1
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Yu B, Bolik-Coulon N, Rangadurai AK, Kay LE, Iwahara J. Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules. J Am Chem Soc 2024; 146:20788-20801. [PMID: 39028837 PMCID: PMC11295196 DOI: 10.1021/jacs.4c04433] [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: 03/31/2024] [Revised: 06/09/2024] [Accepted: 06/28/2024] [Indexed: 07/21/2024]
Abstract
NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of 1H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (ϕENS) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ϕENS values and demonstrate its utility through applications to a number of biomolecular systems. The use of Gd-based cosolutes offers several advantages over nitroxides for ϕENS measurements. First, unlike nitroxide compounds, Gd chelates enable electrostatic potential measurements on oxidation-sensitive proteins that require reducing agents. Second, the large electron spin quantum number of Gd (7/2) results in notably larger PREs for Gd chelates when used at the same concentrations as nitroxide radicals. Thus, it is possible to measure ϕENS values exclusively from + and - charged compounds even for highly charged biomolecules, avoiding the use of neutral cosolutes that, as we further establish here, limits the accuracy of the measured electrostatic potentials. In addition, the smaller concentrations of cosolutes required minimize potential binding to sites on macromolecules. Fourth, the closer proximity of the paramagnetic center and charged groups within Gd chelates, in comparison to the corresponding nitroxide compounds, enables more accurate predictions of ϕENS potentials for cross-validation of the experimental results. The Gd-based method described here, thus, broadens the applicability of studies of biomolecular electrostatics using solution NMR spectroscopy.
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Affiliation(s)
- Binhan Yu
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Nicolas Bolik-Coulon
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Atul K. Rangadurai
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Lewis E. Kay
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program
in Molecular Medicine, Hospital for Sick
Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Junji Iwahara
- Department
of Biochemistry & Molecular Biology, Sealy Center for Structural
Biology & Molecular Biophysics, University
of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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2
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Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JT, Ramakrishnan G, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow SC, Irizarry RA, Bulyk ML. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun 2024; 15:3110. [PMID: 38600112 PMCID: PMC11006913 DOI: 10.1038/s41467-024-47396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.
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Affiliation(s)
- Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Patrick K Kimes
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Gayatri Ramakrishnan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Boston Bangalore Biosciences Beginnings Program, Harvard University, Cambridge, MA, USA
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dongyuan Song
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA
| | - Stephen C Blacklow
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Yu B, Iwahara J. Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation. Biopolymers 2024; 115:e23553. [PMID: 37254885 PMCID: PMC10687310 DOI: 10.1002/bip.23553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023]
Abstract
Before reaching their targets, sequence-specific DNA-binding proteins nonspecifically bind to DNA through electrostatic interactions and stochastically change their locations on DNA. Investigations into the dynamics of DNA-scanning by proteins are nontrivial due to the simultaneous presence of multiple translocation mechanisms and many sites for the protein to nonspecifically bind to DNA. Nuclear magnetic resonance (NMR) spectroscopy can provide information about the target DNA search processes at an atomic level. Paramagnetic relaxation enhancement (PRE) is particularly useful to study how the proteins scan DNA in the search process. Previously, relatively simple two-state or three-state exchange models were used to explain PRE data reflecting the target search process. In this work, using more realistic discrete-state stochastic kinetics models embedded into an NMR master equation, we analyzed the PRE data for the HoxD9 homeodomain interacting with DNA. The kinetic models that incorporate sliding, dissociation, association, and intersegment transfer can reproduce the PRE profiles observed at some different ionic strengths. The analysis confirms the previous interpretation of the PRE data and shows that the protein's probability distribution among nonspecific sites is nonuniform during the target DNA search process.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068
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4
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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5
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Yu B, Wang X, Wang T, Iwahara J. DNA base order parameter determination without influence of chemical exchange. Methods 2023; 210:1-9. [PMID: 36596431 PMCID: PMC9898221 DOI: 10.1016/j.ymeth.2022.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/01/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool used to investigate the dynamic properties of biological macromolecules and their complexes. NMR relaxation data can provide order parameters S2, which represent the mobility of bond vectors reorienting within a molecular frame. Determination of S2 parameters typically involves the use of transverse NMR relaxation rates. However, the accuracy in S2 determination can be diminished by elevation of the transverse relaxation rates through conformational or chemical exchange involving protonation/deprotonation or non-Watson-Crick base-pair states of nucleic acids. Here, we propose an approach for determination of S2 parameters without the influence of exchange processes. This approach utilizes transverse and longitudinal 13C chemical shift anisotropy (CSA) - dipole-dipole (DD) cross-correlation rates instead of 13C transverse relaxation rates. Anisotropy in rotational diffusion is taken into consideration. An application of this approach to nucleotide base CH groups of a uniformly 13C/15N-labeled DNA duplex is demonstrated.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xi Wang
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tianzhi Wang
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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6
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Wang X, Yu B, Iwahara J. Hindered Rotations of Protein Asparagine/Glutamine Side-Chain NH 2 Groups: Impact of Hydrogen Bonding with DNA. J Phys Chem Lett 2021; 12:11378-11382. [PMID: 34784468 PMCID: PMC8643942 DOI: 10.1021/acs.jpclett.1c03467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hindered rotation about an sp2 C-N bond is known to occur in arginine (Arg), asparagine (Asn), and glutamine (Gln) side chains of proteins. However, very little is known about the rotational dynamics of Asn and Gln side-chain NH2 groups. Here, using a unique NMR method, we quantitatively characterized the hindered rotations of protein Asn/Gln side-chain NH2 groups. This NMR method yields simple NH2-selective spectra that allow for an accurate determination of the kinetic rate constants for the hindered rotations. Through the NMR measurements at different temperatures, we investigated the energy barriers that restrict the C-N bond rotations of protein side-chain NH2 groups. Through a comparison of the kinetic data for the free and DNA-bound states of the Antp homeodomain, we also examined the impact of hydrogen bonding on the hindered rotations of the side-chain NH2 groups. Our data suggest that the hydrogen bonding increases the energy barriers by 1-6 kJ/mol.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
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7
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Pathak PK, Zhang F, Peng S, Niu L, Chaturvedi J, Elliott J, Xiang Y, Tadege M, Deng J. Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA. Acta Crystallogr D Struct Biol 2021; 77:1050-1063. [PMID: 34342278 PMCID: PMC8329861 DOI: 10.1107/s205979832100632x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/18/2021] [Indexed: 12/21/2022] Open
Abstract
Homeobox transcription factors are key regulators of morphogenesis and development in both animals and plants. In plants, the WUSCHEL-related homeobox (WOX) family of transcription factors function as central organizers of several developmental programs ranging from embryo patterning to meristematic stem-cell maintenance through transcriptional activation and repression mechanisms. The Medicago truncatula STENOFOLIA (STF) gene is a master regulator of leaf-blade lateral development. Here, the crystal structure of the homeodomain (HD) of STF (STF-HD) in complex with its promoter DNA is reported at 2.1 Å resolution. STF-HD binds DNA as a tetramer, enclosing nearly the entire bound DNA surface. The STF-HD tetramer is partially stabilized by docking of the C-terminal tail of one protomer onto a conserved hydrophobic surface on the head of another protomer in a head-to-tail manner. STF-HD specifically binds TGA motifs, although the promoter sequence also contains TAAT motifs. Helix α3 not only serves a canonical role as a base reader in the major groove, but also provides DNA binding in the minor groove through basic residues located at its C-terminus. The structural and functional data in planta reported here provide new insights into the DNA-binding mechanisms of plant-specific HDs from the WOX family of transcription factors.
