1
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Li M, Rieck J, Noheda B, Roerdink JBTM, Wilkinson MHF. Stripe noise removal in conductive atomic force microscopy. Sci Rep 2024; 14:3931. [PMID: 38365918 PMCID: PMC10873331 DOI: 10.1038/s41598-024-54094-w] [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: 09/22/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Conductive atomic force microscopy (c-AFM) can provide simultaneous maps of the topography and electrical current flow through materials with high spatial resolution and it is playing an increasingly important role in the characterization of novel materials that are being investigated for novel memory devices. However, noise in the form of stripe features often appear in c-AFM images, challenging the quantitative analysis of conduction or topographical information. To remove stripe noise without losing interesting information, as many as sixteen destriping methods are investigated in this paper, including three additional models that we propose based on the stripes characteristics, and thirteen state-of-the-art destriping methods. We have also designed a gradient stripe noise model and obtained a ground truth dataset consisting of 800 images, generated by rotating and cropping a clean image, and created a noisy image dataset by adding random intensities of simulated noise to the ground truth dataset. In addition to comparing the results of the stripe noise removal visually, we performed a quantitative image quality comparison using simulated datasets and 100 images with very different strengths of simulated noise. All results show that the Low-Rank Recovery method has the best performance and robustness for removing gradient stripe noise without losing useful information. Furthermore, a detailed performance comparison of Polynomial fitting and Low-Rank Recovery at different levels of real noise is presented.
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Affiliation(s)
- Mian Li
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands.
| | - Jan Rieck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Beatriz Noheda
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Jos B T M Roerdink
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands
| | - Michael H F Wilkinson
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands
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2
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Retureau R, Foloppe N, Elbahnsi A, Oguey C, Hartmann B. A dynamic view of DNA structure within the nucleosome: Biological implications. J Struct Biol 2020; 211:107511. [PMID: 32311461 DOI: 10.1016/j.jsb.2020.107511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Most of eukaryotic cellular DNA is packed in nucleosome core particles (NCPs), in which the DNA (DNANCP) is wrapped around histones. The influence of this organization on the intrinsic local dynamics of DNA is largely unknown, in particular because capturing such information from experiments remains notoriously challenging. Given the importance of dynamical properties in DNA functions, we addressed this issue using CHARMM36 MD simulations of a nucleosome containing the NCP positioning 601 sequence and four related free dodecamers. Comparison between DNANCP and free DNA reveals a limited impact of the dense DNA-histone interface on correlated motions of dinucleotide constituents and on fluctuations of inter base pair parameters. A characteristic feature intimately associated with the DNANCP super-helical path is a set of structural periodicities that includes a marked alternation of regions enriched in backbone BI and BII conformers. This observation led to uncover a convincing correspondence between the sequence effect on BI/BII propensities in both DNANCP and free DNA, strengthening the idea that the histone preference for particular DNA sequences relies on those intrinsic structural properties. These results offer for the first time a detailed view of the DNA dynamical behavior within NCP. They show in particular that the DNANCP dynamics is substantial enough to preserve the ability to structurally adjust to external proteins, for instance remodelers. Also, fresh structural arguments highlight the relevance of relationships between DNA sequence and structural properties for NCP formation. Overall, our work offers a more rational framework to approach the functional, biological roles of NCP.
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Affiliation(s)
- Romain Retureau
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | | | - Ahmad Elbahnsi
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France; LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Christophe Oguey
- LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Brigitte Hartmann
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France.
