A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs.

Abstract:

:This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC using original authors' methodology. Established profiles reflect the high similarity between the courses of these processes. Basing on the scrupulous analysis of the profiles of their geometric and electron-topological parameters, it was established that the dipole-active WC↔w tautomerizations of the Watson-Crick-like 2AP·T(WC)/2AP·C*(WC) mispairs, stabilized by the two classical N3H⋯N1, N2H⋯O2 and one weak C6H⋯O4/N4 H-bonds, into the wobble 2AP·T*(w)/2AP·C(w) base pairs, respectively, joined by the two classical N2H⋯N3 and O4/N4H⋯N1 H-bonds, proceed via the concerted stepwise mechanism through the sequential intrapair proton transfer and subsequent large-scale shifting of the bases relative each other, through the planar, highly stable, zwitterionic transition states stabilized by the participation of the four H-bonds - N1+H⋯O4-/N4-, N1+H⋯N3-, N2+H⋯N3-, and N2+H⋯O2-. Moreover, it was found out that the 2AP·T(WC)↔2AP·T*(w)/2AP·C*(WC)↔2AP·C(w) tautomerization reactions occur non-dissociatively and are accompanied by the consequent replacement of the 10 unique patterns of the specific intermolecular interactions along the IRC. Obtained data are of paramount importance in view of their possible application for the control and management of the proton transfer, e.g. by external electric or laser fields.

journal_name

J Biomol Struct Dyn

authors

Brovarets' OO,Voiteshenko IS,Pérez-Sánchez H,Hovorun DM

doi

10.1080/07391102.2017.1331864

subject

Has Abstract

pub_date

2018-05-01 00:00:00

pages

1649-1665

issue

7

eissn

0739-1102

issn

1538-0254

journal_volume

36

pub_type

杂志文章
  • Ursolic acid and carvacrol may be potential inhibitors of dormancy protein small heat shock protein16.3 of Mycobacterium tuberculosis.

    abstract::Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell-wall thickening. sHSP16.3 is also a promising candidate for vaccine, ser...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1389305

    authors: Jee B,Kumar S,Yadav R,Singh Y,Kumar A,Sharma N

    更新日期:2018-10-01 00:00:00

  • Possible role of long-range interactions in the proton transfer of model DNA systems.

    abstract::The possible role of the long-range interactions has been examined within the semiempirical approach for model doubly stranded DNA systems involving the screw symmetry operation. The interaction energy terms seem to be sensitive to the sequence of base pairs. The essential influence of long-range corrections to the pr...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10506322

    authors: Chojnacki H,Laskowski Z

    更新日期:1985-02-01 00:00:00

  • Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies.

    abstract::Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1817788

    authors: Raval B,Srivastav AK,Gupta SK,Kumar U,Mahapatra SK,Gajjar PN,Banerjee I

    更新日期:2020-09-11 00:00:00

  • Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis.

    abstract::A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Treatment efforts have been severely impeded due to the lack of specific effective antiviral drugs for the treatment of COVID-associated pathologies. In the pre...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1794972

    authors: Naidoo D,Roy A,Kar P,Mutanda T,Anandraj A

    更新日期:2020-07-21 00:00:00

  • Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies.

    abstract::Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.674184

    authors: Majumder R,Roy S,Thakur AR

    更新日期:2012-01-01 00:00:00

  • Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine.

    abstract::A family of covalent complexes between oligonucleotides and derivatives of the intercalating agent 9-amino acridine has been synthesized (Asseline, U., Thuong, N.T. and Helene, C. (1983) C.R.Acad. Sci. (Paris) 297 (III), 369-372) and studied (Lancelot, G., Asseline, U., Thuong, N.T., and Helene, C. (1985) Biochemistry...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10506400

    authors: Cieplak P,Rao SN,Hélène C,Montenay-Garestier T,Kollman PA

    更新日期:1987-10-01 00:00:00

  • HMG box proteins interact with multiple tandemly repeated (GCC)n (GGC)m DNA sequences.

    abstract::A number of tandemly repeated DNA sequences have the ability to form hairpin structures by forming non-standard base pairs. When (GCC)15 and (GGC)15 strands are annealed together, the expected duplex is the only product. However, when (GCC)15 is annealed with (GCC)10, depending on the relative concentrations, up to fi...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1996.10508113

    authors: Zhao Y,Cheng W,Gibb CL,Gupta G,Kallenbach NR

    更新日期:1996-10-01 00:00:00

  • Investigation of domain motions in bacteriophage T4 lysozyme.

    abstract::Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508751

    authors: Arnold GE,Manchester JI,Townsend BD,Ornstein RL

    更新日期:1994-10-01 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

  • Tris (phenanthroline) metal complexes: probes for DNA helicity.

    abstract::The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of hel...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1983.10507469

    authors: Barton JK

    更新日期:1983-12-01 00:00:00

  • Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A.

    abstract::Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. o...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.698218

    authors: Lei Y,Kang SK,Gao J,Jia XS,Chen LL

    更新日期:2013-03-01 00:00:00

  • Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'.

    abstract::A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecyl...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.762724

    authors: Kutyshenko VP,Prokhorov DA,Molochkov NV,Sharapov MG,Kolesnikov I,Uversky VN

    更新日期:2014-01-01 00:00:00

  • DFT and docking studies of designed conjugates of noscapines & repurposing drugs: promising inhibitors of main protease of SARS-CoV-2 and falcipan-2.

