Wobble↔Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: a key to the intimate mechanisms of the spontaneous transversions.

Abstract:

:The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechanisms of the spontaneous transversions.

journal_name

J Biomol Struct Dyn

authors

Brovarets' OO,Hovorun DM

doi

10.1080/07391102.2015.1077737

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

2710-5

issue

12

eissn

0739-1102

issn

1538-0254

journal_volume

33

pub_type

杂志文章
  • Study on the binding characteristics of hydroxylated polybrominated diphenyl ethers and thyroid transporters using the multispectral technique and computational simulation.

    abstract::Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1461134

    authors: Wei Y,Yi Z,Xu J,Yang W,Yang L,Liu H

    更新日期:2019-04-01 00:00:00

  • Structure and energetics in the complexes of a double-stranded B-DNA dodecamer with netropsin derivatives of a tricationic water-soluble porphyrin: a theoretical investigation.

    abstract::The structural and energetical characteristics of the complexes formed between two auto-complementary DNA dodecamers, d(CGCGAATTCGCG)2, and d(GCGCAATTGCGC)2, and two novel netropsin (I) and glycine-netropsin (II) conjugates of a tricationic water-soluble porphyrin are investigated in detail by means of theoretical com...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508064

    authors: Perrée-Fauvet M,Gresh N

    更新日期:1994-06-01 00:00:00

  • Molecular modeling of sialyloligosaccharide fragments into the active site of influenza virus N9 neuraminidase.

    abstract::Molecular modeling studies have been carried out to investigate the interactions between substrate sialyloligosaccharide (SOS) fragments bearing different glycosidic linkages and influenza virus N9 neuraminidase, a surface glycoprotein of influenza virus subtype N9. The studies revealed that the allowed orientation fo...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2001.10506718

    authors: Veluraja K,Suresh MX,Christlet TH,Rafi ZA

    更新日期:2001-08-01 00:00:00

  • Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies.

    abstract::The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of α...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2013.855144

    authors: Anwer K,Sonani R,Madamwar D,Singh P,Khan F,Bisetty K,Ahmad F,Hassan MI

    更新日期:2015-01-01 00:00:00

  • A novel major groove binding site in B-form DNA for ethidium cation.

    abstract::A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2007.10507160

    authors: Monaco RR

    更新日期:2007-10-01 00:00:00

  • In silico 3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase.

    abstract::Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2014.968622

    authors: Tanneeru K,Balla AR,Guruprasad L

    更新日期:2015-01-01 00:00:00

  • Density functional geometry optimization and energy calculations of calcium(II)-triphosphate complexes. Polyphosphates as possible dissolving agents for calcium pyrophosphate dihydrate crystals in chondrocalcinosis disease.

    abstract::Geometry optimizations and energy calculations have been carried out via molecular orbital methods at the density functional B3LYP/LANL2DZ level on the molecules PO3-, OPO3(3-), HOPO3(2-), CH3OPO3(2-), H(CH3OPO3)-, O(PO3)2(4-), HO(PO3)2(3-), CH2(PO3)2(4-), (CH3OPO2)O(PO3)3-, O(PO3)3(5-), HO(PO3)3(4-), (PO3)3(3-), (CH3...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506655

    authors: Cini R,Chindamo D,Catenaccio M,Lorenzini S,Marcolongo R

    更新日期:2000-08-01 00:00:00

  • Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

    abstract::Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing am...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1323015

    authors: Kim Y,Lee M,Choi H,Baek I,Kim JI,Na S

    更新日期:2018-04-01 00:00:00

  • Conformational studies on calcium binding by tBoc-Leu-Pro-Tyr-Ala-NHCH3, a tyrosine kinase substrate, in a nonpolar solvent.

    abstract::With a view to understanding the structural requirement for tyrosine phosphorylation, we have examined the free and Ca(2+)-bound conformations of the synthetic peptide tBoc-Leu-Pro-Tyr-Ala-NHCH3, a substrate for a protein tyrosine kinase, using circular dichroism (CD), 1H and 13C nuclear magnetic resonance (NMR) and m...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1993.10508012

    authors: Ananthanarayanan VS,Saint-Jean A,Cheesman BV,Hughes DW,Bain AD

    更新日期:1993-12-01 00:00:00

  • In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro.

