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Wetzler DE, Fuchs Wightman F, Bucci HA, Rinaldi J, Caramelo JJ, Iusem ND, Ricardi MM. Conformational plasticity of the intrinsically disordered protein ASR1 modulates its function as a drought stress-responsive gene. PLoS One 2018; 13:e0202808. [PMID: 30138481 PMCID: PMC6107238 DOI: 10.1371/journal.pone.0202808] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/09/2018] [Indexed: 11/18/2022] Open
Abstract
Plants in arid zones are constantly exposed to drought stress. The ASR protein family (Abscisic, Stress, Ripening) -a subgroup of the late embryogenesis abundant superfamily- is involved in the water stress response and adaptation to dry environments. Tomato ASR1, as well as other members of this family, is an intrinsically disordered protein (IDP) that functions as a transcription factor and a chaperone. Here we employed different biophysical techniques to perform a deep in vitro characterization of ASR1 as an IDP and showed how both environmental factors and in vivo targets modulate its folding. We report that ASR1 adopts different conformations such as α-helix or polyproline type II in response to environmental changes. Low temperatures and low pH promote the polyproline type II conformation (PII). While NaCl increases PII content and slightly destabilizes α-helix conformation, PEG and glycerol have an important stabilizing effect of α-helix conformation. The binding of Zn2+in the low micromolar range promotes α-helix folding, while extra Zn2+ results in homo-dimerization. The ASR1-DNA binding is sequence specific and dependent on Zn2+. ASR1 chaperone activity does not change upon the structure induction triggered by the addition of Zn2+. Furthermore, trehalose, which has no effect on the ASR1 structure by itself, showed a synergistic effect on the ASR1-driven heat shock protection towards the reporter enzyme citrate synthase (CS). These observations prompted the development of a FRET reporter to sense ASR1 folding in vivo. Its performance was confirmed in Escherichia coli under saline and osmotic stress conditions, representing a promising probe to be used in plant cells. Overall, this work supports the notion that ASR1 plasticity is a key feature that facilitates its response to drought stress and its interaction with specific targets.
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Affiliation(s)
- Diana E. Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail: (DW); (MR)
| | - Federico Fuchs Wightman
- Departamento de Fisiología y Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Hernan A. Bucci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir, Buenos Aires, Argentina e Instituto de investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Julio J. Caramelo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Fundación Instituto Leloir, Buenos Aires, Argentina e Instituto de investigaciones Bioquímicas de Buenos Aires (IIBBA- CONICET), Buenos Aires, Argentina
| | - Norberto D. Iusem
- Departamento de Fisiología y Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martiniano M. Ricardi
- Departamento de Fisiología y Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail: (DW); (MR)
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Yarawsky AE, English LR, Whitten ST, Herr AB. The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. J Mol Biol 2017; 429:261-279. [PMID: 27890783 PMCID: PMC5363081 DOI: 10.1016/j.jmb.2016.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022]
Abstract
Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a 135-aa-long, proline/glycine-rich region (PGR) that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the PGR using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide with unusually high polyproline type II helix propensity. In contrast to many intrinsically disordered polypeptides, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon the addition of the osmolyte trimethylamine N-oxide or the cosolvent 2,2,2-trifluoroethanol. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B Herr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Chin AF, Toptygin D, Elam WA, Schrank TP, Hilser VJ. Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein. Biophys J 2016; 110:362-371. [PMID: 26789759 DOI: 10.1016/j.bpj.2015.12.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/24/2015] [Accepted: 12/07/2015] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered regions of proteins, which lack unique tertiary structure under physiological conditions, are enriched in phosphorylation sites and in significant local bias toward the polyproline II conformation. The overrepresented coincidence of this posttranslational regulatory signal and local conformational bias within unstructured regions raises a question: can phosphorylation serve to manipulate the conformational preferences of a disordered protein? In this study, we use time-resolved fluorescence resonance energy transfer and a, to our knowledge, novel data analysis method to directly measure the end-to-end distance distribution of a phosphorylatable peptide derived from the human microtubule associated protein tau. Our results show that phosphorylation at threonine or serine extends the end-to-end distance and increases the effective persistence length of the tested model peptides. Unexpectedly, the extension is independent of salt concentration, suggestive of a nonelectrostatic origin. The phosphorylation extension and stiffening effect provides a peptide-scale physical interpretation for the posttranslational regulation of the highly abundant protein-protein interactions found in disordered proteins, as well as a potential insight into the regulatory mechanism of the tau protein's microtubule binding activity.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - W Austin Elam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Travis P Schrank
- Department of Otolaryngology, Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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Chemes LB, Alonso LG, Noval MG, de Prat-Gay G. Circular dichroism techniques for the analysis of intrinsically disordered proteins and domains. Methods Mol Biol 2012; 895:387-404. [PMID: 22760329 DOI: 10.1007/978-1-61779-927-3_22] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Circular dichroism (CD) spectroscopy is a simple and powerful technique, which allows for the assessment of the conformational properties of a protein or protein domain. Intrinsically disordered proteins (IDPs), as discussed throughout this series, differ from random coil polypeptides in that different regions present specific conformational preferences, exhibiting dynamic secondary structure content [1]. These dynamic secondary structure elements can be stabilized or perturbed by different chemical (solvent, ionic strength, pH) or physical (temperature) agents, by posttranslational modifications, and by ligands. This information is important for defining ID nature. As IDPs present dynamic conformations, circular dichroism measurements (and other approaches as well) should be carried out not as single spectra performed in unique conditions, but instead changing the chemical conditions and observing the behavior, as part of the determination of the ID nature.In this chapter, we present the basic methodology for performing Far-UV CD measurements on a protein of interest and for identifying and characterizing intrinsically disordered regions, and several protocols for the analysis of residual secondary structure present in the protein under study. These techniques are straightforward to perform; they require minimal training and can be preliminary to more complex methodologies such as NMR.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure, Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas, Buenos Aires, Argentina.
