Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

Abstract:

:The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol.

journal_name

J Biomol Struct Dyn

authors

Florián J,Leszczyński J

doi

10.1080/07391102.1995.10508797

subject

Has Abstract

pub_date

1995-04-01 00:00:00

pages

1055-62

issue

5

eissn

0739-1102

issn

1538-0254

journal_volume

12

pub_type

杂志文章
  • Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2.

    abstract::Drug re-purposing might be a fast and efficient way of drug development against the novel coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We applied a bioinformatics approach using molecular dynamics and docking to identify FDA-approved drugs that can be re-purposed to ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1811773

    authors: Chandel V,Sharma PP,Raj S,Choudhari R,Rathi B,Kumar D

    更新日期:2020-08-24 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

  • 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

  • Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles.

    abstract::The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2014.1003195

    authors: Ebrahimi M,Khayamian T,Hadadzadeh H,Sayed Tabatabaei BE,Jannesari Z,Khaksar G

    更新日期:2015-01-01 00:00:00

  • Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations.

    abstract::The With-No-Lysine (WNK) kinase family plays a significant role in regulating cation-chloride cotransporters, blood pressure and body fluid homeostasis. Mutations in the gene of WNK family, especially in WNK1 and WNK4 are responsible for pseudohypoaldosteronism type II (PHAII), characterized by hypertension. The selec...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1602079

    authors: Jonniya NA,Kar P

    更新日期:2020-03-01 00:00:00

  • Cryo-electron microscopy reveals the membrane insertion mechanism of V. cholerae hemolysin.

    abstract::Vibrio cholerae hemolysin (HlyA) is a 65 kDa pore-forming toxin which causes lysis of target eukaryotic cells by forming heptameric channels in the plasma membrane. Deletion of the 15 kDa C-terminus β-prism carbohydrate-binding domain generates a 50 kDa truncated variant (HlyA50) with 1000-fold-reduced pore-forming ac...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2013.823564

    authors: Dutta S,Banerjee KK,Ghosh AN

    更新日期:2014-01-01 00:00:00

  • Elucidating the molecular interaction of sinigrin, a potent anticancer glucosinolate from cruciferous vegetables with bovine serum albumin: effect of methylglyoxal modification.

    abstract::The present study employed the spectroscopic techniques, i.e. fluorescence, and circular dichroism (CD) and the molecular docking approach to investigate the mechanism of interaction of a potent anticancer glucosinolate, sinigrin (SIN), with bovine serum albumin (BSA). SIN binding to BSA resulted in the quenching of i...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1110835

    authors: Awasthi S,Saraswathi NT

    更新日期:2016-10-01 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

  • A full-automatic sequence design algorithm for branched DNA structures.

    abstract::Production of various structures by self-assembling single stranded DNA molecules is a widely used technology in the filed of DNA nanotechnology. Base sequences of single strands do predict the shape of the resulting nanostructure. Therefore, sequence design is crucial for the successful structure fabrication. This pa...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507193

    authors: Seiffert J,Huhle A

    更新日期:2008-04-01 00:00:00

  • Synthesis, characterization, in silico ADMET prediction, and protein binding analysis of a novel zinc(II) Schiff-base complex: Application of multi-spectroscopic and computational techniques.

    abstract::By reaction of 1,2-diaminocyclohexane with the 2,3-butanedione monoxime in the presence of ZnCl2, a new Schiff base complex was obtained. This complex was characterized by elemental analyses, FT-IR, 1H NMR, UV-Vis, and conductivity measurements. The reactivity of this complex to human serum albumin (HSA) under simulat...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1334595

    authors: Shahraki S,Shiri F,Saeidifar M

    更新日期:2018-05-01 00:00:00

  • 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

  • Comparison of the structures of the metal-thiolate binding site in Zn(II)-, Cd(II)-, and Hg(II)-metallothioneins using molecular modeling techniques.

    abstract::The first fully energy-minimized structures for a series of structurally related metal complexes of the important mammalian metal binding protein metallothionein are described. The structures were calculated based on structural information obtained from existing spectroscopic and crystallographic data, and minimized u...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1997.10508139

    authors: Fowle DA,Stillman MJ

    更新日期:1997-02-01 00:00:00

  • Human microtubule affinity-regulating kinase 4 is stable at extremes of pH.

    abstract::MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-ter...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1074942

    authors: Naz F,Singh P,Islam A,Ahmad F,Imtaiyaz Hassan M

    更新日期:2016-06-01 00:00:00

  • Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study.