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Affiliation(s)
- Prabhat Kumar Pathak
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fei Zhang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Shuxia Peng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lifang Niu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Juhi Chaturvedi
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Justin Elliott
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yan Xiang
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Junpeng Deng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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8
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Nepravishta R, Pletka CC, Iwahara J. Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes. JOURNAL OF BIOMOLECULAR NMR 2020; 74:421-429. [PMID: 32683519 PMCID: PMC7511421 DOI: 10.1007/s10858-020-00333-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/09/2020] [Indexed: 05/05/2023]
Abstract
A major driving force for protein-nucleic acid association is electrostatic interactions via ion pairs of the positively charged basic side chains and negatively charged phosphates. For a better understanding of how proteins scan DNA and recognize particular signatures, it is important to gain atomic-level insight into the behavior of basic side chains at the protein-DNA interfaces. NMR spectroscopy is a powerful tool for investigating the structural, dynamic, and kinetic aspects of protein-DNA interactions. However, resonance assignment of basic side-chain cationic moieties at the molecular interfaces remains to be a major challenge. Here, we propose a fast, robust, and inexpensive approach that greatly facilitates resonance assignment of interfacial moieties and also allows for kinetic measurements of protein translocation between two DNA duplexes. This approach utilizes site-specific incorporation of racemic phosphorothioate at the position of a phosphate that interacts with a protein side chain. This modification retains the electric charge of phosphate and therefore is mild, but causes significant chemical shift perturbations for the proximal protein side chains, which facilitates resonance assignment. Due to the racemic nature of the modification, two different chemical shifts are observed for the species with different diastereomers RP and SP of the incorporated phosphorothioate group. Kinetic information on the exchange of the protein molecule between RP and SP DNA duplexes can be obtained by 15Nz exchange spectroscopy. We demonstrate the applications of this approach to the Antennapedia homeodomain-DNA complex and the CREB1 basic leucine-zipper (bZIP)-DNA complex.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA.
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9
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Yu B, Pletka CC, Iwahara J. NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups. J Phys Chem B 2020; 124:1065-1070. [PMID: 31958014 PMCID: PMC7021563 DOI: 10.1021/acs.jpcb.9b10987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Channing C. Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA
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10
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Shaik T, Rather GM, Bansal N, Minko T, Garbuzenko O, Szekely Z, Abali EE, Banerjee D, Kerrigan JE, Scotto KW, Bertino JR. Modeling and antitumor studies of a modified L-penetratin peptide targeting E2F in lung cancer and prostate cancer. Oncotarget 2018; 9:33249-33257. [PMID: 30279956 PMCID: PMC6161789 DOI: 10.18632/oncotarget.26064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/15/2018] [Indexed: 01/05/2023] Open
Abstract
E2F1-3a overexpression due to amplification or to mutation or loss of the retinoblastoma gene, induces genes involved in DNA synthesis and leads to abnormal cellular proliferation, tumor growth, and invasion. Therefore, inhibiting the overexpression of one or more of these activating E2Fs is a recognized target in cancer therapeutics. In previous studies we identified by phage display, a novel 7-mer peptide (PEP) that bound tightly to an immobilized consensus E2F1 promoter sequence, and when conjugated to penetratin to increase its uptake into cells, was cytotoxic to several malignant cell lines and human prostate and small cell lung cancer xenografts. Based on molecular simulation studies that showed that the D-Arg penetratin peptide (D-Arg PEP) secondary structure is more stable than the L-Arg PEP, the L-Arg in the peptide was substituted with D-Arg. In vitro studies confirmed that it was more stable than the L- form and was more cytotoxic as compared to the L-Arg PEP when tested against the human castrate resistant cell line, DU145 and the human lung cancer H196 cell line. When encapsulated in PEGylated liposomes, the D-Arg-PEP potently inhibited growth of the DU145 xenograft in mice. Our findings validate D- Arg PEP, an inhibitor of E2F1and 3a transcription, as an improved second generation drug candidate for targeted molecular therapy of cancers with elevated levels of activated E2F(s).
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Affiliation(s)
- Tazeem Shaik
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Gulam M Rather
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Nitu Bansal
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Tamara Minko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers: The State University of New Jersey, Piscataway, NJ, USA
| | - Olga Garbuzenko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers: The State University of New Jersey, Piscataway, NJ, USA
| | - Zoltan Szekely
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers: The State University of New Jersey, Piscataway, NJ, USA
| | - Emine E Abali
- Department of Biochemistry & Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Debabrata Banerjee
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - John E Kerrigan
- Information Technology Division of Life Sciences and Chemistry, Rutgers School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kathleen W Scotto
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Joseph R Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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11
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Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M. Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes As Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations. Biochemistry 2018; 57:2796-2813. [PMID: 29664630 DOI: 10.1021/acs.biochem.8b00195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics and may, therefore, play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain/DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a nonconsensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.