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3
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Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018; 18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022] Open
Abstract
Abstract
DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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4
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Petronijević J, Janković N, Stanojković TP, Joksimović N, Grozdanić NĐ, Vraneš M, Tot A, Bugarčić Z. Biological evaluation of selected 3,4-dihydro-2(1H
)-quinoxalinones and 3,4-dihydro-1,4-benzoxazin-2-ones: Molecular docking study. Arch Pharm (Weinheim) 2018; 351:e1700308. [DOI: 10.1002/ardp.201700308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Nenad Janković
- Department of Chemistry; University of Kragujevac; Kragujevac Serbia
| | | | - Nenad Joksimović
- Department of Chemistry; University of Kragujevac; Kragujevac Serbia
| | | | - Milan Vraneš
- Department of Chemistry, Biochemistry and Environmental Protection; University of Novi Sad; Novi Sad Serbia
| | - Aleksandar Tot
- Department of Chemistry, Biochemistry and Environmental Protection; University of Novi Sad; Novi Sad Serbia
| | - Zorica Bugarčić
- Department of Chemistry; University of Kragujevac; Kragujevac Serbia
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5
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Radisavljević S, Bratsos I, Scheurer A, Korzekwa J, Masnikosa R, Tot A, Gligorijević N, Radulović S, Rilak Simović A. New gold pincer-type complexes: synthesis, characterization, DNA binding studies and cytotoxicity. Dalton Trans 2018; 47:13696-13712. [DOI: 10.1039/c8dt02903b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex [Au(H2LtBu)Cl]Cl2(1) induced perturbations of the cell cycle and led to apoptosis in human melanoma A375 cells.
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Affiliation(s)
| | - Ioannis Bratsos
- I.N.N
- Department of Physical Chemistry
- NCSR “Demokritos”
- Athens
- Greece
| | - Andreas Scheurer
- Inorganic Chemistry
- Department of Chemistry and Pharmacy
- University of Erlangen-Nürnberg
- Erlangen
- Germany
| | - Jana Korzekwa
- Inorganic Chemistry
- Department of Chemistry and Pharmacy
- University of Erlangen-Nürnberg
- Erlangen
- Germany
| | - Romana Masnikosa
- Department of Physical Chemistry
- Vinča Institute of Nuclear Sciences
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - Aleksandar Tot
- University of Novi Sad
- Faculty of Sciences
- Department of Chemistry
- Biochemistry and Environmental Protection
- 21000 Novi Sad
| | | | - Siniša Radulović
- Institute for Oncology and Radiology of Serbia
- 11000 Belgrade
- Serbia
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6
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Bhattacharya D, Cao R, Cheng J. UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinformatics 2016; 32:2791-9. [PMID: 27259540 PMCID: PMC5018369 DOI: 10.1093/bioinformatics/btw316] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/15/2016] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Recent experimental studies have suggested that proteins fold via stepwise assembly of structural units named 'foldons' through the process of sequential stabilization. Alongside, latest developments on computational side based on probabilistic modeling have shown promising direction to perform de novo protein conformational sampling from continuous space. However, existing computational approaches for de novo protein structure prediction often randomly sample protein conformational space as opposed to experimentally suggested stepwise sampling. RESULTS Here, we develop a novel generative, probabilistic model that simultaneously captures local structural preferences of backbone and side chain conformational space of polypeptide chains in a united-residue representation and performs experimentally motivated conditional conformational sampling via stepwise synthesis and assembly of foldon units that minimizes a composite physics and knowledge-based energy function for de novo protein structure prediction. The proposed method, UniCon3D, has been found to (i) sample lower energy conformations with higher accuracy than traditional random sampling in a small benchmark of 6 proteins; (ii) perform comparably with the top five automated methods on 30 difficult target domains from the 11th Critical Assessment of Protein Structure Prediction (CASP) experiment and on 15 difficult target domains from the 10th CASP experiment; and (iii) outperform two state-of-the-art approaches and a baseline counterpart of UniCon3D that performs traditional random sampling for protein modeling aided by predicted residue-residue contacts on 45 targets from the 10th edition of CASP. AVAILABILITY AND IMPLEMENTATION Source code, executable versions, manuals and example data of UniCon3D for Linux and OSX are freely available to non-commercial users at http://sysbio.rnet.missouri.edu/UniCon3D/ CONTACT: chengji@missouri.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Jianlin Cheng
- Department of Computer Science Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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Barati M, Faramarzi MA, Nafissi-Varcheh N, Khoshayand MR, Houshdar Tehrani MH, Vahidi H, Adrangi S. L-Asparaginase Activity in Cell Lysates and Culture Media of Halophilic Bacterial Isolates. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2016; 15:435-440. [PMID: 27980578 PMCID: PMC5149030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The objective of this study was to isolate halophilic bacteria with the ability to produce intracellular or extracellular L-asparaginase. A total number of 120 halophilic bacteria were isolated from 17 different saline habitats of Iran including salt lakes, wetlands, brine springs and deserts. Among these, 68 were able to grow in the presence of 1.5 M NaCl and 52 demonstrated the ability to grow in the selection medium containing 3.5 M NaCl. None of the isolates appeared to produce appreciable amounts of extracellular L-asparaginase. Among the isolates that produced intracellular L-asparaginase, 5 moderate and 1 extreme halophiles were selected for further study based on their observed activity level. The moderately halophilic isolates were shown to belong to the genus Halomonas while the extreme halophile was identified as a member of the genus Aidingimonas.
