scholarly journals Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies.

1998 ◽  
Vol 45 (1) ◽  
pp. 221-231 ◽  
Author(s):  
J Brzeski ◽  
T Grycuk ◽  
A W Lipkowski ◽  
W Rudnicki ◽  
B Lesyng ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Dna Binding ◽  
Experimental Studies ◽  
Binding Mode ◽  
Binding Modes ◽  
Binding Properties ◽  
Peptide Motifs ◽  
Gel Shift Assay ◽  
Molecular Modeling Studies ◽  
Gel Shift

The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK-type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

Synthesis and DNA-binding Properties of a Cationic Seven-coordinate Manganese(II) Complex Formed with the Tripodal Ligand Tris(Nmethylbenzimidazol- 2-ylmethyl)amine and Salicylate

2012 ◽  
Vol 67 (8) ◽  
pp. 819-826 ◽  
Author(s):  
Huilu Wu ◽  
Ying Bai ◽  
Jingkun Yuan ◽  
Hua Wang ◽  
Guolong Pan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Mode ◽  
X Ray Diffraction ◽  
Binding Properties ◽  
Tripodal Ligand ◽  
Spectrophotometric Methods ◽  
Physico Chemical ◽  
Dna Binding Properties ◽  
Hydroxyl Radical Scavenge

A ternary cationic Mn(II) complex with the tripodal ligand tris(2-(N-methyl) benzimidazylmethyl)amine (Mentb), salicylate and DMF as ligands and nitrate as counterion, [Mn(Mentb)(salicylate)DMF](NO3), was synthesized and characterized by physico-chemical and spectroscopic methods. The crystal structure of the Mn(II) complex has been determined by single-crystal X-ray diffraction and revealed that the central Mn(II) atom is seven-coordinated. The DNA-binding properties of the Mn(II) complex were investigated by spectrophotometric methods and viscosity measurements, and the results suggest that the Mn(II) complex binds to DNA via an intercalation binding mode. Additionally, the complex exhibited potential hydroxyl radical scavenge properties in in vitro studies

Investigations into the DNA-binding mode of doxorubicinone

2019 ◽  
Vol 17 (7) ◽  
pp. 1992-1998 ◽  
Author(s):  
Samuel Steucek Tartakoff ◽  
Jennifer M. Finan ◽  
Ellis J. Curtis ◽  
Haley M. Anchukaitis ◽  
Danielle J. Couture ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Mode ◽  
Calorimetric Study ◽  
Binding Modes ◽  
Structural Homology

Spectroscopic and calorimetric study of DNA-binding by doxorubicin and doxorubicinone found different binding modes for the two molecules, despite their structural homology.

scholarly journals Molecular Modeling Studies on the Interactions of Aflatoxin B1 and Its Metabolites with Human Acetylcholinesterase. Part II: Interactions with the Catalytic Anionic Site (CAS)

Toxins ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 389 ◽  
Author(s):  
Joyce de Almeida ◽  
Rafael Dolezal ◽  
Ondrej Krejcar ◽  
Kamil Kuca ◽  
Kamil Musilek ◽  
...  
Keyword(s):  
Aflatoxin B1 ◽  
Binding Sites ◽  
Mixed Type ◽  
Experimental Studies ◽  
Common Type ◽  
Binding Modes ◽  
Anionic Site ◽  
Chronic Effects ◽  
Molecular Modeling Studies ◽  
Acute And Chronic Effects

The most common type of aflatoxin (AFT) found in nature is aflatoxin B1 (AFB1). This micotoxin is extremely hepatotoxic and carcinogenic to mammals, with acute and chronic effects. It is believed that this could be related to the capacity of AFB1 and its metabolites in inhibiting the enzyme acetylcholinesterase (AChE). In a previous work, we performed an inedited theoretical investigation on the binding modes of these molecules on the peripheral anionic site (PAS) of human AChE (HssAChE), revealing that the metabolites can also bind in the PAS in the same way as AFB1. Here, we investigated the binding modes of these compounds on the catalytic anionic site (CAS) of HssAChE to compare the affinity of the metabolites for both binding sites as well as verify which is the preferential one. Our results corroborated with experimental studies pointing to AFB1 and its metabolites as mixed-type inhibitors, and pointed to the residues relevant for the stabilization of these compounds on the CAS of HssAChE.

scholarly journals Synthesis of novel calix[4]arene p-benzazole derivatives and investigation of their DNA binding and cleavage activities with molecular docking and experimental studies

RSC Advances ◽  
2020 ◽  
Vol 10 (63) ◽  
pp. 38695-38708
Author(s):  
Seyda Cigdem Ozkan ◽  
Fatma Aksakal ◽  
Aydan Yilmaz
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Dna Cleavage ◽  
Experimental Studies ◽  
Binding Properties ◽  
Dna Binding And Cleavage