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Affiliation(s)
- Jamie M Baird-Titus
- Department of Chemistry and Physical Sciences , Mount St. Joseph University , Cincinnati , Ohio 45233 , United States
| | - Mahendra Thapa
- Department of Physics , University of Cincinnati , Cincinnati , Ohio 45220 , United States
| | - Thomas Doerdelmann
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Kelly A Combs
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology , University of Cincinnati College of Medicine , Cincinnati , Ohio 45267 , United States
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12
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Rance M. Exploring a New Approach for Discovery of Conformational Heterogeneity in Homeodomain-DNA Complexes. Biochemistry 2017; 56:5033-5034. [PMID: 28902509 DOI: 10.1021/acs.biochem.7b00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati , Cincinnati, Ohio 45267, United States
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13
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Jia Z, Li L, Chakravorty A, Alexov E. Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem 2017; 38:1974-1979. [PMID: 28602026 PMCID: PMC5495612 DOI: 10.1002/jcc.24831] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/21/2017] [Accepted: 04/22/2017] [Indexed: 11/06/2022]
Abstract
The standard treatment of ions in the framework of the Poisson-Boltzmann equation relies on molecular surfaces, which are commonly constructed along with the Stern layer. The molecular surface determines where ions can be present. In the Gaussian-based smooth dielectric function in DelPhi, smooth boundaries between the solute and solvent take the place of molecular surface. Therefore, this invokes the question of how to model mobile ions in the water phase without a definite solute-solvent boundary. This article reports a natural extension of the Gaussian-based smooth dielectric function approach that treats mobile ions via Boltzmann distribution with an added desolvation penalty. Thus, ion concentration near macromolecules is governed by the local electrostatic potential and the desolvation penalty (from being partially desolvated). The approach is tested against the experimental salt dependence of binding free energy on 7 protein-protein complexes and 12 DNA-protein complexes, resulting in Pearson correlations of 0.95 and 0.88, respectively. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States, 29634
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14
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Faraggi E, Dunker AK, Sussman JL, Kloczkowski A. Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder. J Biomol Struct Dyn 2017; 36:2331-2341. [PMID: 28714803 DOI: 10.1080/07391102.2017.1352539] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure. We find a close statistical correspondence between NMR and X-ray structures if fluctuations inherent to the NMR protocol are taken into account. Intuitively this tends to lend support to the validity of both NMR and X-ray protocols in deriving biomolecular models that correspond to in vivo conditions. We then establish Lindemann-like parameters for NMR derived structures and examine what order/disorder cutoffs for these parameters are most consistent with X-ray data and how consistent are they. Finally, we find critical value of [Formula: see text] for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value [Formula: see text] if a balance between false positive and false negative prediction is sought. We examine a few non-conforming cases, and examine the origin of the structure derived in X-ray. This study could help in assigning meaningful disorder from NMR experiments.
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Affiliation(s)
- Eshel Faraggi
- a Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , Indianapolis , 46202 IN , USA .,b Battelle Center for Mathematical Medicine , The Research Institute at Nationwide Children's Hospital , Columbus , 43205 OH , USA .,c Research and Information Systems , LLC , Carmel , 46032 IN , USA
| | - A Keith Dunker
- a Department of Biochemistry and Molecular Biology , Indiana University School of Medicine , Indianapolis , 46202 IN , USA .,d Center for Computational Biology and Bioinformatics , Indiana University School of Medicine , Indianapolis , 46202 IN , USA
| | - Joel L Sussman
- e Department of Structural Biology , Weizmann Institute of Science , Rehovot , 76100 Israel
| | - Andrzej Kloczkowski
- f Battelle Center for Mathematical Medicine , Nationwide Children's Hospital , Columbus , 43215 OH , USA .,g Department of Pediatrics , The Ohio State University , Columbus , 43215 OH , USA .,h Kavli Institute for Theoretical Physics China , Chinese Academy of Sciences , Beijing , 100190 China
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15
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Gao Y, Mi Y, Lakerveld R. An optimization‐based approach for structural design of self‐assembled DNA tiles. AIChE J 2016. [DOI: 10.1002/aic.15546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yu Gao
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
| | - Yongli Mi
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
| | - Richard Lakerveld
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
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16
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Nojima H, Kanou K, Terashi G, Takeda-Shitaka M, Inoue G, Atsuda K, Itoh C, Iguchi C, Matsubara H. Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor. BMC STRUCTURAL BIOLOGY 2016; 16:11. [PMID: 27491540 PMCID: PMC4974693 DOI: 10.1186/s12900-016-0062-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/29/2016] [Indexed: 12/21/2022]
Abstract
Background We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and whether DPP-4 has a common rule for inhibitor binding. Results All the main and side chains in the inhibitor binding area were minimally altered, except for a few side chains, despite binding to inhibitors of various shapes. Some residues (Arg125, Glu205, Glu206, Tyr662 and Asn710) in the area had binding modes to fix a specific atom of inhibitor to a particular spatial position in DPP-4. We found two specific water molecules that were common to 92 DPP-4 structures. The two water molecules were close to many inhibitors, and seemed to play two roles: maintaining the orientation of the Glu205 and Glu206 side chains through a network via the water molecules, and arranging the inhibitor appropriately at the S2 subsite. Conclusions Our study based on high-quality resources may provide a necessary minimum consensus to help in the discovery of a novel DPP-4 inhibitor that is commercially useful. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0062-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroyuki Nojima
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Kazuhiko Kanou
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.,Present address: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Genki Terashi
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Mayuko Takeda-Shitaka
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Gaku Inoue
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Koichiro Atsuda
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Chihiro Itoh
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Chie Iguchi
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Hajime Matsubara
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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17
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Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J. Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. Biophys J 2016; 109:1026-37. [PMID: 26331260 DOI: 10.1016/j.bpj.2015.07.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022] Open
Abstract
Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.
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Affiliation(s)
- Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Kurtis M Anderson
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - David G Gorenstein
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
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18
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Kachhap S, Priyadarshini P, Singh B. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. J Biomol Struct Dyn 2016; 35:1153-1167. [PMID: 27058822 DOI: 10.1080/07391102.2016.1175967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.
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Affiliation(s)
- Sangita Kachhap
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Pragya Priyadarshini
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Balvinder Singh
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
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Bhattacharjee A, Khurana JP, Jain M. Characterization of Rice Homeobox Genes, OsHOX22 and OsHOX24, and Over-expression of OsHOX24 in Transgenic Arabidopsis Suggest Their Role in Abiotic Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:627. [PMID: 27242831 PMCID: PMC4862318 DOI: 10.3389/fpls.2016.00627] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 04/25/2016] [Indexed: 05/21/2023]
Abstract
Homeobox transcription factors are well known regulators of plant growth and development. In this study, we carried out functional analysis of two candidate stress-responsive HD-ZIP I class homeobox genes from rice, OsHOX22, and OsHOX24. These genes were highly up-regulated under various abiotic stress conditions at different stages of rice development, including seedling, mature and reproductive stages. The transcript levels of these genes were enhanced significantly in the presence of plant hormones, including abscisic acid (ABA), auxin, salicylic acid, and gibberellic acid. The recombinant full-length and truncated homeobox proteins were found to be localized in the nucleus. Electrophoretic mobility shift assay established the binding of these homeobox proteins with specific DNA sequences, AH1 (CAAT(A/T)ATTG) and AH2 (CAAT(C/G)ATTG). Transactivation assays in yeast revealed the transcriptional activation potential of full-length OsHOX22 and OsHOX24 proteins. Homo- and hetero-dimerization capabilities of these proteins have also been demonstrated. Further, we identified putative novel interacting proteins of OsHOX22 and OsHOX24 via yeast-two hybrid analysis. Over-expression of OsHOX24 imparted higher sensitivity to stress hormone, ABA, and abiotic stresses in the transgenic Arabidopsis plants as revealed by various physiological and phenotypic assays. Microarray analysis revealed differential expression of several stress-responsive genes in transgenic lines as compared to wild-type. Many of these genes were found to be involved in transcriptional regulation and various metabolic pathways. Altogether, our results suggest the possible role of OsHOX22/OsHOX24 homeobox proteins as negative regulators in abiotic stress responses.
