1
|
Chen B, Wang H, Wu Z, Duan B, Bai P, Zhang K, Li W, Zheng J, Xing J. Conformational stabilization of FOX-DNA complex architecture to sensitize prostate cancer chemotherapy. Amino Acids 2017; 49:1247-1254. [PMID: 28474127 DOI: 10.1007/s00726-017-2426-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/17/2017] [Indexed: 11/26/2022]
Abstract
The forkhead box (FOX) transcription factor is a family of tumor suppressors that negatively regulates the tumorigenesis activity of prostate cancer; stabilization of FOX-DNA complex architecture has been recognized as a new and promising strategy for sensitizing cancer chemotherapy. Here, we described a systematic method that combined in silico analysis and in vitro assay to investigate the intermolecular interaction between FOX DNA-binding domain (DBD) and its cognate DNA partner. The structural and energetic information harvested from the molecular investigation were used to guide high-throughput virtual screening against a structurally diverse, nonredundant library of natural product compounds, aiming at discovery of novel small-molecule medicines that can conformationally stabilize and promote FOX-DNA recognition and interaction. The screening identified a number of theoretically promising hits, which were then examined by using fluorescence anisotropy assay to determine their binding potency for FOX DBD domain. The antitumor activity of identified high-affinity compounds was also tested at cellular level. Structural dynamics analysis found that the small-molecule stabilizers can shift the conformational equilibrium of FOX DBD to DNA-bound state, thus promoting the protein domain to bind tightly with its DNA partner.
Collapse
Affiliation(s)
- Bin Chen
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Huiqiang Wang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Zhun Wu
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Bo Duan
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Peide Bai
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Kaiyan Zhang
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Wei Li
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jiaxin Zheng
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Jinchun Xing
- Department of Urology and Center of Urology, Xiamen Urinary Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China.
| |
Collapse
|
2
|
Mondal S, Chakraborty K, Bandyopadhyay S. Microscopic understanding of the conformational features of a protein–DNA complex. Phys Chem Chem Phys 2017; 19:32459-32472. [DOI: 10.1039/c7cp05161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein–DNA interactions play crucial roles in different stages of genetic activities, such as replication of genome, initiation of transcription,etc.
Collapse
Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Kaushik Chakraborty
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| |
Collapse
|
3
|
van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2014; 1850:1091-1098. [PMID: 25161164 DOI: 10.1016/j.bbagen.2014.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. SCOPE OF REVIEW This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. MAJOR CONCLUSIONS Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. GENERAL SIGNIFICANCE Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
Collapse
Affiliation(s)
- Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA.
| |
Collapse
|
4
|
Bekesi A, Pukancsik M, Haasz P, Felfoldi L, Leveles I, Muha V, Hunyadi-Gulyas E, Erdei A, Medzihradszky KF, Vertessy BG. Association of RNA with the uracil-DNA-degrading factor has major conformational effects and is potentially involved in protein folding. FEBS J 2010; 278:295-315. [PMID: 21134127 DOI: 10.1111/j.1742-4658.2010.07951.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, a novel uracil-DNA-degrading factor protein (UDE) was identified in Drosophila melanogaster, with homologues only in pupating insects. Its unique uracil-DNA-degrading activity and a potential domain organization pattern have been described. UDE seems to be the first representative of a new protein family with unique enzyme activity that has a putative role in insect development. In addition, UDE may also serve as potential tool in molecular biological applications. Owing to lack of homology with other proteins with known structure and/or function, de novo data are required for a detailed characterization of UDE structure and function. Here, experimental evidence is provided that recombinant protein is present in two distinct conformers. One of these contains a significant amount of RNA strongly bound to the protein, influencing its conformation. Detailed biophysical characterization of the two distinct conformational states (termed UDE and RNA-UDE) revealed essential differences. UDE cannot be converted into RNA-UDE by addition of the same RNA, implying putatively joint processes of RNA binding and protein folding in this conformational species. By real-time PCR and sequencing after random cloning, the bound RNA pool was shown to consist of UDE mRNA and the two ribosomal RNAs, also suggesting cotranslational RNA-assisted folding. This finding, on the one hand, might open a way to obtain a conformationally homogeneous UDE preparation, promoting successful crystallization; on the other hand, it might imply a further molecular function of the protein. In fact, RNA-dependent complexation of UDE was also demonstrated in a fruit fly pupal extract, suggesting physiological relevance of RNA binding of this DNA-processing enzyme.
