1
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Ávila-Moreno F. Nanofitins and their applications in human health and lung diseases. Mol Ther 2023; 31:2813-2814. [PMID: 37729903 PMCID: PMC10556214 DOI: 10.1016/j.ymthe.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Affiliation(s)
- Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED). Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM). México State, Cp. 54090. México; Research Unit, Subdirección de Investigación Básica. Instituto Nacional de Cancerología (INCAN). México City, Cp. 14080. México; Research Unit. Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas. México City, Cp. 14080. México.
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2
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Farooqui AK, Ahmad H, Rehmani MU, Husain A. Quick and easy method for extraction and purification of Pfu-Sso7d, a high processivity DNA polymerase. Protein Expr Purif 2023; 208-209:106276. [PMID: 37156451 DOI: 10.1016/j.pep.2023.106276] [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: 03/17/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023]
Abstract
The polymerase chain reaction is an extensively used technique with numerous applications in the field of biological sciences. In addition to naturally occurring DNA polymerases with varying processivity and fidelity, genetically engineered recombinant DNA polymerases are also used in PCR. The Pfu-Sso7d, a fusion DNA polymerase, is obtained by the fusion of Sso7d, a small DNA binding protein, to the polymerase domain of the Pfu DNA polymerase. Pfu-Sso7d is known for its high processivity, efficiency, and fidelity. Expensive commercial variants of Pfu-Sso7d are sold under various trade names. Here, we report a quick, cost and time-efficient purification protocol and an optimized buffer system for Pfu-Sso7d. We evaluated precipitation efficiencies of varying concentrations of ethanol and acetone and compared the activities of the precipitated enzyme. Although both the solvents efficiently precipitated Pfu-Sso7d, acetone showed better precipitation efficiency. Purified Pfu-Sso7d showed excellent activities in the PCR of templates with varying lengths and GC contents. We also report a buffer system that works with Pfu-Sso7d as efficiently as commercially available buffers. This quick and efficient purification scheme and buffer system will provide researchers cost-efficient access to fusion polymerases.
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Affiliation(s)
- Afreen Kamal Farooqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Haleema Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohd Umar Rehmani
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
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3
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Takahashi S, Oshige M, Katsura S, Nagahara Y. A new fluorescence labeling method for molecular analysis of double-stranded DNA. Anal Biochem 2023; 662:115000. [PMID: 36470466 DOI: 10.1016/j.ab.2022.115000] [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: 09/01/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
In this study, a double-stranded DNA (dsDNA) fluorescent labeling method was developed using the fusion proteins of fluorescent protein (FP), and 7 kDa DNA-binding family members including Sso7d from Sulfolobus solfataricus, Aho7c from Acidianus hospitalis, ATSV7 from Acidianus tailed spindle virus and Sto7 from Sulfolobus tokodaii. Using this fluorescent DNA labeling method, we succeeded in single-molecule imaging of bacteriophage λDNA molecules stretched on glass surfaces. The fluorescence of the λDNA with FP fusion proteins decayed 2.4- to 6.4-fold slower than that of the typical intercalating method with SYTOX Green (SxG). In addition, the dynamic behaviors of FP-fused Aho7c-λDNA were relaxed and stretched with and without buffer flow, respectively, in microflow channels and were similar to that with typical intercalating dye, such as YOYO-1 and SxG. this fluorescent DNA labeling method. This fluorescent DNA labeling method can solve the problem of rapid fluorescence decay due to the intercalating dyes and therefore can be expected as an alternative to compound-based fluorescent dye. Thus, this study establishes FP fusion proteins as useful fluorescent DNA probes at the single-molecule level.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan.
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Yukitoshi Nagahara
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan
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4
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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5
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Essentiality of core hydrophobicity to the structure and function of archaeal chromatin protein Cren7. Int J Biol Macromol 2022; 214:381-390. [PMID: 35728637 DOI: 10.1016/j.ijbiomac.2022.06.114] [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: 12/12/2021] [Revised: 04/29/2022] [Accepted: 06/14/2022] [Indexed: 11/23/2022]
Abstract
Studies on the structure-function relationship of protein greatly help to understand not only the principles of protein folding but also the rationales of protein engineering. Crenarchaeal chromatin protein Cren7 provides an excellent research model for this issue. The small protein adopts a 'β-barrel' fold, formed by the double-stranded antiparallel β-sheet 1 tightly packing with the triple-stranded antiparallel β-sheet 2. The simple structure of Cren7 is stabilized by the hydrophobic core between the β-sheets, consisting of the side chains of V8, V10, L20, V25, F41 and F50. In the present work, mutation analyses by alanine substitution of each of the residues in the hydrophobic core were performed. Circular dichroism spectra and nuclear magnetic resonance analyses showed that mutation of F41 led to a significant misfolding of Cren7 through disruption of the β-sheets. Meanwhile, the mutant F41A showed a reduced thermostatility (Tm of 53.2 °C), as compared with the wild-type Cren7 (Tm > 80 °C). Biolayer interferometry and nick-closure assays showed the largely unchanged activities in DNA binding and supercoiling of F41A, indicating the DNA interface of Cren7 was generally retained in F41A. However, F41A was unable to mediate DNA bridging, probably due to the impairment in forming oligomers/polymers on DNA. Atomic force microscopic images of the F41A-DNA complexes also revealed that F41A nearly completely lost the ability to compact DNA into highly condensed structures. Our results not only reveal the critical role of F41 in protein folding of Cren7 but also provide new insights into the structure-function relationships of thermostable proteins.