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Affiliation(s)
- Mahmood Barati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Ali Faramarzi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Biotechnology Research Center, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran, 14176, Iran.
| | - Nastaran Nafissi-Varcheh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Khoshayand
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | | | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sina Adrangi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. ,Corresponding author: E-mail:
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8
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High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli. Proc Natl Acad Sci U S A 2015; 112:7177-82. [PMID: 26039992 PMCID: PMC4466710 DOI: 10.1073/pnas.1500412112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Double-stranded DNA is one of the stiffest polymers in biology, resisting both bending and twisting over hundreds of base pairs. However, tightly bent DNA loops are formed by proteins that turn off (repress) genes in bacteria. It has been shown that “architectural” proteins capable of kinking any DNA molecule without sequence preference facilitate this kind of gene repression. The mechanism of this effect is unknown for DNA loops involving the well-known Escherichia coli lac repressor. Here we adapt high-resolution protein-mapping techniques to show that an architectural protein directly binds tightly looped DNA to facilitate gene repression by the lac repressor. Double-stranded DNA is a locally inflexible polymer that resists bending and twisting over hundreds of base pairs. Despite this, tight DNA bending is biologically important for DNA packaging in eukaryotic chromatin and tight DNA looping is important for gene repression in prokaryotes. We and others have previously shown that sequence nonspecific DNA kinking proteins, such as Escherichia coli heat unstable and Saccharomyces cerevisiae non-histone chromosomal protein 6A (Nhp6A), facilitate lac repressor (LacI) repression loops in E. coli. It has been unknown if this facilitation involves direct protein binding to the tightly bent DNA loop or an indirect effect promoting global negative supercoiling of DNA. Here we adapt two high-resolution in vivo protein-mapping techniques to demonstrate direct binding of the heterologous Nhp6A protein at a LacI repression loop in living E. coli cells.
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9
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Rosanio G, Widom J, Uhlenbeck OC. In vitro selection of DNAs with an increased propensity to form small circles. Biopolymers 2015; 103:303-20. [DOI: 10.1002/bip.22608] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Gabriel Rosanio
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Jonathan Widom
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
| | - Olke C. Uhlenbeck
- Department of Molecular Biosciences; Northwestern University; Evanston IL 60208
- Department of Chemistry; Northwestern University; Evanston IL 60208
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10
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Analysis of stacking overlap in nucleic acid structures: algorithm and application. J Comput Aided Mol Des 2014; 28:851-67. [DOI: 10.1007/s10822-014-9767-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
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11
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Kulkarni M, Mukherjee A. Sequence dependent free energy profiles of localized B- to A-form transition of DNA in water. J Chem Phys 2014; 139:155102. [PMID: 24160545 DOI: 10.1063/1.4825175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA carries an inherent polymorphism, which surfaces under various external conditions. While B-form remains predominant under normal physiological conditions for most of the DNA sequences, low humidity and increased ion concentration cause B- to A-form transition. Certain proteins and molecules also sometimes cause local deformation of the DNA to the specific A-form. Previous experimental and computational studies focused on the overall B- to A-form transition. Here for the first time we investigated thermodynamics and mechanism of B- to A-form transition in water for various DNA sequences at a local dinucleotide base pair level. We introduced a new reaction coordinate Zp', based on the unique order parameter Zp, to drive B- to A-form transition locally and thereby calculate free energy profiles for the same for all the ten different dinucleotide steps embedded in a twelve base pair DNA. Results show that the trend of "A" and "B" philicity observed in experiment is preserved even at this local dinucleotide level, indicating its localized origin. Higher free energy cost obtained here is attributed to the cost of creating B∕A junctions along with formation of B->A transition at dimer level. We find that while water energetically stabilizes A-form for all the ten different dinucleotide steps to various extents, entropy acts against it. Therefore, we find that the stability of B-form DNA in water is entropic in origin. Mechanism of the conversion appears to be triggered by Slide; however, backbone parameters change concertedly.