Collapse
Affiliation(s)
- Angela Bekesi
- Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Frimpong AK, Abzalimov RR, Uversky VN, Kaltashov IA. Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: conformational heterogeneity of alpha-synuclein. Proteins 2010; 78:714-22. [PMID: 19847913 DOI: 10.1002/prot.22604] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformational heterogeneity of alpha-synuclein was studied with electrospray ionization mass spectrometry by analyzing protein ion charge state distributions, where the extent of multiple charging reflects compactness of the protein conformations in solution. Although alpha-synuclein lacks a single well-defined structure under physiological conditions, it was found to sample four distinct conformational states, ranging from a highly structured one to a random coil. The compact highly structured state of alpha-synuclein is present across the entire range of conditions tested (pH ranging from 2.5 to 10, alcohol content from 0% to 60%), but is particularly abundant in acidic solutions. The only other protein state populated in acidic solutions is a partially folded intermediate state lacking stable tertiary structure. Another, more compact intermediate state is induced by significant amounts of ethanol used as a co-solvent and appears to represent a partially folded conformation with high beta-sheet content. Protein dimerization is observed throughout the entire range of conditions tested, although only acidic solutions favor formation of highly structured dimers of alpha-synuclein. These dimers are likely to present the earliest stages in protein aggregation leading to globular oligomers and, subsequently, protofibrils.
Collapse
Affiliation(s)
- Agya K Frimpong
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | | | | |
Collapse
|
6
|
Kamadurai HB, Jain R, Foster MP. Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:470-3. [PMID: 18540053 PMCID: PMC2496856 DOI: 10.1107/s174430910801381x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 05/08/2008] [Indexed: 11/11/2022]
Abstract
Bacteriophage lambda integrase catalyzes site-specific DNA recombination. A helical bundle domain in the enzyme, called the core-binding domain (Int(CB)), promotes the catalysis of an intermediate DNA-cleavage reaction that is critical for recombination and is not well folded in solution in the absence of DNA. To gain structural insights into the mechanism behind the accessory role of this domain in catalysis, an attempt was made to crystallize an Int(CB)-DNA complex, but crystals of free Int(CB) were fortuitously obtained. The three-dimensional structure of DNA-free Int(CB) was solved at 2.0 A resolution by molecular replacement using as the search model the previously available DNA-bound 2.8 A structure of the Int(CB) domain in a larger construct of lambda integrase. The crystal structure of DNA-free Int(CB) resembles the DNA-bound structure of Int(CB), but exhibits subtle differences in the DNA-binding face and lacks electron density for ten residues in the C-terminus that form a portion of a linker connecting Int(CB) to the C-terminal catalytic domain of the enzyme. Thus, this work reveals the domain in the absence of DNA and allows comparison with the DNA-bound form of this catalytically activating domain.
Collapse
Affiliation(s)
- Hari B. Kamadurai
- Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43201, USA
| | - Rinku Jain
- Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43201, USA
| | - Mark P. Foster
- Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, OH 43201, USA
| |
Collapse
|
7
|
Chapter 2 Characterization of Protein Higher Order Structure and Dynamics with ESI MS. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
8
|
Subramaniam S, Kamadurai HB, Foster MP. Trans cooperativity by a split DNA recombinase: the central and catalytic domains of bacteriophage lambda integrase cooperate in cleaving DNA substrates when the two domains are not covalently linked. J Mol Biol 2007; 370:303-14. [PMID: 17531268 PMCID: PMC2034338 DOI: 10.1016/j.jmb.2007.04.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 04/05/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
Site-specific recombinases of the lambda-integrase family recognize and cleave their cognate DNA sites through cooperative binding to opposite sides of the DNA substrate by a C-terminal catalytic domain and a flexibly linked "core-binding" domain; regulation of this cleavage is achieved via the formation of higher-order complexes. We report that the core-binding domain of lambda-integrase is able to stimulate the activity of the catalytic domain even when the two domains are not linked. This trans stimulation is accomplished without significantly increasing the affinity of the catalytic domain for its DNA substrate. Moreover, we show that mutations in the DNA substrate can abrogate this effect while retaining specificity determinants for cleavage. Since the domains do not significantly interact directly, this finding implies that trans activation is achieved via the DNA substrate in a manner that may be mechanistically important in this and similar DNA binding and cleaving enzymes.
Collapse
Affiliation(s)
| | | | - Mark P. Foster
- * Corresponding author contact: (614) 292-1377, FAX: (614) 292-6773,
| |
Collapse
|
9
|
Vindigni A. Biochemical, biophysical, and proteomic approaches to study DNA helicases. MOLECULAR BIOSYSTEMS 2007; 3:266-74. [PMID: 17372655 DOI: 10.1039/b616145f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Helicases are a family of enzymes that play an essential role in nearly all DNA metabolic processes, catalyzing the transient opening of DNA duplexes. These motor proteins couple the chemical energy of ATP binding and hydrolysis to the separation of the complementary strands of a DNA or RNA duplex substrate. A full understanding of their mechanism of DNA unwinding can be achieved only through careful investigation of the thermodynamic and kinetic parameters that control this ATP-driven process, as well as through analysis of the helicases' tertiary and quaternary structures associated with nucleic acids and/or nucleotide recognition. This review describes the various biochemical, biophysical, and, more recently, proteomic techniques that have been developed to shed light on the still controversial, and in some aspects elusive, helicase-catalyzed mechanism of DNA unwinding.