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Affiliation(s)
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South CampusNew Delhi, India
| | - Mukesh Jain
- National Institute of Plant Genome ResearchNew Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- *Correspondence: Mukesh Jain,
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20
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Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes. J Phys Chem Lett 2015; 6:2733-2737. [PMID: 26207171 PMCID: PMC4507475 DOI: 10.1021/acs.jpclett.5b01134] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/24/2015] [Indexed: 05/21/2023]
Abstract
Intermolecular ion pairs (salt bridges) are crucial for protein-DNA association. For two protein-DNA complexes, we demonstrate that the ion pairs of protein side-chain NH3+ and DNA phosphate groups undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. While the crystal structures of the complexes show only the solvent-separated ion pair (SIP) state for some interfacial lysine side chains, our NMR hydrogen-bond scalar coupling data clearly indicate the presence of the contact ion pair (CIP) state for the same residues. The 0.6-μs molecular dynamics (MD) simulations confirm dynamic transitions between the CIP and SIP states. This behavior is consistent with our NMR order parameters and scalar coupling data for the lysine side chains. Using the MD trajectories, we also analyze the free energies of the CIP-SIP equilibria. This work illustrates the dynamic nature of short-range electrostatic interactions in DNA recognition by proteins.
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Affiliation(s)
| | | | | | | | | | - Junji Iwahara
- J.I.: [Phone] 409-747-1403; [E-mail] ; [Fax] 409-772-6334
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21
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Anderson KM, Nguyen D, Esadze A, Zandarashvili L, Gorenstein DG, Iwahara J. A chemical approach for site-specific identification of NMR signals from protein side-chain NH₃⁺ groups forming intermolecular ion pairs in protein-nucleic acid complexes. JOURNAL OF BIOMOLECULAR NMR 2015; 62:1-5. [PMID: 25690740 PMCID: PMC4433575 DOI: 10.1007/s10858-015-9909-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/09/2015] [Indexed: 05/21/2023]
Abstract
Protein-nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein-DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH3 (+) groups forming the intermolecular ion pairs. A characteristic change in their (1)H and (15)N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain (15)N and DNA phosphorodithiaote (31)P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein-RNA complexes as well.
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Affiliation(s)
- Kurtis M. Anderson
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - David G. Gorenstein
- Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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22
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Echeverria I, Papoian GA. DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates. PLoS Comput Biol 2015; 11:e1003980. [PMID: 25675216 PMCID: PMC4326129 DOI: 10.1371/journal.pcbi.1003980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022] Open
Abstract
DNA molecules are highly charged semi-flexible polymers that are involved in a wide variety of dynamical processes such as transcription and replication. Characterizing the binding landscapes around DNA molecules is essential to understanding the energetics and kinetics of various biological processes. We present a curvilinear coordinate system that fully takes into account the helical symmetry of a DNA segment. The latter naturally allows to characterize the spatial organization and motions of ligands tracking the minor or major grooves, in a motion reminiscent of sliding. Using this approach, we performed umbrella sampling (US) molecular dynamics (MD) simulations to calculate the three-dimensional potentials of mean force (3D-PMFs) for a Na+ cation and for methyl guanidinium, an arginine analog. The computed PMFs show that, even for small ligands, the free energy landscapes are complex. In general, energy barriers of up to ~5 kcal/mol were measured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the minor groove. We shed light on the way the minor groove geometry, defined mainly by the DNA sequence, shapes the binding landscape around DNA, providing heterogeneous environments for recognition by various ligands. For example, we identified the presence of dissociation points or "exit ramps" that naturally would terminate sliding. We discuss how our findings have important implications for understanding how proteins and ligands associate and slide along DNA.
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Affiliation(s)
- Ignacia Echeverria
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
| | - Garegin A. Papoian
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
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23
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Fogolari F, Corazza A, Esposito G. Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes. J Comput Chem 2015; 36:585-96. [DOI: 10.1002/jcc.23832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/15/2014] [Accepted: 12/12/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze Mediche e Biologiche; Universita' di Udine; Piazzale Kolbe 4-33100 Udine Italy
- Istituto Nazionale Biostrutture e Biosistemi; Viale medaglie d'Oro 305-00136 Roma Italy
| | - Alessandra Corazza
- Dipartimento di Scienze Mediche e Biologiche; Universita' di Udine; Piazzale Kolbe 4-33100 Udine Italy
- Istituto Nazionale Biostrutture e Biosistemi; Viale medaglie d'Oro 305-00136 Roma Italy
| | - Gennaro Esposito
- Dipartimento di Scienze Mediche e Biologiche; Universita' di Udine; Piazzale Kolbe 4-33100 Udine Italy
- Istituto Nazionale Biostrutture e Biosistemi; Viale medaglie d'Oro 305-00136 Roma Italy
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24
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Dunker AK, Oldfield CJ. Back to the Future: Nuclear Magnetic Resonance and Bioinformatics Studies on Intrinsically Disordered Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:1-34. [PMID: 26387098 DOI: 10.1007/978-3-319-20164-1_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
From the 1970s to the present, regions of missing electron density in protein structures determined by X-ray diffraction and the characterization of the functions of these regions have suggested that not all protein regions depend on prior 3D structure to carry out function. Motivated by these observations, in early 1996 we began to use bioinformatics approaches to study these intrinsically disordered proteins (IDPs) and IDP regions. At just about the same time, several laboratory groups began to study a collection of IDPs and IDP regions using nuclear magnetic resonance. The temporal overlap of the bioinformatics and NMR studies played a significant role in the development of our understanding of IDPs. Here the goal is to recount some of this history and to project from this experience possible directions for future work.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 46202, Indianapolis, IN, USA.