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Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
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12
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Kailasam S, Bhattacharyya D, Bansal M. Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps. BMC Res Notes 2014; 7:83. [PMID: 24502340 PMCID: PMC3930292 DOI: 10.1186/1756-0500-7-83] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/31/2014] [Indexed: 01/21/2023] Open
Abstract
Background Sequence determines the three-dimensional structure of RNAs, and thereby plays an important role in carrying out various biological functions. RNA duplexes containing Watson-Crick (WC) basepairs, interspersed with non-Watson-Crick basepairs, are the dominant structural unit and form the scaffold for the 3-dimensional structure of RNA. It is therefore crucial to understand the geometric variation in the dinucleotide steps that form the helices. We have carried out a detailed analysis of the dinucleotide steps formed by AU and GC Watson-Crick basepairs in RNA structures (both free and protein bound) and compared the results to that seen in DNA. Further, the effect of protein binding on these steps was examined by comparing steps in free RNA structures with protein bound RNA structures. Results Characteristic sequence dependent geometries are observed for the RR, RY and YR type of dinucleotide steps in RNA. Their geometric parameters show correlated variations that are different from those observed in B-DNA helices. Subtle, but statistically significant differences are seen in roll, slide and average propeller-twist values, between the dinucleotide steps of free RNA and protein bound RNA structures. Many non-canonical cross-strand and intra-strand hydrogen bonds were identified that can stabilise the RNA dinucleotide steps, among which YR steps show presence of many new unreported interactions. Conclusions Our work provides for the first time a detailed analysis of the conformational preferences exhibited by Watson-Crick basepair containing steps in RNA double helices. Overall, the WC dinucleotide steps show considerable conformational variability. Furthermore, we have identified hydrogen bond interactions in several of the dinucleotide steps that could play a role in determining the preferred geometry, in addition to the intra-basepair hydrogen bonds and stacking interactions. Protein binding affects the conformation of the steps that are in direct contact, as well as allosterically affect the steps that are not in direct physical contact.
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Affiliation(s)
| | | | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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13
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Kühl T, Wißbrock A, Goradia N, Sahoo N, Galler K, Neugebauer U, Popp J, Heinemann SH, Ohlenschläger O, Imhof D. Analysis of Fe(III) heme binding to cysteine-containing heme-regulatory motifs in proteins. ACS Chem Biol 2013; 8:1785-93. [PMID: 23730736 DOI: 10.1021/cb400317x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Regulatory heme binds to specific motifs in proteins and controls a variety of biochemical processes. Several of these proteins were recently shown to form complexes with ferric and/or ferrous heme via a cysteine residue as axial ligand. The objective of this study was to examine the heme-binding properties of a series of cysteine-containing peptides with focus on CP motif sequences. The peptides displayed different binding behavior upon Fe(III) heme application with characteristic wavelength shifts of the Soret band to 370 nm or 420-430 nm and in some cases to both wavelengths. Whereas for most of the peptides containing a cysteine only a shift to 420-430 nm was observed, CP-containing peptides exhibited a preference for a shift to 370 nm. Detailed structural investigation using Raman and NMR spectroscopy on selected representatives revealed different binding modes with respect to iron ion coordination, which reflected the results of the UV-vis studies. A predicted short sequence stretch derived from dipeptidyl peptidase 8 was additionally examined with respect to CP motif binding to heme on the peptide as well as on the protein level. The heme association was confirmed with the first solution structure of a CP-peptide-heme complex and, moreover, an inhibitory effect of Fe(III) heme on the enzyme's activity. The relevance of both the use of model compounds to elucidate the molecular mechanism underlying regulatory heme binding and its potential for the investigation of regulatory heme control is discussed.
