domains, the bridge–helix, exert a key regulatory role on the rate of the NAC (nucleotide-addition cycle). Mutations that increase the probability and/or half-life of kink formation in the BH-HC (bridge–helix C-terminal hinge) cause a substantial increase in specific activity (‘superactivity’). Fully atomistic molecular dynamics simulations show that kinking of the BH-HC appears to be driven by cation–π interactions and involve amino acid side chains that are exceptionally highly conserved in all prokaryotic and eukaryotic species.
- Published
- 2011
44. Largest subunit of Drosophila transcription factor IID directs assembly of a complex containing TBP and a coactivator
- Author
-
Robert Tjian, Robert O. J. Weinzierl, and Brian David Dynlacht
- Subjects
Transcriptional Activation ,Sp1 Transcription Factor ,Protein subunit ,Molecular Sequence Data ,genetic processes ,information science ,macromolecular substances ,Homology (biology) ,law.invention ,law ,Drosophilidae ,Coactivator ,Animals ,Amino Acid Sequence ,Cloning, Molecular ,Histone Acetyltransferases ,Genetics ,TATA-Binding Protein Associated Factors ,Multidisciplinary ,biology ,Nuclear Proteins ,TATA-Box Binding Protein ,biology.organism_classification ,Recombinant Proteins ,Cell biology ,DNA-Binding Proteins ,enzymes and coenzymes (carbohydrates) ,health occupations ,Recombinant DNA ,Drosophila ,Transcription Factor TFIID ,Transcription factor II D ,Transcription factor II A ,Transcription Factors - Abstract
The TFIID complex consists of the TATA-binding protein (TBP) and associated factors (TAFs) serving to mediate transcriptional activation by promoter-specific regulators. Here we report the cloning of Drosophila TAFII250 and the assembly of a partial complex containing recombinant TBP, TAFII110 and the C-terminal domain of TAFII250. This triple complex supports Sp1 activation and reveals specific interactions between TAFII250, TBP and TAFII110.
- Published
- 1993
45. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain
- Author
-
Robert O. J. Weinzierl
- Subjects
Models, Molecular ,Protein Conformation ,Physiology ,Molecular Sequence Data ,Protein domain ,Plant Science ,Molecular Dynamics Simulation ,Biology ,Catalysis ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein structure ,Structural Biology ,Transcription (biology) ,RNA polymerase ,Amino Acid Sequence ,lcsh:QH301-705.5 ,Ecology, Evolution, Behavior and Systematics ,Polymerase ,030304 developmental biology ,0303 health sciences ,Agricultural and Biological Sciences(all) ,Base Sequence ,Biochemistry, Genetics and Molecular Biology(all) ,RNA ,DNA-Directed RNA Polymerases ,Sequence Analysis, DNA ,Cell Biology ,Molecular machine ,Protein Structure, Tertiary ,lcsh:Biology (General) ,Biochemistry ,chemistry ,Mutagenesis ,Biophysics ,biology.protein ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,DNA ,Research Article ,Developmental Biology ,Biotechnology - Abstract
Background: Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results: Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions: The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains. Background RNA polymerases (RNAPs) play a central role in the regulation of gene expression. Like the majority of the enzymes involved in fundamental biological information-processing functions (for example, replication, transcription, recombination, repair), RNAPs are probably best viewed as intricate molecular machines. The movement of nucleic acid substrates, coupled with various types of active site chemistries, requires a precisely orchestrated sequence of conformational changes of protein domains during the transcription cycle (for recent reviews see [1-4]). The nanomechanical mechanisms guiding the structural rearrangements of domains within the active site are still very poorly understood. Thus far, models of the fundamental reaction catalyzed by RNAPs, the nucleotide addition cycle (NAC), have predominantly been derived from a series of crystal structures that contain RNAPs as apoenzymes (for example [5-9]), or complexed with various