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25
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Zandarashvili L, Iwahara J. Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds. Biochemistry 2014; 54:538-45. [PMID: 25489884 DOI: 10.1021/bi5012749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although charged side chains play important roles in protein function, their dynamic properties are not well understood. Nuclear magnetic resonance methods for investigating the dynamics of lysine side-chain NH3(+) groups were established recently. Using this methodology, we have studied the temperature dependence of the internal motions of the lysine side-chain NH3(+) groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain-DNA complex. For these NH3(+) groups, we determined order parameters and correlation times for bond rotations and reorientations at 15, 22, 28, and 35 °C. The order parameters were found to be virtually constant in this temperature range. In contrast, the bond-rotation correlation times of the NH3(+) groups were found to depend strongly on temperature. On the basis of transition state theory, the energy barriers for NH3(+) rotations were analyzed and compared to those for CH3 rotations. Enthalpies of activation for NH3(+) rotations were found to be significantly higher than those for CH3 rotations, which can be attributed to the requirement of hydrogen bond breakage. However, entropies of activation substantially reduce the overall free energies of activation for NH3(+) rotations to a level comparable to those for CH3 rotations. This entropic reduction in energy barriers may accelerate molecular processes requiring hydrogen bond breakage and play a kinetically important role in protein function.
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Affiliation(s)
- Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555-1068, United States
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26
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Ferguson L, Marlétaz F, Carter JM, Taylor WR, Gibbs M, Breuker CJ, Holland PWH. Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation. PLoS Genet 2014; 10:e1004698. [PMID: 25340822 PMCID: PMC4207634 DOI: 10.1371/journal.pgen.1004698] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/22/2014] [Indexed: 01/15/2023] Open
Abstract
Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five lepidopteran species (Polygonia c-album, Pararge aegeria, Callimorpha dominula, Cameraria ohridella, Hepialus sylvina) plus a caddisfly outgroup (Glyphotaelius pellucidus) to trace the evolution of the lepidopteran Shx genes. We demonstrate that Shx genes originated by tandem duplication of zen early in the evolution of large clade Ditrysia; Shx are not found in a caddisfly and a member of the basally diverging Hepialidae (swift moths). Four distinct Shx genes were generated early in ditrysian evolution, and were stably retained in all descendent Lepidoptera except the silkmoth which has additional duplications. Despite extensive sequence divergence, molecular modelling indicates that all four Shx genes have the potential to encode stable homeodomains. The four Shx genes have distinct spatiotemporal expression patterns in early development of the Speckled Wood butterfly (Pararge aegeria), with ShxC demarcating the future sites of extraembryonic tissue formation via strikingly localised maternal RNA in the oocyte. All four genes are also expressed in presumptive serosal cells, prior to the onset of zen expression. Lepidopteran Shx genes represent an unusual example of Hox cluster expansion and integration of novel genes into ancient developmental regulatory networks.
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Affiliation(s)
- Laura Ferguson
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Jean-Michel Carter
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Headington, Oxford, United Kingdom
| | - William R. Taylor
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Melanie Gibbs
- NERC Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
| | - Casper J. Breuker
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Headington, Oxford, United Kingdom
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Pröpper K, Meindl K, Sammito M, Dittrich B, Sheldrick GM, Pohl E, Usón I. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1743-57. [PMID: 24914984 PMCID: PMC4051508 DOI: 10.1107/s1399004714007603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/04/2014] [Indexed: 11/11/2022]
Abstract
Protein-DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein-DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein-DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein-DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.
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Affiliation(s)
- Kevin Pröpper
- University of Göttingen, Germany
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Kathrin Meindl
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | - Massimo Sammito
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
| | | | | | | | - Isabel Usón
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Spain
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Spain
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On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:77-120. [PMID: 24629186 DOI: 10.1016/b978-0-12-800168-4.00004-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are the bricks and mortar of cells, playing structural and functional roles. In order to perform their function, they interact with each other as well as with other biomolecules such as DNA or RNA. Therefore, to fathom the function of a protein, we require knowing its partners and the atomic details of its interactions (i.e., the structure of the complex). However, the amount of protein interactions with an experimentally determined three-dimensional structure is scarce. Therefore, computational techniques such as homology modeling are foremost to fill this gap. Protein interactions can be modeled using as templates the interactions of homologous proteins, if the structure of the complex is known, or using docking methods. In both approaches, the estimation of the quality of models is essential. There are several ways to address this problem. In this review, we focus on the use of knowledge-based potentials for the analysis of protein interactions. We describe the procedure to derive statistical potentials and split them into different energetic terms that can be used for different purposes. We extensively discuss the fields where knowledge-based potentials have been successfully applied to (1) model protein-protein, protein-DNA, and protein-RNA interactions and (2) predict binding sites (in the protein and in the DNA). Moreover, we provide ready-to-use resources for docking and benchmarking protein interactions.
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29
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Brison N, Debeer P, Tylzanowski P. Joining the fingers: AHOXD13story. Dev Dyn 2013; 243:37-48. [DOI: 10.1002/dvdy.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nathalie Brison
- Center for Human Genetics; University Hospitals Leuven, University of Leuven; Belgium
| | - Philippe Debeer
- Department of Development and Regeneration; University of Leuven; Belgium
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Qin Y, Yang Y, Zhang L, Fowler JD, Qiu W, Wang L, Suo Z, Zhong D. Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex. J Phys Chem A 2013; 117:13926-34. [PMID: 24308461 DOI: 10.1021/jp410051w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.
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Affiliation(s)
- Yangzhong Qin
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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Abstract
Sparsely populated transient states of proteins and their complexes play an important role in many biological processes including protein-protein and protein-DNA recognition, allostery, conformational selection, induced fit and self-assembly. These states are difficult to study as their low population and transient nature makes them effectively invisible to conventional structural and biophysical techniques. In the present article, I summarize recent NMR developments in our laboratory, including the use of paramagnetic relaxation enhancement, lifetime line broadening and dark-state exchange saturation transfer spectroscopy, that have permitted such sparsely populated states to be detected, characterized and, in some instances, visualized. I illustrate the application of these methods to the elucidation of mechanisms whereby transcription factors locate their specific target sites within an overwhelming sea of non-specific DNA, to the characterization of encounter complexes in protein-protein recognition, to large-scale interdomain motions involved in ligand binding, and to the interaction of monomeric amyloid β-peptide with the surface of amyloid protofibrils and the internal cavity surface of the chaperonin GroEL.