Collapse
Affiliation(s)
- Alessandro Vindigni
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy.
| |
Collapse
|
10
|
Receveur-Bréchot V, Bourhis JM, Uversky VN, Canard B, Longhi S. Assessing protein disorder and induced folding. Proteins 2005; 62:24-45. [PMID: 16287116 DOI: 10.1002/prot.20750] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins (IDPs) defy the structure-function paradigm as they fulfill essential biological functions while lacking well-defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the use of multiples techniques.
Collapse
Affiliation(s)
- Véronique Receveur-Bréchot
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Universités Aix-Marseille I et II, Campus de Luminy, Marseille Cedex 09, France
| | | | | | | | | |
Collapse
|
11
|
Hanson CL, Robinson CV. Protein-nucleic acid interactions and the expanding role of mass spectrometry. J Biol Chem 2004; 279:24907-10. [PMID: 15056667 DOI: 10.1074/jbc.r300037200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mass spectrometry methods are being developed that enable detection of protein interactions with nucleic acids. By mass measuring complexes a direct determination of the stoichiometry of protein-nucleic acid interactions is revealed. For more complex assemblies, using a different approach it is possible to gain information about subcomplexes and even the spatial arrangement of proteins in macromolecular machines. To illustrate these different approaches we review progress and problems encountered in evaluating complexes from bimolecular interactions through to macromolecular machines such as ribosomes.
Collapse
Affiliation(s)
- Charlotte L Hanson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | |
Collapse
|
12
|
Lee L, Sadowski PD. Identification of Cre residues involved in synapsis, isomerization, and catalysis. J Biol Chem 2003; 278:36905-15. [PMID: 12851389 DOI: 10.1074/jbc.m305464200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Cre protein of bacteriophage P1 is a tyrosine recombinase and catalyzes recombination via formation of a covalent protein-DNA complex and a Holliday junction intermediate. Several co-crystal structures of Cre bound to its target lox site have provided novel insights into its biochemical activities. We have used these structures to guide the mutagenesis of several Cre residues that contact the lox spacer region and/or are involved in intersubunit protein-protein interactions. None of the mutant proteins had significant defects in DNA binding, DNA bending, or strand-specific initiation of recombination. We have identified novel functions of several amino acids that are involved in three aspects of the Cre reaction. 1) Single mutation of several NH2-terminal basic residues that contact the spacer region of loxP caused the accumulation of Holliday junction (HJ) intermediates but only a modest impairment of recombination. These residues may be involved in the isomerization of the Holliday intermediate. 2) We identified three new residues (Arg-118, Lys-122, and Glu-129) that are involved in synapsis. Cre R118A, K122A, and E129Q were catalytically competent. 3) Mutations E129R, Q133H, and K201A inactivated catalysis by the protein. The function of these Cre residues in recombination is discussed.
Collapse
Affiliation(s)
- Linda Lee
- Department of Molecular and Medical Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | | |
Collapse
|
13
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:781-792. [PMID: 12898659 DOI: 10.1002/jms.410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
|
14
|
Subramaniam S, Tewari AK, Nunes-Duby SE, Foster MP. Dynamics and DNA substrate recognition by the catalytic domain of lambda integrase. J Mol Biol 2003; 329:423-39. [PMID: 12767827 DOI: 10.1016/s0022-2836(03)00469-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Bacteriophage lambda integrase (lambda-Int) is the prototypical member of a large family of enzymes that catalyze site-specific DNA recombination via the formation of a Holliday junction intermediate. DNA strand cleavage by lambda-Int is mediated by nucleophilic attack on the scissile phosphate by a conserved tyrosine residue, forming an intermediate with the enzyme covalently attached to the 3'-end of the cleaved strand via a phosphotyrosine linkage. The crystal structure of the catalytic domain of lambda-Int (C170) obtained in the absence of DNA revealed the tyrosine nucleophile at the protein's C terminus to be located on a beta-hairpin far from the other conserved catalytic residues and adjacent to a disordered loop. This observation suggested that a conformational change in the C terminus of the protein was required to generate the active site in cis, or alternatively, that the active site could be completed in trans by donation of the tyrosine nucleophile from a neighboring molecule in the recombining synapse. We used NMR spectroscopy together with limited proteolysis to examine the dynamics of the lambda-Int catalytic domain in the presence and absence of DNA half-site substrates with the goal of characterizing the expected conformational change. Although the C terminus is indeed flexible in the absence of DNA, we find that conformational changes in the tyrosine-containing beta-hairpin are not coupled to DNA binding. To gain structural insights into C170/DNA complexes, we took advantage of mechanistic conservation with Cre and Flp recombinases to model C170 in half-site and tetrameric Holliday junction complexes. Although the models do not reveal the nature of the conformational change required for cis cleavage, they are consistent with much of the available experimental data and provide new insights into the how trans complementation could be accommodated.
Collapse
|