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6
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Tashiro R, Sugiyama H. Photoreaction of DNA Containing 5-Halouracil and its Products. Photochem Photobiol 2022; 98:532-545. [PMID: 34543451 PMCID: PMC9197447 DOI: 10.1111/php.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-Cyo, Suzuka, Mie, 513-8670, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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7
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Teufl M, Zajc CU, Traxlmayr MW. Engineering Strategies to Overcome the Stability-Function Trade-Off in Proteins. ACS Synth Biol 2022; 11:1030-1039. [PMID: 35258287 PMCID: PMC8938945 DOI: 10.1021/acssynbio.1c00512] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In addition to its
biological function, the stability of a protein
is a major determinant for its applicability. Unfortunately, engineering
proteins for improved functionality usually results in destabilization
of the protein. This so-called stability–function trade-off
can be explained by the simple fact that the generation of a novel
protein function—or the improvement of an existing one—necessitates
the insertion of mutations, i.e., deviations from
the evolutionarily optimized wild-type sequence. In fact, it was demonstrated
that gain-of-function mutations are not more destabilizing than other
random mutations. The stability–function trade-off is a universal
phenomenon during protein evolution that has been observed with completely
different types of proteins, including enzymes, antibodies, and engineered
binding scaffolds. In this review, we discuss three types of strategies
that have been successfully deployed to overcome this omnipresent
obstacle in protein engineering approaches: (i) using highly stable
parental proteins, (ii) minimizing the extent of destabilization during
functional engineering (by library optimization and/or coselection
for stability and function), and (iii) repairing damaged mutants through
stability engineering. The implementation of these strategies in protein
engineering campaigns will facilitate the efficient generation of
protein variants that are not only functional but also stable and
therefore better-suited for subsequent applications.
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Affiliation(s)
- Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Charlotte U. Zajc
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
| | - Michael W. Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
- CD Laboratory for Next Generation CAR T Cells, 1190 Vienna, Austria
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8
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Wicke N, Bedford MR, Howarth M. Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid. Commun Biol 2021; 4:960. [PMID: 34381153 PMCID: PMC8358037 DOI: 10.1038/s42003-021-02487-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 07/23/2021] [Indexed: 02/04/2023] Open
Abstract
Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Two stable scaffold proteins (nanobody and nanofitin), previously developed to be protease-resistant, were completely digested in less than 10 min at 100-fold lower concentration of pepsin than found in the stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI's evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. Gastrobodies show resilience to exceptionally harsh conditions, which should provide a foundation for targeting and modulating function within the GI tract.
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Affiliation(s)
- Niels Wicke
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
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9
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Li X, Xu F, Yang D, Wang P. A DNA-binding, albumin-targeting fusion protein promotes the cellular uptake and bioavailability of framework DNA nanostructures. NANOSCALE 2021; 13:6038-6042. [PMID: 33885601 DOI: 10.1039/d0nr07967g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Framework DNA nanostructures exhibit unique characteristics such as precisely controllable physicochemical properties (i.e. size, shape, and surface functionality) and have been used as carriers for the delivery of a variety of therapeutics. Nevertheless, pristine DNA nanostructures encounter challenges such as low cellular uptake efficiency and short in vivo retention time that largely hinder their biomedical applications. Here in this report, a fusion protein is designed to complex with a tetrahedral DNA nanostructure (TDN) to circumvent these challenges by recruiting serum albumins. This bi-functional fusion protein (ABS) is composed of an albumin-binding domain (ABD) and a DNA-binding domain (Sso-7d), which can serve as a linker to bridge the TDN with albumin. It was revealed that ABS-tethered TDN can readily recruit serum albumins to achieve significantly enhanced uptake in cancer cells and longer retention time in mice, suggesting that ABS may serve as a potent agent to facilitate the biological applications of DNA nanostructures.
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Affiliation(s)
- Xue Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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10
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Laursen SP, Bowerman S, Luger K. Archaea: The Final Frontier of Chromatin. J Mol Biol 2020; 433:166791. [PMID: 33383035 PMCID: PMC7987875 DOI: 10.1016/j.jmb.2020.166791] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022]
Abstract
The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.
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Affiliation(s)
- Shawn P Laursen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, United States
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States; Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.
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11
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Zhang Z, Zhan Z, Wang B, Chen Y, Chen X, Wan C, Fu Y, Huang L. Archaeal Chromatin Proteins Cren7 and Sul7d Compact DNA by Bending and Bridging. mBio 2020; 11:e00804-20. [PMID: 32518188 PMCID: PMC7373190 DOI: 10.1128/mbio.00804-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/06/2020] [Indexed: 11/20/2022] Open
Abstract
Archaeal chromatin proteins Cren7 and Sul7d from Sulfolobus are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA compaction by Cren7 and Sis7d, a Sul7d family member, from Sulfolobus islandicus at the single-molecule (SM) level by total single-molecule internal reflection fluorescence microscopy (SM-TIRFM) and atomic force microscopy (AFM). We show that both Cren7 and Sis7d were able to compact singly tethered λ DNA into a highly condensed structure in a three-step process and that Cren7 was over an order of magnitude more efficient than Sis7d in DNA compaction. The two proteins were similar in DNA bending kinetics but different in DNA condensation patterns. At saturating concentrations, Sis7d formed randomly distributed clusters whereas Cren7 generated a single and highly condensed core on plasmid DNA. This observation is consistent with the greater ability of Cren7 than of Sis7d to bridge DNA. Our results offer significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaea.IMPORTANCE A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting DNA, albeit with different efficiencies and in different manners, at the single molecule level. We demonstrate for the first time that the two proteins, which have long been regarded as DNA binders and benders, are able to mediate DNA bridging, and this previously unknown property of the proteins allows DNA to be packaged into highly condensed structures. Therefore, our results provide significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaeota.
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Affiliation(s)
- Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Zhan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yuanyuan Chen
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cuihong Wan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yu Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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12
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Sarangi MK, Zvoda V, Holte MN, Becker NA, Peters JP, Maher LJ, Ansari A. Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A. Nucleic Acids Res 2019; 47:2871-2883. [PMID: 30698746 PMCID: PMC6451137 DOI: 10.1093/nar/gkz022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 01/17/2023] Open
Abstract
The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.