    abstract::SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodoc...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1845980

    authors: Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik I

    更新日期:2020-11-17 00:00:00

  • Statistical mechanical approach for predicting the transition to non-B DNA structures in supercoiled DNA.

    abstract::Supercoiling causes global twist of DNA structure and the supercoiled state has wide influence on conformational transition. A statistical mechanical approach was made for prediction of the transition probability to non-B DNA structures under torsional stress. A conditional partition function was defined as the sum ov...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1993.10507997

    authors: Katsura S,Makishima F,Nishimura H

    更新日期:1993-02-01 00:00:00

  • Blocking the DNA repair system by traditional Chinese medicine?

    abstract::Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from trad...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2011.10508616

    authors: Sun MF,Chang TT,Chang KW,Huang HJ,Chen HY,Tsai FJ,Lin JG,Chen CY

    更新日期:2011-06-01 00:00:00

  • Correlation of secondary structures of bradykinin B1 receptor antagonists with their activity.

    abstract::The secondary structure of a bradykinin B(1)receptor antagonist B-10324 (F5C-Lys-(1)- Lys(0)-Arg(1)-Pro(2)- Hyp(3)-Gly(4)-CpG(5)- Ser(6)-DTic(7)-CpG(8)) was determined by NMR at 800MHz. The conformational data are compared with those obtained previously for two bradykinin B(1) receptor antagonists, namely B-9858 (Lys-...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506765

    authors: Miskolzie M,Gera L,Stewart JM,Kotovych G

    更新日期:2002-02-01 00:00:00

  • Probing the binding sites of resveratrol, genistein, and curcumin with milk β-lactoglobulin.

    abstract::We determined the binding sites of curcumin (cur), resveratrol (res), and genistein (gen) with milk β-lactoglobulin (β-LG) at physiological conditions. Fourier transform infrared spectroscopy, circular dichroism, and fluorescence spectroscopic methods as well as molecular modeling were used to determine the binding of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.742461

    authors: Kanakis CD,Tarantilis PA,Polissiou MG,Tajmir-Riahi HA

    更新日期:2013-12-01 00:00:00

  • Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19.

    abstract::Medicinal herbs have proved along history to be a source of multiple cures. In this paper, we demonstrate how hydroxychloroquine can act as a good inhibitor of SARS-CoV-2 Spike protein receptor-binding-domain using molecular docking studies. We also unveil how hydroxychloroquine can interfere in the prevention of Lys3...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1796809

    authors: Sehailia M,Chemat S

    更新日期:2020-07-22 00:00:00

  • Mid-infrared study of deoxyadenosine at high pressures: evidence of phase transitions.

    abstract::Room temperature mid-infrared experiments between 500 and 1800 cm(-1) have been performed on crystalline deoxyadenosine as a function of pressure up to about 10 GPa. Discontinuities observed near 2 and 4 GPa indicate that two separate phase transitions occur at these pressures. Changes in the spectra suggest that both...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2007.10507147

    authors: Lee SA,Lettress L,Anderson A

    更新日期:2007-06-01 00:00:00

  • Molecular modeling and molecular dynamics simulation studies of Delta-Notch complex.

    abstract::Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章,收录出版

    doi:10.1080/07391102.2011.10507386

    authors: Majumder R,Roy S,Thakur A

    更新日期:2011-10-01 00:00:00

  • An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies.

    abstract::Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1567388

    authors: Kashyap K,Kakkar R

    更新日期:2020-01-01 00:00:00

  • Exploring the structural interaction of BSA with amine functionalized ruthenium(II) metal complex.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2019.1683071

    authors: Anish Babu A,Karthick K,Subramanian R,Swarnalatha K

    更新日期:2020-08-01 00:00:00

  • DNA Structure and Polymerase Fidelity: A New Role for A-DNA.

