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Article ; Online: Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery.

Romanuka, Julija / Folkers, Gert E / Gnida, Manuel / Kovačič, Lidija / Wienk, Hans / Kaptein, Robert / Boelens, Rolf

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 49, Page(s) e2311240120

Abstract: High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the ... ...

Abstract	High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric
MeSH term(s)	Lac Repressors/genetics ; Lac Repressors/metabolism ; Escherichia coli Proteins/metabolism ; Allosteric Regulation/genetics ; Escherichia coli/metabolism ; DNA/metabolism ; Protein Structure, Secondary ; Lac Operon/genetics
Chemical Substances	Lac Repressors ; Escherichia coli Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2311240120
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Article ; Online: Comparison of PAC and MOAH for understanding the carcinogenic and developmental toxicity potential of mineral oils.

Carrillo, Juan-Carlos / Kamelia, Lenny / Romanuka, Julija / Kral, Olaf / Isola, Allison / Niemelä, Helena / Steneholm, Anna

Regulatory toxicology and pharmacology : RTP

2022 Volume 132, Page(s) 105193

Abstract: The carcinogenicity and developmental toxicity of unrefined mineral oil is related to its 3-7 ring polycyclic aromatic compounds (PAC) content. Therefore, refining operations focus on the targeted removal PAC from mineral oil that may contain aromatics ... ...

Abstract	The carcinogenicity and developmental toxicity of unrefined mineral oil is related to its 3-7 ring polycyclic aromatic compounds (PAC) content. Therefore, refining operations focus on the targeted removal PAC from mineral oil that may contain aromatics of low toxicological concern. There are thus, two types of aromatic substances in mineral oil: hazardous and non-hazardous. The first type consists of 3-7 ring PAC which may be naked (unsubstituted) or lowly alkylated. The second type or non-hazardous consists of 1-7 ring aromatics with high degree of alkylation or lack of bay or fjord regions. Although these are toxicologically different, they may both elute in the same fraction when using chromatography. To understand how these two aromatic types are related we have assessed the entire mineral oil refinement process by measuring total mineral oil aromatic hydrocarbons (MOAH) content by chromatography next to regulatory hazard tests which focus on 3-7 ring PAC. MOAH content is positively correlated to its molecular weight resulting in aromatic content bias for high viscosity substances. Hazard to 3-7 ring PAC is best controlled by the validated IP346 or modified Ames test. We explain the concept of high vs low alkylation by shortly reviewing new data on alkylated PAC.
MeSH term(s)	Carcinogenesis ; Carcinogens/toxicity ; Humans ; Hydrocarbons, Aromatic/analysis ; Mineral Oil/chemistry ; Mineral Oil/toxicity ; Minerals ; Oils ; Polycyclic Compounds
Chemical Substances	Carcinogens ; Hydrocarbons, Aromatic ; Minerals ; Oils ; Polycyclic Compounds ; Mineral Oil (8020-83-5)
Language	English
Publishing date	2022-05-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604672-1
ISSN	1096-0295 ; 0273-2300
ISSN (online)	1096-0295
ISSN	0273-2300
DOI	10.1016/j.yrtph.2022.105193
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Article ; Online: Amine Adsorbents Stability for Post-Combustion CO

Leenders, Stefan H A M / Pankratova, Galina / Wijenberg, John / Romanuka, Julija / Gharavi, Farahnaz / Tsou, Joana / Infantino, Melina / van Haandel, Lennart / van Paasen, Sander / Just, Paul-Emmanuel

ChemSusChem

2023 Volume 16, Issue 24, Page(s) e202300930

Abstract: Alternative to current liquid amine technologies for post-combustion ... ...

Abstract	Alternative to current liquid amine technologies for post-combustion CO
Language	English
Publishing date	2023-09-27
Publishing country	Germany
Document type	Journal Article
ISSN	1864-564X
ISSN (online)	1864-564X
DOI	10.1002/cssc.202300930
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Article ; Online: Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system.

Loth, Karine / Gnida, Manuel / Romanuka, Julija / Kaptein, Robert / Boelens, Rolf

Journal of biomolecular NMR

2013 Volume 56, Issue 1, Page(s) 41–49

Abstract: In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be ... ...

Abstract	In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.
MeSH term(s)	Binding Sites/genetics ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Kinetics ; Lac Operon/genetics ; Lac Repressors/chemistry ; Lac Repressors/metabolism ; Macromolecular Substances/chemistry ; Macromolecular Substances/metabolism ; Models, Biological ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Interaction Mapping ; Substrate Specificity
Chemical Substances	DNA, Bacterial ; DNA-Binding Proteins ; Lac Repressors ; Macromolecular Substances
Language	English
Publishing date	2013-04-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1081696-3
ISSN	1573-5001 ; 0925-2738
ISSN (online)	1573-5001
ISSN	0925-2738
DOI	10.1007/s10858-013-9723-0
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Zs.A 4132: Show issues

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Article ; Online: Novel strategies to overcome expression problems encountered with toxic proteins: application to the production of Lac repressor proteins for NMR studies.