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Affiliation(s)
- Manas Kumar Sarangi
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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13
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Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses. Viruses 2019; 11:v11090770. [PMID: 31443391 PMCID: PMC6784120 DOI: 10.3390/v11090770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Foamy viruses (FV) are retroviruses belonging to the Spumaretrovirinae subfamily. They are non-pathogenic viruses endemic in several mammalian hosts like non-human primates, felines, bovines, and equines. Retroviral DNA integration is a mandatory step and constitutes a prime target for antiretroviral therapy. This activity, conserved among retroviruses and long terminal repeat (LTR) retrotransposons, involves a viral nucleoprotein complex called intasome. In the last decade, a plethora of structural insights on retroviral DNA integration arose from the study of FV. Here, we review the biochemistry and the structural features of the FV integration apparatus and will also discuss the mechanism of action of strand transfer inhibitors.
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14
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Lee CH, Shih YP, Ho MR, Wang AHJ. The C-terminal D/E-rich domain of MBD3 is a putative Z-DNA mimic that competes for Zα DNA-binding activity. Nucleic Acids Res 2019; 46:11806-11821. [PMID: 30304469 PMCID: PMC6294567 DOI: 10.1093/nar/gky933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/04/2018] [Indexed: 12/25/2022] Open
Abstract
The Z-DNA binding domain (Zα), derived from the human RNA editing enzyme ADAR1, can induce and stabilize the Z-DNA conformation. However, the biological function of Zα/Z-DNA remains elusive. Herein, we sought to identify proteins associated with Zα to gain insight into the functional network of Zα/Z-DNA. By pull-down, biophysical and biochemical analyses, we identified a novel Zα-interacting protein, MBD3, and revealed that Zα interacted with its C-terminal acidic region, an aspartate (D)/glutamate (E)-rich domain, with high affinity. The D/E-rich domain of MBD3 may act as a DNA mimic to compete with Z-DNA for binding to Zα. Dimerization of MBD3 via intermolecular interaction of the D/E-rich domain and its N-terminal DNA binding domain, a methyl-CpG-binding domain (MBD), attenuated the high affinity interaction of Zα and the D/E-rich domain. By monitoring the conformation transition of DNA, we found that Zα could compete with the MBD domain for binding to the Z-DNA forming sequence, but not vice versa. Furthermore, co-immunoprecipitation experiments confirmed the interaction of MBD3 and ADAR1 in vivo. Our findings suggest that the interplay of Zα and MBD3 may regulate the transition of the DNA conformation between B- and Z-DNA and thereby modulate chromatin accessibility, resulting in alterations in gene expression.
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Affiliation(s)
- Chi-Hua Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yan-Ping Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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15
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Zorzi A, Linciano S, Angelini A. Non-covalent albumin-binding ligands for extending the circulating half-life of small biotherapeutics. MEDCHEMCOMM 2019; 10:1068-1081. [PMID: 31391879 PMCID: PMC6644573 DOI: 10.1039/c9md00018f] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/01/2019] [Indexed: 12/13/2022]
Abstract
Peptides and small protein scaffolds are gaining increasing interest as therapeutics. Similarly to full-length antibodies, they can bind a target with a high binding affinity and specificity while remaining small enough to diffuse into tissues. However, despite their numerous advantages, small biotherapeutics often suffer from a relatively short circulating half-life, thus requiring frequent applications that ultimately restrict their ease of use and user compliance. To overcome this limitation, a large variety of half-life extension strategies have been developed in the last decades. Linkage to ligands that non-covalently bind to albumin, the most abundant serum protein with a circulating half-life of ∼19 days in humans, represents one of the most successful approaches for the generation of long-lasting biotherapeutics with improved pharmacokinetic properties and superior efficacy in the clinic.
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Affiliation(s)
- Alessandro Zorzi
- Institute of Chemical Sciences and Engineering , School of Basic Sciences , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Lausanne CH-1015 , Switzerland
| | - Sara Linciano
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
- European Centre for Living Technologies (ECLT) , San Marco 2940 , Venice 30124 , Italy .
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16
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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019; 58:5967-5972. [DOI: 10.1002/anie.201900935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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17
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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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18
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Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Das R, Gosavi S. A five-residue motif for the design of domain swapping in proteins. Nat Commun 2019; 10:452. [PMID: 30692525 PMCID: PMC6349918 DOI: 10.1038/s41467-019-08295-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 12/28/2018] [Indexed: 11/09/2022] Open
Abstract
Domain swapping is the process by which identical monomeric proteins exchange structural elements to generate dimers/oligomers. Although engineered domain swapping is a compelling strategy for protein assembly, its application has been limited due to the lack of simple and reliable design approaches. Here, we demonstrate that the hydrophobic five-residue 'cystatin motif' (QVVAG) from the domain-swapping protein Stefin B, when engineered into a solvent-exposed, tight surface loop between two β-strands prevents the loop from folding back upon itself, and drives domain swapping in non-domain-swapping proteins. High-resolution structural studies demonstrate that engineering the QVVAG stretch independently into various surface loops of four structurally distinct non-domain-swapping proteins enabled the design of different modes of domain swapping in these proteins, including single, double and open-ended domain swapping. These results suggest that the introduction of the QVVAG motif can be used as a mutational approach for engineering domain swapping in diverse β-hairpin proteins.
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Affiliation(s)
- Neha Nandwani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Parag Surana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Hitendra Negi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.,Sastra University, Thanjavur, 613402, India
| | - Nahren M Mascarenhas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.,Sacred Heart College, Tirupattur, Tamil Nadu, 635601, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India. .,Indian Institute of Science Education and Research, Pune, 411008, India.
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
| | - Shachi Gosavi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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19
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Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong Y, Huang L. Architectural roles of Cren7 in folding crenarchaeal chromatin filament. Mol Microbiol 2019; 111:556-569. [PMID: 30499242 DOI: 10.1111/mmi.14173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
Abstract
Archaea have evolved various strategies in chromosomal organization. While histone homologues exist in most archaeal phyla, Cren7 is a chromatin protein conserved in the Crenarchaeota. Here, we show that Cren7 preferentially binds DNA with AT-rich sequences over that with GC-rich sequences with a binding size of 6~7 bp. Structural studies of Cren7 in complex with either an 18-bp or a 20-bp double-stranded DNA fragment reveal that Cren7 binds to the minor groove of DNA as monomers in a head-to-tail manner. The neighboring Cren7 monomers are located on the opposite sides of the DNA duplex, with each introducing a single-step sharp kink by intercalation of the hydrophobic side chain of Leu28, bending the DNA into an S-shape conformation. A structural model for the chromatin fiber folded by Cren7 was established and verified by the analysis of cross-linked Cren7-DNA complexes by atomic force microscopy. Our results suggest that Cren7 differs significantly from Sul7, another chromatin protein conserved among Sulfolobus species, in both DNA binding and deformation. These data shed significant light on the strategy of chromosomal DNA organization in crenarchaea.