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Affiliation(s)
- G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R. Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res 2013; 42:430-41. [PMID: 24078250 PMCID: PMC3874178 DOI: 10.1093/nar/gkt862] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Protein–DNA recognition is a critical component of gene regulatory processes but the underlying molecular mechanisms are not yet completely understood. Whereas the DNA binding preferences of transcription factors (TFs) are commonly described using nucleotide sequences, the 3D DNA structure is recognized by proteins and is crucial for achieving binding specificity. However, the ability to analyze DNA shape in a high-throughput manner made it only recently feasible to integrate structural information into studies of protein–DNA binding. Here we focused on the homeodomain family of TFs and analyzed the DNA shape of thousands of their DNA binding sites, investigating the covariation between the protein sequence and the sequence and shape of their DNA targets. We found distinct homeodomain regions that were more correlated with either the nucleotide sequence or the DNA shape of their preferred binding sites, demonstrating different readout mechanisms through which homeodomains attain DNA binding specificity. We identified specific homeodomain residues that likely play key roles in DNA recognition via shape readout. Finally, we showed that adding DNA shape information when characterizing binding sites improved the prediction accuracy of homeodomain binding specificities. Taken together, our findings indicate that DNA shape information can generally provide new mechanistic insights into TF binding.
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Affiliation(s)
- Iris Dror
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA and Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel
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Babin V, Wang D, Rose RB, Sagui C. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. PLoS Comput Biol 2013; 9:e1003160. [PMID: 23950697 PMCID: PMC3738460 DOI: 10.1371/journal.pcbi.1003160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022] Open
Abstract
The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold. This is one of several small DNA binding motifs that, in spite of limited DNA binding specificity, adopts crucial, specific roles when incorporated in a transcription factor. The homeodomain is composed of a 3-helix domain and a mobile N-terminal arm. Helix 3 (the recognition helix) interacts with the DNA bases through the major groove, while the N-terminal arm becomes ordered upon binding a specific sequence through the minor groove. Although many structural studies have characterized the DNA binding properties of homeodomains, the factors behind the binding specificity are still difficult to elucidate. A crystal structure of the Pdx1 homeodomain bound to DNA (PDB 2H1K) obtained previously in our lab shows two complexes with differences in the conformation of the N-terminal arm, major groove contacts, and backbone contacts, raising new questions about the DNA recognition process by homeodomains. Here, we carry out fully atomistic Molecular Dynamics simulations both in crystal and aqueous environments in order to elucidate the nature of the difference in binding contacts. The crystal simulations reproduce the X-ray experimental structures well. In the absence of crystal packing constraints, the differences between the two complexes increase during the solution simulations. Thus, the conformational differences are not an artifact of crystal packing. In solution, the homeodomain with a disordered N-terminal arm repositions to a partially specific orientation. Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity. We propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations. This flexibility in DNA binding may facilitate multiple functions for the same transcription factor.
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Affiliation(s)
- Volodymyr Babin
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, United States of America
| | - Dongli Wang
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert B. Rose
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (RBR); (CS)
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Xie X, Kerrigan JE, Minko T, Garbuzenko O, Lee KC, Scarborough A, Abali EE, Budak-Alpdogan T, Johnson-Farley N, Banerjee D, Scotto KW, Bertino JR. Antitumor and modeling studies of a penetratin-peptide that targets E2F-1 in small cell lung cancer. Cancer Biol Ther 2013; 14:742-51. [PMID: 23792570 DOI: 10.4161/cbt.25184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
E2F-1, a key transcription factor necessary for cell growth, DNA repair, and differentiation, is an attractive target for development of anticancer drugs in tumors that are E2F "oncogene addicted". We identified a peptide isolated from phage clones that bound tightly to the E2F-1 promoter consensus sequence. The peptide was coupled to penetratin to enhance cellular uptake. Modeling of the penetratin-peptide (PEP) binding to the DNA E2F-1 promoter demonstrated favorable interactions that also involved the participation of most of the penetratin sequence. The penetratin-peptide (PEP) demonstrated potent in vitro cytotoxic effects against a range of cancer cell lines, particularly against Burkitt lymphoma cells and small cell lung cancer (SCLC) cells. Further studies in the H-69 SCLC cell line showed that the PEP inhibited transcription of E2F-1 and also several important E2F-regulated enzymes involved in DNA synthesis, namely, thymidylate synthase, thymidine kinase, and ribonucleotide reductase. As the PEP was found to be relatively unstable in serum, it was encapsulated in PEGylated liposomes for in vivo studies. Treatment of mice bearing the human small cell lung carcinoma H-69 with the PEP encapsulated in PEGylated liposomes (PL-PEP) caused tumor regression without significant toxicity. The liposome encapsulated PEP has promise as an antitumor agent, alone or in combination with inhibitors of DNA synthesis.
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Affiliation(s)
- Xiaoqi Xie
- Department of Pharmacology and Medicine, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ USA
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35
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Polyproline-II Helix in Proteins: Structure and Function. J Mol Biol 2013; 425:2100-32. [DOI: 10.1016/j.jmb.2013.03.018] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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Zou C, Levine EM. Vsx2 controls eye organogenesis and retinal progenitor identity via homeodomain and non-homeodomain residues required for high affinity DNA binding. PLoS Genet 2012; 8:e1002924. [PMID: 23028343 PMCID: PMC3447932 DOI: 10.1371/journal.pgen.1002924] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/05/2012] [Indexed: 12/26/2022] Open
Abstract
The homeodomain and adjacent CVC domain in the visual system homeobox (VSX) proteins are conserved from nematodes to humans. Humans with missense mutations in these regions of VSX2 have microphthalmia, suggesting both regions are critical for function. To assess this, we generated the corresponding mutations in mouse Vsx2. The homeodomain mutant protein lacked DNA binding activity and the knock-in mutant phenocopied the null mutant, ocular retardation J. The CVC mutant protein exhibited weakened DNA binding; and, although the corresponding knock-in allele was recessive, it unexpectedly caused the strongest phenotype, as indicated by severe microphthalmia and hyperpigmentation of the neural retina. This occurred through a cryptic transcriptional feedback loop involving the transcription factors Mitf and Otx1 and the Cdk inhibitor p27Kip1. Our data suggest that the phenotypic severity of the CVC mutant depends on the weakened DNA binding activity elicited by the CVC mutation and a previously unknown protein interaction between Vsx2 and its regulatory target Mitf. Our data also suggest that an essential function of the CVC domain is to assist the homeodomain in high-affinity DNA binding, which is required for eye organogenesis and unhindered execution of the retinal progenitor program in mammals. Finally, the genetic and phenotypic behaviors of the CVC mutation suggest it has the characteristics of a recessive neomorph, a rare type of genetic allele. Problems with the early development of the mammalian retina can cause congenital eye defects such as microphthalmia, in which the eye is dramatically smaller and functionally compromised. Severe microphthalmia is associated with mutations in the retinal-expressed visual system homeobox 2 (Vsx2) gene, but how Vsx2 controls retinal development, and ultimately eye formation, has remained unclear. We assessed the impact of two missense mutations, discovered in humans, on Vsx2 function and eye development in mice. One mutation altered a highly conserved residue of the homeodomain, and the other altered a highly conserved residue in the CVC domain, a region of unresolved function. Both mutations impacted the DNA binding properties of the protein, although to differing extents. Likewise, both mutations caused microphthalmia and disruptions in retinal development, also to differing extents and by distinct mechanisms. Our data suggest that Vsx2 acts as a gatekeeper of the retinal gene expression program by preventing the activation of interfering or competing gene expression programs. We propose that the evolutionary stable association between the VSX-class homeodomain and CVC domain set the stage for Vsx2 or its archetype to assume a gatekeeper function for retinal development and ultimately eye organogenesis.