- Published
- 2010
46. Nanomechanical constraints acting on the catalytic site of cellular RNA polymerases
- Author
-
Robert O. J. Weinzierl
- Subjects
Models, Molecular ,Cells ,Mutant ,Molecular Sequence Data ,Molecular Conformation ,Saccharomyces cerevisiae ,Biology ,Biochemistry ,Catalytic Domain ,Humans ,Nucleotide ,Amino Acid Sequence ,Polymerase ,chemistry.chemical_classification ,Sequence Homology, Amino Acid ,RNA ,Methanocaldococcus jannaschii ,Active site ,DNA-Directed RNA Polymerases ,Methanococcaceae ,biology.organism_classification ,Molecular machine ,Biomechanical Phenomena ,Nanostructures ,chemistry ,Nucleic acid ,Biophysics ,biology.protein - Abstract
RNAPs (RNA polymerases) are complex molecular machines containing structural domains that co-ordinate the movement of nucleic acid and nucleotide substrates through the catalytic site. X-ray images of bacterial, archaeal and eukaryotic RNAPs have provided a wealth of structural detail over the last decade, but many mechanistic features can only be derived indirectly from such structures. We have therefore implemented a robotic high-throughput structure–function experimental system based on the automatic generation and assaying of hundreds of site-directed mutants in the archaeal RNAP from Methanocaldococcus jannaschii. In the present paper, I focus on recent insights obtained from applying this experimental strategy to the bridge–helix domain. Our work demonstrates that the bridge–helix undergoes substantial conformational changes within a narrowly confined region (mjA′ Ala822-Gln823-Ser824) during the nucleotide-addition cycle. Naturally occurring radical sequence variations in plant RNAP IV and V enzymes map to this region. In addition, many mutations within this domain cause a substantial increase in the RNAP catalytic activity (‘superactivity’), suggesting that the RNAP active site is conformationally constrained.
- Published
- 2010
47. T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site
- Author
-
Steve Matthews, Jonathan Reynolds, Beatriz Cámara, Peter C. Simpson, Minhao Liu, Siva R. Wigneshweraraj, Ernesto Cota, Andrey M. Shadrin, Robert O. J. Weinzierl, Konstantin Severinov, King Kwok, and Bing Liu
- Subjects
DNA, Bacterial ,Models, Molecular ,Genes, Viral ,Protein Conformation ,Static Electricity ,RNA polymerase II ,Biology ,chemistry.chemical_compound ,Transcription (biology) ,RNA polymerase ,Bacteriophage T7 ,Escherichia coli ,Promoter Regions, Genetic ,Nuclear Magnetic Resonance, Biomolecular ,Transcription bubble ,Multidisciplinary ,Binding Sites ,General transcription factor ,Escherichia coli Proteins ,Promoter ,DNA-Directed RNA Polymerases ,Biological Sciences ,Molecular biology ,Cell biology ,Repressor Proteins ,chemistry ,Genes, Bacterial ,Coding strand ,Multiprotein Complexes ,Mutation ,biology.protein ,Transcription Initiation Site ,DNA - Abstract
Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the host RNA polymerase (RNAP)—a multi-subunit enzyme responsible for gene transcription—by a small (∼7 kDa) phage-encoded protein called Gp2. Gp2 is also a potent inhibitor of E. coli RNAP in vitro. Here we describe the first atomic resolution structure of Gp2, which reveals a distinct run of surface-exposed negatively charged amino acid residues on one side of the molecule. Our comprehensive mutagenesis data reveal that two conserved arginine residues located on the opposite side of Gp2 are important for binding to and inhibition of RNAP. Based on a structural model of the Gp2-RNAP complex, we propose that inhibition of transcription by Gp2 involves prevention of RNAP-promoter DNA interactions required for stable DNA strand separation and maintenance of the “transcription bubble” near the transcription start site, an obligatory step in the formation of a transcriptionally competent promoter complex.