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Affiliation(s)
- Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Mohan Zhao
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yuanyuan Chen
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Li Wang
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Qinghua Liu
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yuhui Dong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Yong Gong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, 100049, China
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20
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Rocha MS, Storm IM, Bazoni RF, Ramos ÉB, Hernandez-Garcia A, Cohen Stuart MA, Leermakers F, de Vries R. Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes. Macromolecules 2018; 51:204-212. [PMID: 29339838 PMCID: PMC5763285 DOI: 10.1021/acs.macromol.7b01795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/13/2017] [Indexed: 11/30/2022]
Abstract
![]()
As a model system
to study the elasticity of bottle-brush polymers,
we here introduce self-assembled DNA bottle brushes, consisting of
a DNA main chain that can be very long and still of precisely defined
length, and precisely monodisperse polypeptide side chains that are
physically bound to the DNA main chains. Polypeptide side chains have
a diblock architecture, where one block is a small archaeal nucleoid
protein Sso7d that strongly binds to DNA. The other block is a net
neutral, hydrophilic random coil polypeptide with a length of exactly
798 amino acids. Light scattering shows that for saturated brushes
the grafting density is one side chain per 5.6 nm of DNA main chain.
According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle
brushes using AFM, we find that the effective persistence of the saturated
DNA bottle brushes is Peff = 95 nm, but
from force–extension curves of single DNA bottle brushes measured
using optical tweezers we find Peff =
15 nm. The latter is equal to the value expected for DNA coated by
the Sso7d binding block alone. The apparent discrepancy between the
two measurements is rationalized in terms of the scale dependence
of the bottle-brush elasticity using theory previously developed to
analyze the scale-dependent electrostatic stiffening of DNA at low
ionic strengths.
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Affiliation(s)
- Márcio Santos Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ingeborg M Storm
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Raniella Falchetto Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Ésio Bessa Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa Viçosa, Minas Gerais, Brazil
| | - Armando Hernandez-Garcia
- Departamento de Química de Biomacromoleculas, Instituto de Química, Universidad Nacional Autónoma de México, México City, México
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Frans Leermakers
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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21
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DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Sci Rep 2017; 7:4756. [PMID: 28684739 PMCID: PMC5500549 DOI: 10.1038/s41598-017-02578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol. Guided by structural simulation, a fused pol Sdbh with non-specific dsDNA binding protein Sso7d in the N-terminus was designed. This modification increased in vitro processivity 4-fold as compared to the wild-type Dbh. Additionally, bioinformatics was used to identify amino acid mutations that would increase stabilization of Dbh bound to DNA. The variant SdbhM76I further improved the processivity of Dbh by 10 fold. The variant SdbhKSKIP241–245RVRKS showed higher activity than Dbh on the incorporation of dCTP (correct) and dATP (incorrect) opposite the G (normal) or 8-oxoG(damaged) template base. These results demonstrate the capability to rationally design increases in pol processivity and catalytic efficiency through computational DNA binding predictions and the addition of non-specific DNA binding domains.
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22
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Yu X, Yang YP, Dikici E, Deo SK, Daunert S. Beyond Antibodies as Binding Partners: The Role of Antibody Mimetics in Bioanalysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:293-320. [PMID: 28375702 PMCID: PMC5895458 DOI: 10.1146/annurev-anchem-061516-045205] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence of novel binding proteins or antibody mimetics capable of binding to ligand analytes in a manner analogous to that of the antigen-antibody interaction has spurred increased interest in the biotechnology and bioanalytical communities. The goal is to produce antibody mimetics designed to outperform antibodies with regard to binding affinities, cellular and tumor penetration, large-scale production, and temperature and pH stability. The generation of antibody mimetics with tailored characteristics involves the identification of a naturally occurring protein scaffold as a template that binds to a desired ligand. This scaffold is then engineered to create a superior binder by first creating a library that is then subjected to a series of selection steps. Antibody mimetics have been successfully used in the development of binding assays for the detection of analytes in biological samples, as well as in separation methods, cancer therapy, targeted drug delivery, and in vivo imaging. This review describes recent advances in the field of antibody mimetics and their applications in bioanalytical chemistry, specifically in diagnostics and other analytical methods.
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Affiliation(s)
- Xiaowen Yu
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Yu-Ping Yang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Sapna K Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136;
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23
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Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA. Biochem J 2017; 474:1727-1739. [PMID: 28377493 DOI: 10.1042/bcj20170036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/30/2017] [Accepted: 04/03/2017] [Indexed: 12/31/2022]
Abstract
Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologs, intercalates into the kinked DNA step. In the present study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e. L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (∼43°), nearly as sharp as that produced by wild-type Cren7 (∼48°), in the bound DNA fragment despite the lack of side chain intercalation. In another duplex DNA fragment, L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (∼39°) than that formed by the wild-type protein (∼50°). Mutation of Leu28 into methionine yields two protein conformers differing in loop β3-β4 orientation, DNA-binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop β3-β4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.
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24
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Zhao N, Spencer J, Schmitt MA, Fisk JD. Hyperthermostable binding molecules on phage: Assay components for point-of-care diagnostics for active tuberculosis infection. Anal Biochem 2017; 521:59-71. [DOI: 10.1016/j.ab.2016.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/25/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
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25
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Estrich NA, Hernandez-Garcia A, de Vries R, LaBean TH. Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly. ACS NANO 2017; 11:831-842. [PMID: 28048935 DOI: 10.1021/acsnano.6b07291] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.