In this study, p-benzazole-derived calix[4]arene compounds with aromatic structures are synthesized and their DNA cleavage/binding properties are investigated.

scholarly journals Gel Shift Assay of Nuclear Extracts from Histoplasma capsulatum Demonstrates the Presence of Several DNA Binding Proteins

2002 ◽  
Vol 70 (4) ◽  
pp. 2238-2241 ◽  
Author(s):  
Atanas Ignatov ◽  
Elizabeth J. Keath
Keyword(s):  
Dna Binding ◽  
Fungal Pathogens ◽  
Binding Proteins ◽  
Histoplasma Capsulatum ◽  
Protein S ◽  
Dna Binding Proteins ◽  
Mobility Shift ◽  
Nuclear Extracts ◽  
Gel Shift Assay ◽  
Gel Shift

ABSTRACT A gel shift assay was optimized to detect several general DNA binding proteins from Histoplasma capsulatum strain G217B. The electrophoretic mobility shift assay (EMSA) technique also detected protein(s) recognizing a pyrimidine-rich motif found in several Histoplasma promoters. Establishment of EMSA conditions provides an important framework to evaluate regulation of homeostatic or phase-specific genes that may influence virulence in Histoplasma and other dimorphic fungal pathogens.

Synthesis, Crystal Structure, DNA-binding Properties and Antioxidant Activities of a Lutetium(III) Complex with the Bis(N-salicylidene)-3- oxapentane-1,5-diamine Ligand

2013 ◽  
Vol 68 (3) ◽  
pp. 257-266 ◽  
Author(s):  
Guolong Pan ◽  
Yuchen Bai ◽  
Hua Wang ◽  
Jin Kong ◽  
Furong Shi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Antioxidant Activities ◽  
Radical Scavenging ◽  
Binding Mode ◽  
Binding Properties ◽  
Metal Centers ◽  
Spectrophotometric Methods ◽  
Dna Binding Properties

A Schiff base ligand bis(N-salicylidene)-3-oxapentane-1,5-diamine (H2L) and its lutetium(III) complex, with composition Lu2(L)2(NO3)2, were synthesized and characterized by physico-chemical and spectroscopic methods. The crystal structure of the Lu(III) complex has been determined by single-crystal X-ray diffraction. It reveals a centrosymmetric binuclear neutral entity where Lu(III) metal centers are bridged by two phenoxo oxygen atoms. The DNA-binding properties of the Lu(III) complex were investigated by spectrophotometric methods and viscosity measurements, and the results suggest that the Lu(III) complex binds to DNA via a groove binding mode. Additionally, the antioxidant activity of the Lu(III) complex was determined by the superoxide and hydroxyl radical scavenging methods in vitro, which indicate that it is a scavenger for OH· and O-· 2 radicals.

The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1

2016 ◽  
Vol 473 (19) ◽  
pp. 3321-3339 ◽  
Author(s):  
Kazuhiko Yamasaki ◽  
Tomoko Yamasaki
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Tertiary Structure ◽  
Specific Binding ◽  
Binding Mode ◽  
Matrix Attachment Region ◽  
Titration Calorimetry ◽  
Affinity Constant ◽  
Target Sequence ◽  
Binding Modes

Transcription factor SATB1 (special AT-rich sequence binding protein 1) contains multiple DNA-binding domains (DBDs), i.e. two CUT-domain repeats (CUTr1 and CUTr2 from the N-terminus) and a homeodomain, and binds to the matrix attachment region (MAR) of DNA. Although CUTr1 and the homeodomain, but not CUTr2, are known to contribute to DNA binding, different research groups have not reached a consensus on which DBD is responsible for recognition of the target sequence in MAR, 5′-TAATA-3′. Here, we used isothermal titration calorimetry to demonstrate that CUTr1 has binding specificity to this motif, whereas the homeodomain shows affinity for a variety of DNAs without specificity. In line with nonspecific DNA-binding properties of the homeodomain, a mutation of the invariant Asn at position 51 of the homeodomain (typically in contact with the A base in a sequence-specific binding mode) did not affect the binding affinity significantly. The NMR analyses and computational modeling of the homeodomain, however, revealed the tertiary structure and DNA-binding mode that are typical of homeodomains capable of sequence-specific binding. We believe that the lack of highly conserved basic residues in the helix relevant to the base recognition loosens its fitting into the DNA groove and impairs the specific binding. The two DBDs, when fused in tandem, showed strong binding to DNA containing the 5′-TAATA-3′ motif with an affinity constant >108 M−1 and retained nonspecific binding activity. The combination of the sequence-specific and nonspecific DNA-binding modes of SATB1 should be advantageous in a search for target loci during transcriptional regulation.

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