- Published
- 2010
48. Bridge helix and trigger loop perturbations generate superactive RNA polymerases
- Author
-
Robert O. J. Weinzierl, Simone C. Wiesler, Dominika Trzaska, Hannah C. Carney, and Lin Tan
- Subjects
Models, Molecular ,Protein Conformation ,Protein subunit ,Molecular Sequence Data ,RNA, Archaeal ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,RNA polymerase ,Amino Acid Sequence ,lcsh:QH301-705.5 ,Polymerase ,030304 developmental biology ,0303 health sciences ,biology ,Agricultural and Biological Sciences(all) ,Biochemistry, Genetics and Molecular Biology(all) ,030302 biochemistry & molecular biology ,Methanocaldococcus jannaschii ,RNA ,DNA-Directed RNA Polymerases ,biology.organism_classification ,Archaea ,Biochemistry ,chemistry ,lcsh:Biology (General) ,Helix ,biology.protein ,Biophysics ,Nucleic acid ,Mutagenesis, Site-Directed ,General Agricultural and Biological Sciences ,Research Article - Abstract
Background Cellular RNA polymerases are highly conserved enzymes that undergo complex conformational changes to coordinate the processing of nucleic acid substrates through the active site. Two domains in particular, the bridge helix and the trigger loop, play a key role in this mechanism by adopting different conformations at various stages of the nucleotide addition cycle. The functional relevance of these structural changes has been difficult to assess from the relatively small number of static crystal structures currently available. Results Using a novel robotic approach we characterized the functional properties of 367 site-directed mutants of the Methanocaldococcus jannaschii RNA polymerase A' subunit, revealing a wide spectrum of in vitro phenotypes. We show that a surprisingly large number of single amino acid substitutions in the bridge helix, including a kink-inducing proline substitution, increase the specific activity of RNA polymerase. Other 'superactivating' substitutions are located in the adjacent base helices of the trigger loop. Conclusion The results support the hypothesis that the nucleotide addition cycle involves a kinked bridge helix conformation. The active center of RNA polymerase seems to be constrained by a network of functional interactions between the bridge helix and trigger loop that controls fundamental parameters of RNA synthesis.
- Published
- 2008
49. Modulation of RNA polymerase core functions by basal transcription factor TFB/TFIIB
- Author
-
Sven Nottebaum, Robert O. J. Weinzierl, Finn Werner, and Simone C. Wiesler
- Subjects
Models, Molecular ,Archaeal Proteins ,Molecular Sequence Data ,RNA polymerase II ,Biochemistry ,Models, Biological ,Evolution, Molecular ,Transcription (biology) ,Animals ,Humans ,Amino Acid Sequence ,RNA polymerase II holoenzyme ,Genetics ,biology ,General transcription factor ,Base Sequence ,Sequence Homology, Amino Acid ,Eukaryotic transcription ,DNA ,DNA-Directed RNA Polymerases ,Archaea ,DNA, Archaeal ,Eukaryotic Cells ,biology.protein ,Transcription Factor TFIIB ,Transcription factor II D ,Transcription factor II B ,Transcription factor II A - Abstract
The archaeal basal transcriptional machinery consists of TBP (TATA-binding protein), TFB (transcription factor B; a homologue of eukaryotic TFIIB) and an RNA polymerase that is structurally very similar to eukaryotic RNA polymerase II. This constellation of factors is sufficient to assemble specifically on a TATA box-containing promoter and to initiate transcription at a specific start site. We have used this system to study the functional interaction between basal transcription factors and RNA polymerase, with special emphasis on the post-recruitment function of TFB. A bioinformatics analysis of the B-finger of archaeal TFB and eukaryotic TFIIB reveals that this structure undergoes rapid and apparently systematic evolution in archaeal and eukaryotic evolutionary domains. We provide a detailed analysis of these changes and discuss their possible functional implications.
- Published
- 2006
50. Imaging Capability of Terahertz and Millimeter-Wave Instrumentations for NDT of Polymer Materials
- Author
-
J. Beckmann, He. Richter, U. Zscherpel, U. Ewert, J. Weinzierl, L.-P. Schmidt, F. Rutz, M. Koch, and H.-W. Hübers
- Published
- 2006
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