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Affiliation(s)
- Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Armando Hernandez-Garcia
- Simpson Querrey Institute for Bionanotechnology, Northwestern University , Evanston, Illinois 60208, United States
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
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26
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Hernandez-Garcia A, Estrich NA, Werten MWT, Van Der Maarel JRC, LaBean TH, de Wolf FA, Cohen Stuart MA, de Vries R. Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain. ACS NANO 2017; 11:144-152. [PMID: 27936577 DOI: 10.1021/acsnano.6b05938] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA coating agent, called C8-BSso7d, which binds to and coats with high specificity and affinity, individual DNA molecules as well as folded origami nanostructures. C8-BSso7d coats and protects without condensing, collapsing or destroying the spatial structure of the underlying DNA template. C8-BSso7d combines the specific nonelectrostatic DNA binding affinity of an archeal-derived DNA binding domain (Sso7d, 7 kDa) with a long hydrophilic random coil polypeptide (C8, 73 kDa), which provides colloidal stability (solubility) through formation of polymer brushes around the DNA templates. C8-BSso7d is produced recombinantly in yeast and has a precise (but engineerable) amino acid sequence of precise length. Using electrophoresis, AFM, and fluorescence microscopy we demonstrate protein coat formation with stiffening of one-dimensional templates (linear dsDNA, supercoiled dsDNA and circular ssDNA), as well as coat formation without any structural distortion or disruption of two-dimensional DNA origami template. Combining the programmability of DNA with the nonperturbing precise coating capability of the engineered protein C8-BSso7d holds promise for future applications such as the creation of DNA-protein hybrid networks, or the efficient transfection of individual DNA nanostructures into cells.
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Affiliation(s)
- Armando Hernandez-Garcia
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Marc W T Werten
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | | | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Frits A de Wolf
- Wageningen UR Food and Biobased Research, Wageningen University and Research , Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University and Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
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27
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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA. PLoS One 2017; 12:e0169627. [PMID: 28068385 PMCID: PMC5222340 DOI: 10.1371/journal.pone.0169627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022] Open
Abstract
The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.
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28
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Kalichuk V, Béhar G, Renodon-Cornière A, Danovski G, Obal G, Barbet J, Mouratou B, Pecorari F. The archaeal "7 kDa DNA-binding" proteins: extended characterization of an old gifted family. Sci Rep 2016; 6:37274. [PMID: 27853299 PMCID: PMC5112516 DOI: 10.1038/srep37274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/27/2016] [Indexed: 01/06/2023] Open
Abstract
The “7 kDa DNA-binding” family, also known as the Sul7d family, is composed of chromatin proteins from the Sulfolobales archaeal order. Among them, Sac7d and Sso7d have been the focus of several studies with some characterization of their properties. Here, we studied eleven other proteins alongside Sac7d and Sso7d under the same conditions. The dissociation constants of the purified proteins for binding to double-stranded DNA (dsDNA) were determined in phosphate-buffered saline at 25 °C and were in the range from 11 μM to 22 μM with a preference for G/C rich sequences. In accordance with the extremophilic origin of their hosts, the proteins were found highly stable from pH 0 to pH 12 and at temperatures from 85.5 °C to 100 °C. Thus, these results validate eight putative “7 kDa DNA-binding” family proteins and show that they behave similarly regarding both their function and their stability among various genera and species. As Sac7d and Sso7d have found numerous uses as molecular biology reagents and artificial affinity proteins, this study also sheds light on even more attractive proteins that will facilitate engineering of novel highly robust reagents.
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Affiliation(s)
- Valentina Kalichuk
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Université catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, Brussels, Belgium
| | - Ghislaine Béhar
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | - Georgi Danovski
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Jacques Barbet
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Barbara Mouratou
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Frédéric Pecorari
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
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29
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Abstract
PCR has become an essential tool in biological science. However, researchers often encounter problems with difficult targets, inhibitors accompanying the samples, or PCR trouble related to DNA polymerase. Therefore, PCR optimization is necessary to obtain better results. One solution is using modified DNA polymerases with desirable properties for the experiments. In this article, PCR troubleshooting, depending on the DNA polymerase used, is shown. In addition, the reasons that might justify the need for modification of DNA polymerases, type of modifications, and links between modified DNA polymerases and PCR efficiency are described.
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30
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Turaga G, Edmondson SP, Smith K, Shriver JW. Insights into the Structure of Sulfolobus Nucleoid Using Engineered Sac7d Dimers with a Defined Orientation. Biochemistry 2016; 55:6230-6237. [PMID: 27766846 DOI: 10.1021/acs.biochem.6b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structure of Archaeal chromatin or nucleoid is believed to have characteristics similar to that found in both eukaryotes and bacteria. Recent comparative studies have suggested that DNA compaction in Archaea requires a bridging protein (e.g., Alba) along with either a wrapping protein (e.g., a histone) or a bending protein such as Sac7d. While X-ray crystal structures demonstrate that Sac7d binds as a monomer to create a significant kink in duplex DNA, the structure of a multiprotein-DNA complex has not been established. Using cross-linked dimers of Sac7d with a defined orientation, we present evidence that indicates that Sac7d is able to largely coat duplex DNA in vivo by binding in alternating head-to-head and tail-to-tail orientations. Although each Sac7d monomer promotes a significant kink of nearly 70°, coated DNA is expected to be largely extended because of compensation of repetitive kinks with helical symmetry.