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Affiliation(s)
- Changjiang Zou
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ. Crystal structure of the human NKX2.5 homeodomain in complex with DNA target. Biochemistry 2012; 51:6312-9. [PMID: 22849347 PMCID: PMC3448007 DOI: 10.1021/bi300849c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 Å resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.
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Affiliation(s)
- Lagnajeet Pradhan
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Caroli Genis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, United States
| | - Peyton Scone
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, United States
| | - Ellen O. Weinberg
- Cardiovascular Research, Boston University Medical Center, Boston, Massachusetts 02118, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida 32610, United States
| | - Hyun-Joo Nam
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States,Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, United States,Corresponding Author: Address: University of Texas at Dallas, 800 W Campbell Road, RL10, Richardson, TX 75080. Telephone: (972) 883-5786.
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A novel non-synonymous mutation in the homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Clin Chim Acta 2012; 413:1049-52. [DOI: 10.1016/j.cca.2012.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 02/16/2012] [Accepted: 02/16/2012] [Indexed: 11/21/2022]
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Limb skeletal malformations – What the HOX is going on? Eur J Med Genet 2012; 55:1-7. [DOI: 10.1016/j.ejmg.2011.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/10/2011] [Indexed: 11/21/2022]
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40
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Zhang Y, Larsen CA, Stadler HS, Ames JB. Structural basis for sequence specific DNA binding and protein dimerization of HOXA13. PLoS One 2011; 6:e23069. [PMID: 21829694 PMCID: PMC3148250 DOI: 10.1371/journal.pone.0023069] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 – 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 – 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes.
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Affiliation(s)
- Yonghong Zhang
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Christine A. Larsen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - H. Scott Stadler
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - James B. Ames
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
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41
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Roy S, Thakur AR. Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. J Biomol Struct Dyn 2011; 28:729-42. [DOI: 10.1080/07391102.2011.10508602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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42
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Sikic K, Tomic S, Carugo O. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J 2010; 4:83-95. [PMID: 21293729 PMCID: PMC3032220 DOI: 10.2174/1874091x01004010083] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/20/2010] [Accepted: 06/14/2010] [Indexed: 11/22/2022] Open
Abstract
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.
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Affiliation(s)
- Kresimir Sikic
- Departement of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, Austria
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Miyazono KI, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M. Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. EMBO J 2010; 29:1613-23. [PMID: 20389279 DOI: 10.1038/emboj.2010.53] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 03/08/2010] [Indexed: 11/09/2022] Open
Abstract
To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.
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Affiliation(s)
- Ken-ichi Miyazono
- Department of Applied Biological Chemistry, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Roy S, Thakur AR. 20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: water interaction and DNA structure analysis. J Biomol Struct Dyn 2010; 27:443-56. [PMID: 19916566 DOI: 10.1080/07391102.2010.10507329] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Homeodomains are one of the important families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. The crystal structure and NMR structure of the antennapedia homeodomain-DNA complex and comparison between them is available. Although earlier works have shown that the direct contacts and water mediated contacts are important for the binding and specificity. The detail dynamical structural characteristics of the complex, water mediating interactions in the complex and also the detail study of the free DNA and protein has not done. In the present paper we have reported the results of 20ns MD simulation of this complex with the presence of explicit water and also the 20ns MD simulation of the protein and the DNA separately in explicit water. The results show that the complex remains stable during the last 8ns of the simulation. The part of the protein which is interacting with the DNA has fewer fluctuations than other part of the protein. The pattern of water distribution around the interacting center has a typical pattern for this complex and it is quite different from the free protein and the free DNA. Water molecules penetrate into the interacting center during the simulation. Several water bridges have been identified which is responsible for recognition but not observed in the crystal structure. The recognized DNA sequence (14 mer) has been characterized by helical and step parameters. The correlated motions of the DNA and the protein in the complexed form and the free form has been analyzed.
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Affiliation(s)
- Sujata Roy
- Department of Bioinformatics, West Bengal University of Technology BF-142. Sector-I Salt Lake Kolkata-700064 India
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45
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Sheftic SR, Croke RL, LaRochelle JR, Alexandrescu AT. Electrostatic contributions to the stabilities of native proteins and amyloid complexes. Methods Enzymol 2009; 466:233-58. [PMID: 21609864 DOI: 10.1016/s0076-6879(09)66010-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to predict electrostatic contributions to protein stability from structure has been a long-standing goal of experimentalists and theorists. With recent advances in NMR spectroscopy, it is possible to determine pK(a) values of all ionizable residues for at least small proteins, and to use the pK(a) shift between the folded and unfolded states to calculate the thermodynamic contribution from a change in charge to the change in free energy of unfolding. Results for globular proteins and for α-helical coiled coils show that electrostatic contributions to stability are typically small on an individual basis, particularly for surface-exposed residues. We discuss why NMR often suggests smaller electrostatic contributions to stability than X-ray crystallography or site-directed mutagenesis, and discuss the type of information needed to improve structure-based modeling of electrostatic forces. Large pK(a) shifts from random coil values are observed for proteins bound to negatively charged sodium dodecyl sulfate micelles. The results suggest that electrostatic interactions between proteins and charges on the surfaces of membrane lipid bilayers could be a major driving force in stabilizing the structures of peripheral membrane proteins. Finally, we discuss how changes in ionization states affect amyloid-β fibril formation and suggest that electrostatic repulsion may be a common destabilizing force in amyloid fibrils.