    abstract::Abstract Although the recent structural studies on polymerases have brought new insights on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots for polymerase slippage shows that, in the B- form, these sequences share common str...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506617

    authors: Timsit Y

    更新日期:2000-01-01 00:00:00

  • Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations.

    abstract::Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章,评审

    doi:10.1080/07391102.2000.10506597

    authors: Sponer J,Berger I,Spačková N,Leszczynski J,Hobza P

    更新日期:2000-01-01 00:00:00

  • Human dopamine transporter: the first implementation of a combined in silico/in vitro approach revealing the substrate and inhibitor specificities.

    abstract::Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the hum...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1426044

    authors: Djikic T,Martí Y,Spyrakis F,Lau T,Benedetti P,Davey G,Schloss P,Yelekci K

    更新日期:2019-02-01 00:00:00

  • An empirical potential study of the interaction of L-lysine-L-alanine-L-alanine tripeptide with four models of B-DNA with different compositions.

    abstract::The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508038

    authors: Vondrásek J,Sponar J,Hobza P

    更新日期:1994-02-01 00:00:00

  • Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays.

    abstract::Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three differ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1404934

    authors: Sutthibutpong T,Rattanarojpong T,Khunrae P

    更新日期:2018-11-01 00:00:00

  • Underlying molecular interaction of bovine serum albumin and linezolid: a biophysical outlook.

    abstract::Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorptio...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1278721

    authors: Roy A,Seal P,Sikdar J,Banerjee S,Haldar R

    更新日期:2018-02-01 00:00:00

  • Structural and biological study of synthesized anthraquinone series of compounds with sulfonamide feature.

    abstract::1, 4 and 5, 8-Positions as well as type of functionalities on these positions at anthraquinone-9, 10-dione are proposed to be significant for anticancer activity. Therefore, keeping this into consideration, a series of 1-substituted anthraquinone-based compounds are designed, synthesized, characterized and biologicall...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1552198

    authors: Awasthi P,Vatsal M,Sharma A

    更新日期:2019-10-01 00:00:00

  • A potent drug candidature of Cu(II) pyrazino[2,3-f][1,10]phenanthroline complexes with bioactive ligands: synthesis, crystal structures, biomolecular interactions, radical scavenging and cytotoxicities.

    abstract::A novel ternary copper(II) complexes, - [Cu(py-phen)(asn)(NO3)(H2O)] (1) and [Cu(py-phen)(trp)(H2O)]NO3 (2)- (py-phen: pyrazino[2,3-f][1,10]phenanthroline, asn: asparagine, trp: tryptophan), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interacti...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1808070

    authors: İnci D,Aydın R,Vatan Ö,Zorlu Y

    更新日期:2020-08-18 00:00:00

  • The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27.

    abstract::Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction w...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1848628

    authors: Timofeev VI,Fateev IV,Kostromina MA,Abramchik YA,Konstantinova ID,Volkov VV,Lykoshin DD,Mikheeva OO,Muravieva TI,Esipov RS,Kuranova IP

    更新日期:2020-11-23 00:00:00

  • Novel coumarin derivatives as potent acetylcholinesterase inhibitors: insight into efficacy, mode and site of inhibition.

    abstract::The inhibitory efficacy of two substituted coumarin derivatives on the activity of neurodegenerative enzyme acetylcholinesterase (AChE) was assessed in aqueous buffer as well as in the presence of human serum albumin (HSA) and compared against standard cholinergic AD drug, Donepezil (DON). The experimental data reveal...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1465853

    authors: Baruah P,Basumatary G,Yesylevskyy SO,Aguan K,Bez G,Mitra S

    更新日期:2019-04-01 00:00:00

  • Unusual stability exhibited by (AT)XN12(AT)Y motif associated with high fetal hemoglobin levels.

    abstract::Quasi-palindromic sequences (AT) X N12(AT) Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1532320

    authors: Roy K,Mahendru S,Kukreti R,Kukreti S

    更新日期:2019-09-01 00:00:00