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Affiliation(s)
- Gokul Turaga
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Stephen P Edmondson
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Kelley Smith
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - John W Shriver
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
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Cruz-Teran CA, Carlin KB, Efimenko K, Genzer J, Rao BM. Targeted Mutagenesis and Combinatorial Library Screening Enables Control of Protein Orientation on Surfaces and Increased Activity of Adsorbed Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8660-8667. [PMID: 27490089 DOI: 10.1021/acs.langmuir.6b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While nonspecific adsorption is widely used for immobilizing proteins on solid surfaces, the random nature of protein adsorption may reduce the activity of immobilized proteins due to occlusion of the active site. We hypothesized that the orientation a protein assumes on a given surface can be controlled by systematically introducing mutations into a region distant from its active site, thereby retaining activity of the immobilized protein. To test this hypothesis, we generated a combinatorial protein library by randomizing six targeted residues in a binding protein derived from highly stable, nonimmunoglobulin Sso7d scaffold; mutations were targeted in a region that is distant from the binding site. This library was screened to isolate binders that retain binding to its cognate target (chicken immunoglobulin Y, cIgY) as well as exhibit adsorption on unmodified silica at pH 7.4 and high ionic strength conditions. A single mutant, Sso7d-2B5, was selected for further characterization. Sso7d-2B5 retained binding to cIgY with an apparent dissociation constant similar to that of the parent protein; both mutant and parent proteins saturated the surface of silica with similar densities. Strikingly, however, silica beads coated with Sso7d-2B5 could achieve up to 7-fold higher capture of cIgY than beads coated with the parent protein. These results strongly suggest that mutations introduced in Sso7d-2B5 alter its orientation relative to the parent protein, when adsorbed on silica surfaces. Our approach also provides a generalizable strategy for introducing mutations in proteins so as to improve their activity upon immobilization, and has direct relevance to development of protein-based biosensors and biocatalysts.
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Affiliation(s)
- Carlos A Cruz-Teran
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Kevin B Carlin
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Kirill Efimenko
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
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Driessen RPC, Lin SN, Waterreus WJ, van der Meulen ALH, van der Valk RA, Laurens N, Moolenaar GF, Pannu NS, Wuite GJL, Goosen N, Dame RT. Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization. Sci Rep 2016; 6:29422. [PMID: 27403582 PMCID: PMC4941522 DOI: 10.1038/srep29422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022] Open
Abstract
Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA. The architectural properties of Sso10a proteins suggest that these proteins fulfil generic roles in chromatin organization and compaction. As these proteins exhibit different binding behaviour depending on their DNA binding stoichiometry, altered levels of expression in the cell can be exploited to drive changes in local genome folding, which may operate to modulate transcription.
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Affiliation(s)
- Rosalie P C Driessen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Szu-Ning Lin
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Willem-Jan Waterreus
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alson L H van der Meulen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Niels Laurens
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Geri F Moolenaar
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Nora Goosen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Zhao N, Schmitt MA, Fisk JD. Phage display selection of tight specific binding variants from a hyperthermostable Sso7d scaffold protein library. FEBS J 2016; 283:1351-67. [DOI: 10.1111/febs.13674] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/21/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Ning Zhao
- Department of Chemical and Biological Engineering; Colorado State University; Fort Collins CO USA
| | - Margaret A. Schmitt
- Department of Chemical and Biological Engineering; Colorado State University; Fort Collins CO USA
| | - John D. Fisk
- Department of Chemical and Biological Engineering; Colorado State University; Fort Collins CO USA
- Department of Chemistry; Colorado State University; Fort Collins CO USA
- School of Biomedical Engineering; Colorado State University; Fort Collins CO USA
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Béhar G, Pacheco S, Maillasson M, Mouratou B, Pecorari F. Switching an anti-IgG binding site between archaeal extremophilic proteins results in Affitins with enhanced pH stability. J Biotechnol 2015; 192 Pt A:123-9. [PMID: 25450641 DOI: 10.1016/j.jbiotec.2014.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/28/2014] [Accepted: 10/07/2014] [Indexed: 12/23/2022]
Abstract
As a useful reagent for biotechnological applications, a scaffold protein needs to be as stable as possible to ensure longer lifetimes. We have developed archaeal extremophilic proteins from the “7 kDa DNA-binding” family as scaffolds to derive affinity proteins (Affitins). In this study, we evaluated a rational structure/sequence-guided approach to stabilize an Affitin derived from Sac7d by transferring its human IgG binding site onto the framework of the more thermally stable Sso7d homolog. The chimera obtained was functional, well expressed in Escherichia coli, but less thermally stable than the original Affitin (T(m) = 74.2 °C vs. T(m) = 80.4 °C). Two single mutations described as thermally stabilizing wild type Sso7d were introduced into chimeras. Only the double mutation nearly restored thermal stability (T(m) = 76.9 °C). Interestingly, the chimera and its double mutant were stable from pH 0 up to at least pH 13. Our results show that it is possible to increase further the stability of Affitins toward alkaline conditions (+2 pH units) while conserving their advantageous properties. As Affitins are based on a growing family of homologs from archaeal extremophiles, we conclude that this approach offers new potential for their improvement, which will be useful in demanding biotechnological applications.
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Ahmad MUD, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W. Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein. J Mol Biol 2015; 427:3216-3229. [PMID: 26299937 DOI: 10.1016/j.jmb.2015.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
Abstract
The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°. While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.
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Affiliation(s)
- Misbha Ud Din Ahmad
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Ingrid Waege
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Michael Thomm
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Winfried Boos
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Kay Diederichs
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Wolfram Welte
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.
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Aiyer S, Rossi P, Malani N, Schneider WM, Chandar A, Bushman FD, Montelione GT, Roth MJ. Structural and sequencing analysis of local target DNA recognition by MLV integrase. Nucleic Acids Res 2015; 43:5647-63. [PMID: 25969444 PMCID: PMC4477651 DOI: 10.1093/nar/gkv410] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 04/16/2015] [Indexed: 01/01/2023] Open
Abstract
Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD). In solution, the isolated MLV IN CTD adopts an SH3 domain fold flanked by a C-terminal unstructured tail. We generated a concordant MLV IN CCD structural model using SWISS-MODEL, MMM-tree and I-TASSER. Using the X-ray crystal structure of the prototype foamy virus IN target capture complex together with our MLV domain structures, residues within the CCD α2 helical region and the CTD β1-β2 loop were predicted to bind target DNA. The role of these residues was analyzed in vivo through point mutants and motif interchanges. Viable viruses with substitutions at the IN CCD α2 helical region and the CTD β1-β2 loop were tested for effects on integration target site selection. Next-generation sequencing and analysis of integration target sequences indicate that the CCD α2 helical region, in particular P187, interacts with the sequences distal to the scissile bonds whereas the CTD β1-β2 loop binds to residues proximal to it. These findings validate our structural model and disclose IN-DNA interactions relevant to target site selection.