Romanuka, Julija / van den Bulke, Heidi / Kaptein, Robert / Boelens, Rolf / Folkers, Gert E

Protein expression and purification

2009 Volume 67, Issue 2, Page(s) 104–112

Abstract: NMR studies of structural aspects of allosteric regulation by the Lac repressor requires overexpression and isotope labeling of the protein. The size of the repressor makes it a challenging target, putting constraints on both expression conditions and ... ...

Abstract	NMR studies of structural aspects of allosteric regulation by the Lac repressor requires overexpression and isotope labeling of the protein. The size of the repressor makes it a challenging target, putting constraints on both expression conditions and sample preparation methods to overcome problems associated with studies of larger proteins by NMR. We optimized protocols for the production of deuterated functionally active thermostable dimeric Lac repressor and its core domain mutants. The Lac repressor core domain has never been obtained as a recombinant protein, possibly due to the observed toxicity to the host cells. We overcame the core domain induced toxicity by co-expression of this domain with the full length Lac repressor, combined with a stringent control of culture conditions. Significant overexpression was only obtained if during all stages of pre-culturing the bacteria were kept in their exponential growth phase at low density. The sensitivity of NMR measurements is dramatically affected by buffer conditions; we therefore used a thermofluor buffer optimization screen to determine the optimal buffer conditions. The combined thermofluor and NMR screening method yielded thermostable fully functional Lac repressor domain samples suitable for high-resolution NMR studies. The optimized procedures to adapt Escherichia coli to growth in D2O, to overcome toxicity, and to optimize protein sample conditions provides a broad range of universally applicable techniques for production of larger proteins for NMR spectroscopy.
MeSH term(s)	Amides/metabolism ; Bacterial Proteins/biosynthesis ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/isolation & purification ; Cell Culture Techniques/methods ; Chromatography, Affinity ; Cloning, Molecular ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins ; Hydrogen-Ion Concentration ; Isopropyl Thiogalactoside/chemistry ; Isopropyl Thiogalactoside/metabolism ; Isotope Labeling ; Lac Repressors ; Nuclear Magnetic Resonance, Biomolecular/methods ; Recombinant Fusion Proteins/biosynthesis ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/biosynthesis ; Repressor Proteins/chemistry ; Repressor Proteins/genetics ; Repressor Proteins/isolation & purification ; Sodium Chloride/chemistry ; Temperature
Chemical Substances	Amides ; Bacterial Proteins ; Escherichia coli Proteins ; Lac Repressors ; LacI protein, E coli ; Recombinant Fusion Proteins ; Repressor Proteins ; Isopropyl Thiogalactoside (367-93-1) ; Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2009-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2009.05.008
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Zs.A 3084: Show issues

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Article ; Online: Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes.

Romanuka, Julija / Folkers, Gert E / Biris, Nikolaos / Tishchenko, Evgeny / Wienk, Hans / Bonvin, Alexandre M J J / Kaptein, Robert / Boelens, Rolf

Journal of molecular biology

2009 Volume 390, Issue 3, Page(s) 478–489

Abstract: The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator ...

Abstract	The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator complexes. Structural analysis of the Lac-O1 and Lac-O2 complexes shows highly similar structures with very similar numbers of specific and nonspecific contacts, in agreement with similar affinities for these two operators. The left monomer of the Lac repressor in the Lac-O3 complex retains most of these specific contacts. However, in the right half-site of the O3 operator, there is a significant loss of protein-DNA contacts, explaining the low affinity of the Lac repressor for the O3 operator. The binding mode in the right half-site resembles that of the nonspecific complex. In contrast to the Lac-nonoperator DNA complex where no hinge helices are formed, the stability of the hinge helices in the weak Lac-O3 complex is the same as in the Lac-O1 and Lac-O2 complexes, as judged from the results of hydrogen/deuterium experiments.
MeSH term(s)	DNA, Bacterial/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Operator Regions, Genetic ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Repressor Proteins/chemistry ; Repressor Proteins/metabolism
Chemical Substances	DNA, Bacterial ; Repressor Proteins
Language	English
Publishing date	2009-07-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2009.05.022
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Article: Structural characterization of an unusually stable cyclic peptide, kalata B2 from Oldenlandia affinis.

Nair, Sudarslal Sadasivan / Romanuka, Julija / Billeter, Martin / Skjeldal, Lars / Emmett, Mark R / Nilsson, Carol L / Marshall, Alan G

Biochimica et biophysica acta

2006 Volume 1764, Issue 10, Page(s) 1568–1576

Abstract: Kalata peptides are isolated from an African medicinal plant, Oldenlandia affinis, an aqueous decoction of which can be ingested to accelerate uterine contraction during childbirth. The closely packed disulfide core of kalata peptides confers unusual ... ...