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Affiliation(s)
- Toni Kühl
- Pharmaceutical
Chemistry I, Institute of Pharmacy, University of Bonn, Brühler Str. 7, D-53119 Bonn, Germany
| | - Amelie Wißbrock
- Pharmaceutical
Chemistry I, Institute of Pharmacy, University of Bonn, Brühler Str. 7, D-53119 Bonn, Germany
| | - Nishit Goradia
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research−Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Nirakar Sahoo
- Center of Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Kerstin Galler
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747
Jena, Germany
- Institute of Photonic Technology, Albert-Einstein-Str.
9, D-07745 Jena, Germany
| | - Ute Neugebauer
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747
Jena, Germany
- Institute of Photonic Technology, Albert-Einstein-Str.
9, D-07745 Jena, Germany
| | - Jürgen Popp
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Erlanger Allee 101, D-07747
Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4,
D-07743 Jena, Germany
| | - Stefan H. Heinemann
- Center of Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research−Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Diana Imhof
- Pharmaceutical
Chemistry I, Institute of Pharmacy, University of Bonn, Brühler Str. 7, D-53119 Bonn, Germany
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Effect of organic solvents on the activity and stability of halophilic alcohol dehydrogenase (ADH2) from Haloferax volcanii. Extremophiles 2012. [PMID: 23179592 DOI: 10.1007/s00792-012-0498-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The effect of various organic solvents on the catalytic activity, stability and substrate specificity of alchohol dehydrogenase from Haloferax volcanii (HvADH2) was evaluated. The HvADH2 showed remarkable stability and catalysed the reaction in aqueous-organic medium containing dimethyl sulfoxide (DMSO) and methanol (MeOH). Tetrahydrofuran and acetonitrile were also investigated and adversely affected the stability of the enzyme. High concentration of salt, essential to maintain the enzymatic activity and structural integrity of the halophilic enzyme under standard conditions may be partially replaced by DMSO and MeOH. The presence of organic solvents did not induce gross changes in substrate specificity. DMSO offered a protective effect for the stability of the enzyme at nonoptimal pHs such as 6 and 10. Salt and solvent effects on the HvADH2 conformation and folding were examined through fluorescence spectroscopy. The fluorescence findings were consistent with the activity and stability results and corroborated the denaturing properties of some solvents. The intrinsic tolerance of this enzyme to organic solvent makes it highly attractive to industry.
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15
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Characterization of alcohol dehydrogenase (ADH12) from Haloarcula marismortui, an extreme halophile from the Dead Sea. Extremophiles 2011; 16:57-66. [DOI: 10.1007/s00792-011-0405-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/06/2011] [Indexed: 10/16/2022]
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16
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Olson WK, Zhurkin VB. Working the kinks out of nucleosomal DNA. Curr Opin Struct Biol 2011; 21:348-57. [PMID: 21482100 DOI: 10.1016/j.sbi.2011.03.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/08/2011] [Accepted: 03/10/2011] [Indexed: 11/17/2022]
Abstract
Condensation of DNA in the nucleosome takes advantage of its double-helical architecture. The DNA deforms at sites where the base pairs face the histone octamer. The largest so-called kink-and-slide deformations occur in the vicinity of arginines that penetrate the minor groove. Nucleosome structures formed from the 601 positioning sequence differ subtly from those incorporating an AT-rich human α-satellite DNA. Restraints imposed by the histone arginines on the displacement of base pairs can modulate the sequence-dependent deformability of DNA and potentially contribute to the unique features of the different nucleosomes. Steric barriers mimicking constraints found in the nucleosome induce the simulated large-scale rearrangement of canonical B DNA to kink-and-slide states. The pathway to these states shows nonharmonic behavior consistent with bending profiles inferred from AFM measurements.
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Affiliation(s)
- Wilma K Olson
- Rutgers- The State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
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