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Affiliation(s)
- Sriram Aiyer
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Paolo Rossi
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Rutgers University, Piscataway, NJ 08854, USA
| | - Nirav Malani
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William M Schneider
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
| | - Ashwin Chandar
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (NESG), Rutgers University, Piscataway, NJ 08854, USA Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Monica J Roth
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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Insights into the interaction between Cren7 and DNA: the role of loop β3-β4. Extremophiles 2015; 19:395-406. [PMID: 25555709 DOI: 10.1007/s00792-014-0725-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
Sulfolobus synthesizes large amounts of small chromatin proteins Cren7 and Sul7d. The two proteins share overall structural similarity, but differ distinctly in the DNA-binding region between β3- and β4-strands. While Sul7d possesses a hinge of two amino acid residues, Cren7 contains a flexible seven-residue loop (loop β3-β4) in the region. Here, we report the role of loop β3-β4 in the interaction of Cren7 with duplex DNA. We show that all residues with a large side chain on the loop, i.e., Pro30, Lys31, Arg33 and Lys34, contributed significantly to the binding of Cren7 to DNA. The three basic amino acids affected the ability of Cren7 to constrain negative DNA supercoils in a residue number-dependent manner. The crystal structure of a complex between a mutant Cren7 protein (GR) with loop β3-β4 replaced by two residues (Gly and Arg) to mimic the hinge at the corresponding position in Sul7d and an 8-bp dsDNA has been determined. Structural comparison between the GR-DNA and Cren7-DNA complexes shows that GR resembles Sul7d more than Cren7 in DNA-binding size and in the effect on the width of the major groove of DNA and the pattern of DNA bending. However, GR induces smaller DNA curvature than Sul7d. Our results suggest that Cren7 and Sul7d package chromosomal DNA in a slightly different fashion, presumably permitting different chromosomal accessibility by proteins functioning in DNA transactions.
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38
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Driessen RPC, Sitters G, Laurens N, Moolenaar GF, Wuite GJL, Goosen N, Dame RT. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry 2014; 53:6430-8. [PMID: 25291500 PMCID: PMC5451147 DOI: 10.1021/bi500344j] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
helical structure of double-stranded DNA is destabilized by
increasing temperature. Above a critical temperature (the melting
temperature), the two strands in duplex DNA become fully separated.
Below this temperature, the structural effects are localized. Using
tethered particle motion in a temperature-controlled sample chamber,
we systematically investigated the effect of increasing temperature
on DNA structure and the interplay between this effect and protein
binding. Our measurements revealed that (1) increasing temperature
enhances DNA flexibility, effectively leading to more compact folding
of the double-stranded DNA chain, and (2) temperature differentially
affects different types of DNA-bending chromatin proteins from mesophilic
and thermophilic organisms. Thus, our findings aid in understanding
genome organization in organisms thriving at moderate as well as extreme
temperatures. Moreover, our results underscore the importance of carefully
controlling and measuring temperature in single-molecule DNA (micromanipulation)
experiments.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Leiden University , 2333 CC Leiden, The Netherlands
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Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea. Int J Mol Sci 2014; 15:17162-87. [PMID: 25257534 PMCID: PMC4200833 DOI: 10.3390/ijms150917162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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Li M, Jurado KA, Lin S, Engelman A, Craigie R. Engineered hyperactive integrase for concerted HIV-1 DNA integration. PLoS One 2014; 9:e105078. [PMID: 25119883 PMCID: PMC4132020 DOI: 10.1371/journal.pone.0105078] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/18/2014] [Indexed: 01/01/2023] Open
Abstract
The DNA cutting and joining reactions of HIV-1 integration are catalyzed by integrase (IN), a viral protein that functions as a tetramer bridging the two viral DNA ends (intasome). Two major obstacles for biochemical and structural studies of HIV-1 intasomes are 1) the low efficiency of assembly with oligonucleotide DNA substrates, and 2) the non-specific aggregation of both intasomes and free IN in the reaction mixture. By fusing IN with a small non-specific DNA binding protein, Sulfolobus solfataricus chromosomal protein Sso7d (PDB: 1BNZ), we have engineered a highly soluble and hyperactive IN. Unlike wild-type IN, it efficiently catalyzes intasome assembly and concerted integration with oligonucleotide DNA substrates. The fusion IN protein also functions to integrate viral reverse transcripts during HIV-infection. The hyperactive HIV-1 IN may assist in facilitating future biochemical and structural studies of HIV-1 intasomes. Understanding the mechanistic basis of the Sso7d-IN fusion protein could provide insight into the factors that have hindered biophysical studies of wild-type HIV-1 IN and intasomes.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kellie A. Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shiqiang Lin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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42
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Grilo IR, Ludovice AM, Tomasz A, de Lencastre H, Sobral RG. The glucosaminidase domain of Atl - the major Staphylococcus aureus autolysin - has DNA-binding activity. Microbiologyopen 2014; 3:247-56. [PMID: 24585695 PMCID: PMC3996572 DOI: 10.1002/mbo3.165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/08/2014] [Accepted: 01/20/2014] [Indexed: 11/08/2022] Open
Abstract
In this communication, we describe evidence demonstrating the capacity of Atl, the major Staphylococcus aureus autolytic enzyme to bind DNA. Electrophoretic mobility shift assays (EMSA) show that both the Atl protein and the endo-β-N-acetylglucosaminidase (GL) domain were able to bind DNA of nonspecific sequence. The implications of this unexpected observation for the physiology of S. aureus remain to be explored.