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Affiliation(s)
- Sarah R Sheftic
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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47
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Chirgadze YN, Zheltukhin EI, Polozov RV, Sivozhelezov VS, Ivanov VV. Binding Regularities in Complexes of Transcription Factors with Operator DNA: Homeodomain Family. J Biomol Struct Dyn 2009; 26:687-700. [DOI: 10.1080/07391102.2009.10507282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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48
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Stanton BC, Giles SS, Kruzel EK, Warren CL, Ansari AZ, Hull CM. Cognate Site Identifier analysis reveals novel binding properties of the Sex Inducer homeodomain proteins of Cryptococcus neoformans. Mol Microbiol 2009; 72:1334-47. [PMID: 19486297 DOI: 10.1111/j.1365-2958.2009.06719.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Homeodomain proteins function in fungi to specify cell types and control sexual development. In the meningoencephalitis-causing fungal pathogen Cryptococcus neoformans, sexual development leads to the production of spores (suspected infectious particles). Sexual development is controlled by the homeodomain transcription factors Sxi1alpha and Sxi2a, but the mechanism by which they act is unknown. To understand how the Sxi proteins regulate development, we characterized their binding properties in vitro, showing that Sxi2a does not require a partner to bind DNA with high affinity. We then utilized a novel approach, Cognate Site Identifier (CSI) arrays, to define a comprehensive DNA-binding profile for Sxi2a, revealing a consensus sequence distinct from those of other fungal homeodomain proteins. Finally, we show that the homeodomains of both Sxi proteins are required for sexual development, a departure from related fungi. Our findings support a model in which Sxi1alpha and Sxi2a control sexual development in a homeodomain-dependent manner by binding to DNA sequences that differ from those defined in previously established fungal paradigms.
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Affiliation(s)
- Brynne C Stanton
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Madison, WI 53706, USA
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Gao M, Skolnick J. From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput Biol 2009; 5:e1000341. [PMID: 19343221 PMCID: PMC2659451 DOI: 10.1371/journal.pcbi.1000341] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/26/2009] [Indexed: 11/19/2022] Open
Abstract
DNA–protein interactions are involved in many essential biological
activities. Because there is no simple mapping code between DNA base pairs and
protein amino acids, the prediction of DNA–protein interactions is a
challenging problem. Here, we present a novel computational approach for
predicting DNA-binding protein residues and DNA–protein interaction
modes without knowing its specific DNA target sequence. Given the structure of a
DNA-binding protein, the method first generates an ensemble of complex
structures obtained by rigid-body docking with a nonspecific canonical B-DNA.
Representative models are subsequently selected through clustering and ranking
by their DNA–protein interfacial energy. Analysis of these encounter
complex models suggests that the recognition sites for specific DNA binding are
usually favorable interaction sites for the nonspecific DNA probe and that
nonspecific DNA–protein interaction modes exhibit some similarity to
specific DNA–protein binding modes. Although the method requires as
input the knowledge that the protein binds DNA, in benchmark tests, it achieves
better performance in identifying DNA-binding sites than three previously
established methods, which are based on sophisticated machine-learning
techniques. We further apply our method to protein structures predicted through
modeling and demonstrate that our method performs satisfactorily on protein
models whose root-mean-square Cα deviation from native is up to 5
Å from their native structures. This study provides valuable
structural insights into how a specific DNA-binding protein interacts with a
nonspecific DNA sequence. The similarity between the specific
DNA–protein interaction mode and nonspecific interaction modes may
reflect an important sampling step in search of its specific DNA targets by a
DNA-binding protein. Many essential biological activities require interactions between DNA and
proteins. These proteins usually use certain amino acids, called DNA-binding
sites, to recognize their specific DNA targets. To facilitate the search of its
specific DNA targets, a DNA-binding protein often associates with nonspecific
DNA and then diffuses along the DNA. Due to the weak interactions between
nonspecific DNA and the protein, structural characterization of nonspecific
DNA–protein complexes is experimentally challenging. This paper
describes a computational modeling study on nonspecific DNA–protein
complexes and comparative analysis with respect to specific
DNA–protein complexes. The study found that the specific DNA-binding
sites on a protein are typically favorable for nonspecific DNA and that
nonspecific and specific DNA–protein interaction modes are quite
similar. This similarity may reflect an important sampling step in the search
for the specific DNA target sequence by a DNA-binding protein. On the basis of
these observations, a novel method was proposed for predicting DNA-binding sites
and binding modes of a DNA-binding protein without knowing its specific DNA
target sequence. Ultimately, the combination of this method and protein
structure prediction may lead the way to high throughput modeling of
DNA–protein interactions.
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Affiliation(s)
- Mu Gao
- Center for the Study of Systems Biology, School of Biology, Georgia
Institute of Technology, Atlanta, Georgia, United States of America
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia
Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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50
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Analysis of the sequence and phenotype of Drosophila Sex combs reduced alleles reveals potential functions of conserved protein motifs of the Sex combs reduced protein. Genetics 2009; 182:191-203. [PMID: 19293143 DOI: 10.1534/genetics.109.100438] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Drosophila Hox gene, Sex combs reduced (Scr), is required for patterning the larval and adult, labial and prothoracic segments. Fifteen Scr alleles were sequenced and the phenotypes analyzed in detail. Six null alleles were nonsense mutations (Scr(2), Scr(4), Scr(11), Scr(13), Scr(13A), and Scr(16)) and one was an intragenic deletion (Scr(17)). Five hypomorphic alleles were missense mutations (Scr(1), Scr(3), Scr(5), Scr(6), and Scr(8)) and one was a small protein deletion (Scr(15)). Protein sequence changes were found in four of the five highly conserved domains of SCR: the DYTQL motif (Scr(15)), YPWM motif (Scr(3)), Homeodomain (Scr(1)), and C-terminal domain (CTD) (Scr(6)), indicating importance for SCR function. Analysis of the pleiotropy of viable Scr alleles for the formation of pseudotracheae suggests that the DYTQL motif and the CTD mediate a genetic interaction with proboscipedia. One allele Scr(14), a missense allele in the conserved octapeptide, was an antimorphic allele that exhibited three interesting genetic properties. First, Scr(14)/Df had the same phenotype as Scr(+)/Df. Second, the ability of the Scr(14) allele to interact intragenetically with Scr alleles mapped to the first 82 amino acids of SCR, which contains the octapeptide motif. Third, Scr(6), which has two missense changes in the CTD, did not interact genetically with Scr(14).
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