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Bharti, Nair MS. Molecular cloning, biophysical and in silico studies of Human papillomavirus 33 E2 DNA binding domain. J Biomol Struct Dyn 2024:1-20. [PMID: 38385450 DOI: 10.1080/07391102.2024.2317996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Human papillomavirus 33, a high-risk HPV strain, is mainly responsible for HPV infection and cervical cancer in Asian countries. The E2 protein of HPV 33 is a DNA-binding protein that plays a crucial role in viral replication and transcription. We have cloned, overexpressed, and purified the DNA binding domain of the E2 protein. Size exclusion chromatography results suggested that the protein exists in a homodimeric state in the native form. Circular dichroism data showed that the protein has a higher content of β-sheet. The melting temperature obtained from differential scanning calorimetry is 52.59 °C, and the protein is stable at pH 8 and is in a dimeric form at basic pH. The protein is monomeric or unfolded at a very low pH. Chemical denaturation studies suggested that the protein denatured and dissociated simultaneously. The DNA binding activity of the protein was also confirmed and it showed binding affinity in the order of 106 M-1. The protein structure was modeled using homology modeling and other bioinformatic tools. The virtual screening and molecular dynamic simulation studies were performed to find compounds that can act as potent inhibitors against E2 DBD. This study expands the understanding of the conserved structural and binding properties of HPV33 E2 DBD and provides the first report on the characterization of the viral protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharti
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Haridwar Uttarakhand, India
| | - Maya S Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Haridwar Uttarakhand, India
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2
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Sreenivasan S, Heffren P, Suh K, Rodnin MV, Kosa E, Fenton AW, Ladokhin AS, Smith PE, Fontes JD, Swint‐Kruse L. The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm? Protein Sci 2024; 33:e4863. [PMID: 38073129 PMCID: PMC10806935 DOI: 10.1002/pro.4863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
During protein evolution, some amino acid substitutions modulate protein function ("tuneability"). In most proteins, the tuneable range is wide and can be sampled by a set of protein variants that each contains multiple amino acid substitutions. In other proteins, the full tuneable range can be accessed by a set of variants that each contains a single substitution. Indeed, in some globular proteins, the full tuneable range can be accessed by the set of site-saturating substitutions at an individual "rheostat" position. However, in proteins with intrinsically disordered regions (IDRs), most functional studies-which would also detect tuneability-used multiple substitutions or small deletions. In disordered transcriptional activation domains (ADs), studies with multiple substitutions led to the "acidic exposure" model, which does not anticipate the existence of rheostat positions. In the few studies that did assess effects of single substitutions on AD function, results were mixed: the ADs of two full-length transcription factors did not show tuneability, whereas a fragment of a third AD was tuneable by single substitutions. In this study, we tested tuneability in the AD of full-length human class II transactivator (CIITA). Sequence analyses and experiments showed that CIITA's AD is an IDR. Functional assays of singly-substituted AD variants showed that CIITA's function was highly tuneable, with outcomes not predicted by the acidic exposure model. Four tested positions showed rheostat behavior for transcriptional activation. Thus, tuneability of different IDRs can vary widely. Future studies are needed to illuminate the biophysical features that govern whether an IDR is tuneable by single substitutions.
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Affiliation(s)
- Shwetha Sreenivasan
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Paul Heffren
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
- Present address:
Department of BiosciencesKansas City UniversityKansas CityMissouriUSA
| | - Kyung‐Shin Suh
- Department of ChemistryKansas State UniversityManhattanKansasUSA
| | - Mykola V. Rodnin
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Edina Kosa
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Aron W. Fenton
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Paul E. Smith
- Department of ChemistryKansas State UniversityManhattanKansasUSA
| | - Joseph D. Fontes
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
| | - Liskin Swint‐Kruse
- Department of Biochemistry and Molecular BiologyUniversity of Kansas Medical CenterKansas CityKansasUSA
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3
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Han L, Liu X, Cheng Z, Cui W, Guo J, Yin J, Zhou Z. Construction and Application of a High-Throughput In Vivo Screening Platform for the Evolution of Nitrile Metabolism-Related Enzymes Based on a Desensitized Repressive Biosensor. ACS Synth Biol 2022; 11:1577-1587. [PMID: 35266713 DOI: 10.1021/acssynbio.1c00642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcription factor (TF)-based biosensors are expected to serve as powerful tools for the high-throughput screening of biocatalytic systems; however, most of them respond to ligands in a narrow concentration range, which limits their application. In this study, we constructed a heterogenous niacin biosensor using the repressive TF BsNadR and its target promoters from Bacillus subtilis. The fine-tunable output of the niacin biosensor was expanded to a wide range of niacin concentrations (0-50 mM) through desensitization engineering, which was suitable for the accurate identification of differences in enzyme activity. Structural mechanism analysis indicated that weakening the affinity of BsNadR with the ligand niacin and with DNA alters its regulatory properties. Based on the desensitized niacin biosensor, a high-throughput in vivo screening platform was developed for evolving nitrile metabolism-related enzymes. The evolved nitrilase, amidase, and nitrile hydratase with 6.6-, 2.1-, and 21.3-fold improvements in activity were achieved, respectively. In addition, these mutants also exhibited elevated activity toward other cognate substrates, indicating the broad applicability of the screening platform. This study not only provided a universal high-throughput screening platform for different nitrile metabolism-related enzymes but also demonstrated the advantages of repressive biosensors and the vital role of desensitization engineering of the TF in the development of high-throughput screening platforms for enzymes.