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Affiliation(s)
- Inês R Grilo
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, 2780, Oeiras, Portugal
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Paquet F, Delalande O, Goffinont S, Culard F, Loth K, Asseline U, Castaing B, Landon C. Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea. PLoS One 2014; 9:e88809. [PMID: 24558431 PMCID: PMC3928310 DOI: 10.1371/journal.pone.0088809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/11/2014] [Indexed: 11/19/2022] Open
Abstract
In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.
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Affiliation(s)
- Françoise Paquet
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
- * E-mail:
| | - Olivier Delalande
- Faculté des Sciences Pharmaceutiques et Biologiques, Institut de Génétique et Développement de Rennes, Centre National de la Recherche Scientifique UMR 6290, Université de Rennes1, Rennes, France
| | - Stephane Goffinont
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
| | - Françoise Culard
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
| | - Karine Loth
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
| | - Ulysse Asseline
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
| | - Celine Landon
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France
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Abstract
The cytoplasmic membrane of most bacteria is surrounded by a more or less thick murein layer (peptidoglycan) that protects the protoplast from mechanical damage, osmotic rupture and lysis. When bacteria are dividing processes are initiated stepwise that involve DNA replication, constriction of the membranes, cell growth, biosynthesis of new murein, and finally the generation of two daughter cells. As the daughter cells are still covalently interlinked by the murein network they must be separated by specific peptidoglycan hydrolases, also referred to as autolysins. In staphylococci, the major autolysin (Atl) and its processed products N-acetylmuramoyl-l-alanine amidase (AM) and endo-β-N-acetylglucosaminidase (GL) have been in the research focus for long time. This review addresses phenotypic consequences of atl mutants, impact of Atl in virulence, the mechanism of targeting to the septum region, regulation of atl, the structure of the amidase and the repeat regions, as well as the phylogeny of Atl and its use in Staphylococcus genus and species typing.
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Zweig M, Schork S, Koerdt A, Siewering K, Sternberg C, Thormann K, Albers SV, Molin S, van der Does C. Secreted single-stranded DNA is involved in the initial phase of biofilm formation by Neisseria gonorrhoeae. Environ Microbiol 2013; 16:1040-52. [PMID: 24119133 DOI: 10.1111/1462-2920.12291] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/23/2013] [Indexed: 11/29/2022]
Abstract
Neisseria gonorrhoeae is an obligate human pathogen that colonizes the genital tract and causes gonorrhoea. Neisseria gonorrhoeae can form biofilms during natural cervical infections, on glass and in continuous flow-chamber systems. These biofilms contain large amounts of extracellular DNA, which plays an important role in biofilm formation. Many clinical isolates contain a gonococcal genetic island that encodes a type IV secretion system (T4SS). The T4SS of N. gonorrhoeae strain MS11 secretes ssDNA directly into the medium. Biofilm formation, studied in continuous flow-chamber systems by confocal laser scanning microscopy (CLSM), was strongly reduced, especially in the initial phases of biofilm formation, in the presence of Exonuclease I, which specifically degrades ssDNA or in a ΔtraB strain that does not secrete ssDNA. To specifically detect ssDNA in biofilms using CLSM, a novel method was developed in which thermostable fluorescently labelled ssDNA- and ss/dsDNA-binding proteins were used to visualize ssDNA and total DNA in biofilms and planktonic cultures. Remarkably, mainly dsDNA was detected in biofilms of the ssDNA secreting strain. We conclude that the secreted ssDNA facilitates initial biofilm formation, but that the secreted ssDNA is not retained in mature biofilms.
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Affiliation(s)
- Maria Zweig
- Department of Ecophysiology, Max-Planck-Institute for terrestrial Microbiology, Marburg, Germany
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46
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Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
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Abstract
Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.
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48
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Wilson RH, Morton SK, Deiderick H, Gerth ML, Paul HA, Gerber I, Patel A, Ellington AD, Hunicke-Smith SP, Patrick WM. Engineered DNA ligases with improved activities in vitro. Protein Eng Des Sel 2013; 26:471-8. [DOI: 10.1093/protein/gzt024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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49
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Béhar G, Bellinzoni M, Maillasson M, Paillard-Laurance L, Alzari PM, He X, Mouratou B, Pecorari F. Tolerance of the archaeal Sac7d scaffold protein to alternative library designs: characterization of anti-immunoglobulin G Affitins. Protein Eng Des Sel 2013; 26:267-75. [PMID: 23315487 DOI: 10.1093/protein/gzs106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Engineered protein scaffolds have received considerable attention as alternatives to antibodies in both basic and applied research, as they can offer superior biophysical properties often associated with a simpler molecular organization. Sac7d has been demonstrated as an effective scaffold for molecular recognition. Here, we used the initial L1 'flat surface' library constructed by randomization of 14 residues, to identify ligands specific for human immunoglobulin G. To challenge the plasticity of the Sac7d protein scaffold, we designed the alternative L2 'flat surface & loops' library whereof only 10 residues are randomized. Representative binders (Affitins) of the two libraries exhibited affinities in the low nanomolar range and were able to recognize different epitopes within human immunoglobulin G. These Affitins were stable up to pH 12 while largely conserving other favorable properties of Sac7d protein, such as high expression yields in Escherichia coli, solubility, thermal stability up to 80.7°C, and acidic stability (pH 0). In agreement with our library designs, mutagenesis study revealed two distinct binding areas, one including loops. Together, our results indicate that the Sac7d scaffold tolerates alternative library designs, which further expands the diversity of Affitins and may provide a general way to create tailored affinity tools for demanding applications.
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Affiliation(s)
- Ghislaine Béhar
- Université de Nantes, UMR CNRS 6204, Ingénierie de la reconnaissance, F-44322 Nantes, France
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50
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Driessen RPC, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar UD, White MF, Schiessel H, van Noort J, Dame RT. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Res 2012; 41:196-205. [PMID: 23155062 PMCID: PMC3592393 DOI: 10.1093/nar/gks1053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein–DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Physics of Life Processes, Leiden Institute of Physics and Cell Observatory, Leiden University, 2333 CC Leiden, The Netherlands
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