Abstract	Kalata peptides are isolated from an African medicinal plant, Oldenlandia affinis, an aqueous decoction of which can be ingested to accelerate uterine contraction during childbirth. The closely packed disulfide core of kalata peptides confers unusual stability against thermal, chemical, and enzymatic degradation. The molecular arrangement may hamper NMR-assisted disulfide connectivity assignment. We have combined NMR with high-resolution mass spectrometry (MS) and MS/MS of native and chemically derivatized kalata B2 to determine its amino acid sequence and disulfide connectivity. Infrared multiphoton dissociation establishes the disulfide bond linkages in kalata B2 as I-IV, II-V and III-VI.
MeSH term(s)	Amino Acid Sequence ; Cyclotides/chemistry ; Cyclotides/isolation & purification ; Mass Spectrometry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Oldenlandia/metabolism ; Peptides, Cyclic/chemistry ; Peptides, Cyclic/isolation & purification ; Protein Conformation
Chemical Substances	Cyclotides ; Peptides, Cyclic ; kalata B2
Language	English
Publishing date	2006-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbapap.2006.07.009
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Article ; Online: Why structurally different cyclic peptides can be glycomimetics of the HNK-1 carbohydrate antigen.

Bhunia, Anirban / Vivekanandan, Subramanian / Eckert, Thomas / Burg-Roderfeld, Monika / Wechselberger, Rainer / Romanuka, Julija / Bächle, Dirk / Kornilov, Andrei V / von der Lieth, Claus-Wilhelm / Jiménez-Barbero, Jesús / Nifantiev, Nikolay E / Schachner, Melitta / Sewald, Norbert / Lütteke, Thomas / Hans-Joachim, Gabius / Siebert, Hans-Christian

Journal of the American Chemical Society

2010 Volume 132, Issue 1, Page(s) 96–105

Abstract: The cyclic peptides c-(LSETTl) and c-(RTLPFS) are of potential clinical interest--they stimulate neurite outgrowth in a way that is similar to the effects of the HNK-1 (human natural killer cell-1) antigenic carbohydrate chains, which are terminated by 3' ...

Abstract	The cyclic peptides c-(LSETTl) and c-(RTLPFS) are of potential clinical interest--they stimulate neurite outgrowth in a way that is similar to the effects of the HNK-1 (human natural killer cell-1) antigenic carbohydrate chains, which are terminated by 3'-sulfated glucuronic acid attached to an N-acetyllactosamine unit. To investigate the structure-activity relationships of the ability of the cyclic peptides to mimic HNK-1 carbohydrates, conformational analysis and examination of hydrophobic and hydrophilic patterns were performed and compared with the characteristics of a synthetic HNK-1 trisaccharide derivative. Data obtained demonstrate that both the trisaccharide and the glycomimetic peptide c-(LSETTl) exhibit a similar relationship between their hydrophobic moieties and their negatively charged sites. However, the second cyclic glycomimetic peptide investigated here, c-(RTLPFS), has a positively charged group as a potential contact point due to its Arg residue. Therefore, we studied the amino acid composition of all known receptor structures in the Protein Data Bank that are in contact with uronic acid and/or sulfated glycans. Interactions of the HNK-1 trisaccharide, c-(LSETTl), and c-(RTLPFS) with a laminin fragment involved in HNK-1 carbohydrate binding (i.e., the 21mer peptide: KGVSSRSYVGCIKNLEISRST) were also analyzed. Because the structure of the HNK-1-binding laminin domain is not available in the Protein Data Bank, we used the HNK-1-binding 21mer peptide fragment of laminin for the construction of a model receptor that enabled us to compare the molecular interplay of the HNK-1 trisaccharide and the two cyclopeptides c-(LSETTl) and c-(RTLPFS) with a reliable receptor structure in considerable detail.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Antigens/chemistry ; Antigens/metabolism ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Computational Biology ; Dimethyl Sulfoxide/chemistry ; Humans ; Killer Cells, Natural ; Laminin/chemistry ; Laminin/metabolism ; Magnetic Resonance Spectroscopy ; Mice ; Molecular Dynamics Simulation ; Molecular Mimicry ; Molecular Sequence Data ; Peptides, Cyclic/chemistry ; Peptides, Cyclic/metabolism ; Protein Structure, Tertiary ; Uronic Acids/chemistry ; Water/chemistry
Chemical Substances	Antigens ; Carbohydrates ; Laminin ; Peptides, Cyclic ; Uronic Acids ; Water (059QF0KO0R) ; Dimethyl Sulfoxide (YOW8V9698H)
Language	English
Publishing date	2010-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja904334s
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