    abstract::First case of the present epidemic, coronavirus disease (COVID-19) is reported in the Wuhan, a city of the China and all the countries throughout the world are being affected. COVID-19 is named by World Health Organization and it stands for coronavirus disease-19. As on 27th October, 2020, 73,776,588 people around the...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1841030

    authors: Kumar A,Kumar D,Kumar R,Singh P,Chandra R,Kumari K

    更新日期:2020-11-03 00:00:00

  • An insight to the dynamics of conserved water molecular triad in IMPDH II (human): recognition of cofactor and substrate to catalytic Arg 322.

    abstract::Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofac...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507304

    authors: Bairagya HR,Mukhopadhyay BP,Sekar K

    更新日期:2009-10-01 00:00:00

  • Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data.

    abstract::The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508074

    authors: Fushman D,Ohlenschläger O,Rüterjans H

    更新日期:1994-06-01 00:00:00

  • Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents.

    abstract::Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1688196

    authors: Pan Z,Wang Y,Gu X,Wang J,Cheng M

    更新日期:2020-10-01 00:00:00

  • Structural characterization of vivapain-2 and vivapain-3, cysteine proteases from Plasmodium vivax: comparative protein modeling and docking studies.

    abstract::Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506968

    authors: Desai PV,Avery MA

    更新日期:2004-06-01 00:00:00

  • Dynamics simulation of the interaction between the novel intercalator diethidium cation and B-form DNA.

    abstract::Previous research has described the interaction between the novel molecule diethidium (2,7-diamino 9-[2,7 diamino 10-N-phenanthridium] 10-N-phenanthridium) (Figure 1) and B-form DNA. Our goal is the elucidation of diethidium as the first member of a novel class of drugs which are potential pharmaceutical agents. This ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1997.10508946

    authors: Monaco RR,Polkosnik W,Dwarakanath S

    更新日期:1997-08-01 00:00:00

  • Design of sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition.

    abstract::The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1996.10508927

    authors: Nikolaev VA,Grokhovsky SL,Surovaya AN,Leinsoo TA,Sidorova NYu,Zasedatelev AS,Zhuze AL,Strahan GA,Shafer RH,Gursky GV

    更新日期:1996-08-01 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

  • Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes.

    abstract::PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 in...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1654410

    authors: Wu J,Sun Y,Zhou H,Ma Y,Wang R

    更新日期:2020-07-01 00:00:00

  • Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities, in poly(deoxythymidylic acid)-poly-L-lysine complexes.

    abstract::Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10508414

    authors: Bobst AM,Kao SC,Bobst EV,Pauly GT

    更新日期:1985-10-01 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

  • Probing the interaction of thionine with human serum albumin by multispectroscopic studies and its in vitro cytotoxic activity toward MCF-7 breast cancer cells.

    abstract::The studies on protein-dye interactions are important in biological process and it is regarded as vital step in rational drug design. The interaction of thionine (TH) with human serum albumin (HSA) was analyzed using isothermal titration calorimetry (ITC), spectroscopic, and molecular docking technique. The emission s...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1235513

    authors: Manivel P,Paulpandi M,Murugan K,Benelli G,Ilanchelian M

    更新日期:2017-11-01 00:00:00

  • An ultraviolet melting study of the stability of the DNA double helix in the NaDNA-bipyridyl-(ethylenediamine)platintum(II) complex.

    abstract::Complexes of NaDNA with the bipyridyl-(ethylenediamine)platintum(II) (abbreviated [(bipy)Pt(en)]2+) molecular ion have been studied in solution via ultraviolet absorption experiments at 260 nm between 50 and 90 degrees C. These measurements, performed as a function of the molar ratio of the [(bipy)Pt(en)]2+ complex to...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507227

    authors: Szabó S,Lee SA

    更新日期:2008-08-01 00:00:00

  • Insights into the structural perturbations of spliced variants of CD44: a modeling and simulation approach.

    abstract::Transient interactions between cancer stem cells and components of the tumor microenvironment initiate various signaling pathways crucial for carcinogenesis. Predominant hyaluronan (HA) receptor, CD44 is structurally and functionally one of the most variable cell surface receptors having the potential to generate a di...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1142476

    authors: Patel S,Shaikh F,Devaraji V,Radadiya A,Shah K,Shah A,Rawal R

    更新日期:2017-02-01 00:00:00

  • 1,2,3-Triazole substituted phthalocyanine metal complexes as potential inhibitors for anticholinesterase and antidiabetic enzymes with molecular docking studies.

    abstract::In recent years, acetylcholinesterase (AChE) and α-glycosidase (α-gly) inhibition have emerged as a promising and important approach for pharmacological intervention in many diseases such as glaucoma, epilepsy, obesity, cancer, and Alzheimer's. In this manner, the preparation and enzyme inhibition activities of periph...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1857842

    authors: Koçyiğit ÜM,Taslimi P,Tüzün B,Yakan H,Muğlu H,Güzel E

    更新日期:2020-12-09 00:00:00

  • Computer-aided drug design of novel PLA2 inhibitor candidates for treatment of snakebite.

    abstract::Phospholipases A(2) (PLA(2)) are enzymes commonly found in snake venoms from Viperidae and Elaphidae families, which are major components thereof. Many plants are used in traditional medicine as active agents against various effects induced by snakebite. This article presents the PLA(2) BthTX-I structure prediction ba...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507293

    authors: Hage-Melim LI,da Silva CH,Semighini EP,Taft CA,Sampaio SV

    更新日期:2009-08-01 00:00:00

  • Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

    abstract::To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guano...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1179594

    authors: Markova N,Pejov L,Stoyanova N,Enchev V

    更新日期:2017-05-01 00:00:00

  • Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection.

    abstract::Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1157037

    authors: Quan Y,Xiong L,Chen J,Zhang HY

    更新日期:2017-02-01 00:00:00