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Wetzler DE, Comin MJ, Krajewski K, Gallo M. New human papilloma virus E2 transcription factor mimics: a tripyrrole-peptide conjugate with tight and specific DNA-recognition. PLoS One 2011; 6:e22409. [PMID: 21799846 PMCID: PMC3143144 DOI: 10.1371/journal.pone.0022409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/21/2011] [Indexed: 12/02/2022] Open
Abstract
Background Human papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions. Methodology/Principal Findings An E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity. Conclusions/Significance These results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection.
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Affiliation(s)
- Diana E. Wetzler
- Department of Biological Chemistry, FCEN, University of Buenos Aires, Buenos Aires, Argentina
| | - Maria J. Comin
- Center for Research and Development in Chemistry, INTI, Buenos Aires, Argentina
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mariana Gallo
- Fundación Instituto Leloir, Buenos Aires, Argentina
- * E-mail:
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Abstract
Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on "dual-role" residues. The nonnative species slow down the reaction allowing for extended functionality.
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Smal C, Wetzler DE, Dantur KI, Chemes LB, Garcia-Alai MM, Dellarole M, Alonso LG, Gaston K, de Prat-Gay G. The human papillomavirus E7-E2 interaction mechanism in vitro reveals a finely tuned system for modulating available E7 and E2 proteins. Biochemistry 2010; 48:11939-49. [PMID: 19899811 DOI: 10.1021/bi901415k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcription of the human papillomavirus E7 oncoprotein is negatively controlled by the viral E2 protein, and loss of this repression leads to irreversible transformation and carcinogenesis. Here we show that interaction of the HPV16 E7 protein with the DNA binding domain of the E2 protein (E2C) leads to ionic strength-dependent hetero-oligomerization even at the lowest concentrations measurable. Titration experiments followed by light scattering and native gel electrophoresis show insoluble oligomeric complexes with a >or=2000 nm diameter and intermediate soluble complexes 40 and 115 nm in diameter, respectively, formed in excess of E2C. A discrete oligomeric soluble complex formed in excess of E7 displays a diameter of 12 nm. The N-terminal domain of E7 interacts with E2C with a K(D) of 0.1 muM, where the stretch of residues 25-40 of E7, encompassing both a PEST motif and phosphorylation sites, is sufficient for the interaction. Displacement of the soluble E7-E2C complex by an E2 site DNA duplex and site-directed mutagenesis indicate that the protein-protein interface involves the DNA binding helix of E2. The formation of complexes of different sizes and properties in excess of either of the viral proteins reveals a finely tuned mechanism that could regulate the intracellular levels of both proteins as infection and transformation progress. Sequestering E2 into E7-E2 oligomers provides a possible additional route to uncontrolled E7 expression, in addition and prior to the disruption of the E2 gene during viral integration into the host genome.
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Affiliation(s)
- Clara Smal
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas, CONICET, Patricias Argentinas 435, 1405 Buenos Aires, Argentina
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Eliseo T, Sánchez IE, Nadra AD, Dellarole M, Paci M, de Prat Gay G, Cicero DO. Indirect DNA Readout on the Protein Side: Coupling between Histidine Protonation, Global Structural Cooperativity, Dynamics, and DNA Binding of the Human Papillomavirus Type 16 E2C Domain. J Mol Biol 2009; 388:327-44. [PMID: 19285507 DOI: 10.1016/j.jmb.2009.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/06/2009] [Accepted: 03/06/2009] [Indexed: 11/26/2022]
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