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Affiliation(s)
- Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyue Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhongyi Cheng
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenjing Cui
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junling Guo
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Yin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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4
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Junghänel S, Karczewski S, Bäcker S, Knauer SK, Schmuck C. A Systematic Structure-Activity Study of a New Type of Small Peptidic Transfection Vector Reveals the Importance of a Special Oxo-Anion-Binding Motif for Gene Delivery. Chembiochem 2017; 18:2268-2279. [PMID: 28914486 DOI: 10.1002/cbic.201700433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 12/16/2022]
Abstract
We discovered a new class of artificial peptidic transfection vectors based on an artificial anion-binding motif, the guanidiniocarbonylpyrrole (GCP) cation. This new type of vector is surprisingly smaller than traditional systems, and our previous work suggested that the GCP group was important for promoting critical endosomal escape. We now present here a systematic comparison of similar DNA ligands featuring our GCP oxo-anion-binding motif with DNA ligands only consisting of naturally occurring amino acids. Structure-activity studies showed that the artificial binding motif clearly outperformed natural amino acids such as histidine, lysine, and arginine. It improved the ability to shuttle foreign genetic material into cells, yet successfully mediated endosomal escape. Also, plasmids that were complexed by our artificial ligands were stabilized against cytosolic degradation to some extent. This resulted in the successful expression of plasmid information (comparable to gold standards such as polyethyleneimine). Hence, our study clearly demonstrates the importance of the tailor-made GCP anion-binding site for efficient gene transfection.
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Affiliation(s)
- Sandra Junghänel
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Sarah Karczewski
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Sandra Bäcker
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Shirley K Knauer
- Institute of Molecular Biology, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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Mondal S, Chakraborty K, Bandyopadhyay S. Microscopic understanding of the conformational features of a protein–DNA complex. Phys Chem Chem Phys 2017; 19:32459-32472. [DOI: 10.1039/c7cp05161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.
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Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Kaushik Chakraborty
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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Gray GM, van der Vaart A. Importance of β2-β3 Loop Motion for the Increased Binding and Decreased Selectivity of the ΔLL Mutant of the Human Papillomavirus Type 6 E2 Protein. Biochemistry 2015; 54:4918-26. [PMID: 26169609 DOI: 10.1021/acs.biochem.5b00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding affinity of the human papillomavirus type 6 E2 protein is strongly mediated by the sequence of the DNA linker region, with high affinity for the AATT linker and low affinity for the CCGG linker. When two terminal leucine residues are removed from the protein, the level of binding to both strands increases, but unequally, resulting in a significant decrease in selectivity for the AATT linker strand. To rationalize this behavior, we performed molecular dynamics simulations of the wild-type and mutant protein in the apo state and bound to DNA with high-affinity AATT and low-affinity CCGG linker strands. While no stable contacts were made between the β2-β3 loop and DNA in the wild type, this loop was repositioned in the mutant complexes and formed electrostatic contacts with the DNA backbone. More contacts were formed when the mutant was bound to the CCGG linker strand than to the AATT linker strand, resulting in a more favorable change in interaction energy for the CCGG strand. In addition, significant differences in correlated motions were found, which further explained the differences in binding. The simulations suggest that β2-β3 loop motions are responsible for the increased affinity and decreased selectivity of the mutant protein.
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Affiliation(s)
- Geoffrey M Gray
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
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7
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Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA. Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species. BMC STRUCTURAL BIOLOGY 2014; 14:23. [PMID: 25315147 PMCID: PMC4209456 DOI: 10.1186/s12900-014-0023-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/03/2014] [Indexed: 11/13/2022]
Abstract
Background The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. Results The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. Conclusions The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.
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Affiliation(s)
- Kirill E Medvedev
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Nikolay A Alemasov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk, 630090, Russia.
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk, 630090, Russia.
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow, 123182, Russia.
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia.
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8
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De S, Chan ACK, Coyne HJ, Bhachech N, Hermsdorf U, Okon M, Murphy MEP, Graves BJ, McIntosh LP. Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6. J Mol Biol 2014; 426:1390-406. [PMID: 24333486 PMCID: PMC4278593 DOI: 10.1016/j.jmb.2013.11.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/05/2013] [Accepted: 11/09/2013] [Indexed: 11/29/2022]
Abstract
DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus (5')GGAA(3') recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing (5')GGAA(3')versus(5')GGAT(3'). These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.
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Affiliation(s)
- Soumya De
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Anson C K Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - H Jerome Coyne
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Niraja Bhachech
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Ulrike Hermsdorf
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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9
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Grant BN, Dourlain EM, Araneda JN, Throneberry ML, McFail-Isom LA. DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures. Nucleic Acids Res 2013; 41:7547-55. [PMID: 23748560 PMCID: PMC3753625 DOI: 10.1093/nar/gkt492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To investigate the role of electrostatics in helical deformation, we quantified the relationship between protein cationic residue density (Cpc) and DNA phosphate crowding (Cpp). The correlation between Cpc and Cpp was then calculated for a subset of 58 high resolution protein-DNA crystal structures. Those structures containing strong Cpc/Cpp correlation (>±0.25) were likely to contain DNA helical curvature. Further, the correlation factor sign predicted the direction of helical curvature with positive (16 structures) and negative (seven structures) correlation containing concave (DNA curved toward protein) and convex (DNA curved away from protein) curvature, respectively. Protein-DNA complexes without significant Cpc/Cpp (36 structures) correlation (-0.25<0<0.25) tended to contain DNA without significant curvature. Interestingly, concave and convex complexes also include more arginine and lysine phosphate contacts, respectively, whereas linear complexes included essentially equivalent numbers of Lys/Arg phosphate contacts. Together, these findings suggest an important role for electrostatic interactions in protein-DNA complexes involving helical curvature.
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Affiliation(s)
- Bryce N Grant
- Department of Chemistry, University of Central Arkansas, Conway, AR 72035, USA
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10
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Ramakrishnan V, Jagannathan S, Shaikh AR, Rajagopalan R. Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. J Biomol Struct Dyn 2012; 29:743-56. [DOI: 10.1080/073911012010525020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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11
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Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I, Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH. Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis. Nucleic Acids Res 2011; 39:8992-9008. [PMID: 21771861 PMCID: PMC3203581 DOI: 10.1093/nar/gkr558] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Iron-inducible transcription of the ap65-1 gene in Trichomonas vaginalis involves at least three Myb-like transcriptional factors (tvMyb1, tvMyb2 and tvMyb3) that differentially bind to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f. Here, we defined a fragment of tvMyb2 comprising residues 40-156 (tvMyb2₄₀₋₁₅₆) as the minimum structural unit that retains near full binding affinity with the promoter DNAs. Like c-Myb in vertebrates, the DNA-free tvMyb2₄₀₋₁₅₆ has a flexible and open conformation. Upon binding to the promoter DNA elements, tvMyb2₄₀₋₁₅₆ undergoes significant conformational re-arrangement and structure stabilization. Crystal structures of tvMyb2₄₀₋₁₅₆ in complex with promoter element-containing DNA oligomers showed that 5'-a/gACGAT-3' is the specific base sequence recognized by tvMyb2₄₀₋₁₅₆, which does not fully conform to that of the Myb binding site sequence. Furthermore, Lys⁴⁹, which is upstream of the R2 motif (amino acids 52-102) also participates in specific DNA sequence recognition. Intriguingly, tvMyb2₄₀₋₁₅₆ binds to the promoter elements in an orientation opposite to that proposed in the HADDOCK model of the tvMyb1₃₅₋₁₄₁/MRE-1-MRE-2r complex. These results shed new light on understanding the molecular mechanism of Myb-DNA recognition and provide a framework to study the molecular basis of transcriptional regulation of myriad Mybs in T. vaginalis.
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Affiliation(s)
- Ingjye Jiang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
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12
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Tripet BP, Goel A, Copie V. Internal dynamics of the tryptophan repressor (TrpR) and two functionally distinct TrpR variants, L75F-TrpR and A77V-TrpR, in their l-Trp-bound forms. Biochemistry 2011; 50:5140-53. [PMID: 21553830 DOI: 10.1021/bi200389k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Backbone amide dynamics of the Escherichia coli tryptophan repressor protein (WT-TrpR) and two functionally distinct variants, L75F-TrpR and A77V-TrpR, in their holo (l-tryptophan corepressor-bound) form have been characterized using (15)N nuclear magnetic resonance (NMR) relaxation. The three proteins possess very similar structures, ruling out major conformational differences as the source of their functional differences, and suggest that changes in protein flexibility are at the origin of their distinct functional properties. Comparison of site specific (15)N-T(1), (15)N-T(2), (15)N-{(1)H} nuclear Overhauser effect, reduced spectral density, and generalized order (S(2)) parameters indicates that backbone dynamics in the three holo-repressors are overall very similar with a few notable and significant exceptions for backbone atoms residing within the proteins' DNA-binding domain. We find that flexibility is highly restricted for amides in core α-helices (i.e., helices A-C and F), and a comparable "stiffening" is observed for residues in the DNA recognition helix (helix E) of the helix D-turn-helix E (HTH) DNA-binding domain of the three holo-repressors. Unexpectedly, amides located in helix D and in adjacent turn regions remain flexible. These data support the concept that residual flexibility in TrpR is essential for repressor function, DNA binding, and molecular recognition of target operators. Comparison of the (15)N NMR relaxation parameters of the holo-TrpRs with those of the apo-TrpRs indicates that the single-point amino acid substitutions, L75F and A77V, perturb the flexibility of backbone amides of TrpR in very different ways and are most pronounced in the apo forms of the three repressors. Finally, we present these findings in the context of other DNA-binding proteins and the role of protein flexibility in molecular recognition.
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Affiliation(s)
- Brian P Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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