    abstract::Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506995

    authors: Murphy D,Doyle H,Eritja R,Redmond G

    更新日期:2004-10-01 00:00:00

  • The effect of spermine binding on the reactivity of DNA towards carcinogenic alkylating agents.

    abstract::The effect of spermine binding on the electrostatic potential of DNA is evaluated. The calculations are performed for the essential reactive sites, atoms N7 and O6 of guanine, N3 and N7 of adenine, of the nucleic acid and for its surface envelope. An important weakening of the potential is found affecting all the impo...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10508433

    authors: Zakrzewska K,Pullman B

    更新日期:1985-12-01 00:00:00

  • A preliminary structure for the DNA binding protein from bacteriophage IKe.

    abstract::A modelling procedure has been utilized to obtain a preliminary three-dimensional structural model for the bacteriophage IKe DNA binding protein (IKe-DBP) based on the known high resolution X-ray diffraction structure of a functionally related protein (G5BP) from bacteriophage fd. The degree of structural homology obs...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10507683

    authors: Brayer GD

    更新日期:1987-04-01 00:00:00

  • Local structural properties of the V3 loop of Thailand HIV-1 isolate.

    abstract::The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506801

    authors: Andrianov AM

    更新日期:2002-06-01 00:00:00

  • Zinc metal carboxylates as potential anti-Alzheimer's candidate: in vitro anticholinesterase, antioxidant and molecular docking studies.

    abstract::In search of suitable therapy for the management of Alzheimer's disease, this study was designed to evaluate metal complexes against its biochemical targets. Zinc metal carboxylates (AAZ1-AAZ6) were evaluated against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The antioxidant in combination with anti...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1724569

    authors: Zafar R,Zubair M,Ali S,Shahid K,Waseem W,Naureen H,Haider A,Jan MS,Ullah F,Sirajuddin M,Sadiq A

    更新日期:2020-02-13 00:00:00

  • Allowance for spatial dispersion of dielectric permittivity in polyelectrolyte model of DNA.

    abstract::In order to allow for real dielectric properties of a solvent in calculating of electrostatic characteristics of strongly charged polyions such as DNA in salt solution we consider a simple model of linear dielectric response of a medium. The interactions between charged particles are treated in the framework of self-c...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1991.10507933

    authors: Lukashin AV,Beglov DB,Frank-Kamenetskii MD

    更新日期:1991-12-01 00:00:00

  • Cooperative thermal denaturation of the assembly origin region of TMV RNA.

    abstract::The assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10506379

    authors: Kelve M,Aruja A,Kooli K,Männik J,Raukas E

    更新日期:1987-08-01 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

  • The interaction of beta-lactoglobulin with ciprofloxacin and kanamycin; a spectroscopic and molecular modeling approach.

    abstract::A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibi...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1203819

    authors: Mehraban MH,Odooli S,Yousefi R,Roghanian R,Motovali-Bashi M,Moosavi-Movahedi AA,Ghasemi Y

    更新日期:2017-07-01 00:00:00

  • Modeling of Neuropeptide Receptors Y1, Y4, Y5, and Docking Studies with Neuropeptide Antagonist Analogues: Implications for Selectivity.

    abstract::Abstract Neuropeptide Y (NPY), receptors belong to the G-protein coupled receptor superfamily. NPY mediates several physiological responses, such as blood pressure, food intake, sedation. These actions of NPY are mediated by six receptor subtypes denoted as Y(1)-Y(5) and y(6). Modeling of receptor subtypes and bindi...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506987

    authors: Jois SD,Nagarajarao LM,Prabhakaran M,Balasubramaniam A

    更新日期:2004-08-01 00:00:00

  • Design, synthesis and biological evaluation of selected 3-[3-(amino) propoxy] benzenamines as acetylcholinesterase inhibitors.

    abstract::The present paper describes design, synthesis, and biological evaluation of a series of some 3-[3-(amino)propoxy]benzenamines as acetylcholinesterase inhibitors using mice as a model and piracetam as a reference drug. The structures of these compounds were confirmed by spectral analysis and compounds were tested for m...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1220330

    authors: Malik R,Gupta R,Srivastava S,Choudhary BS,Sharma M

    更新日期:2017-08-01 00:00:00

  • Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies.

    abstract::Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distributio...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章,评审

    doi:10.1080/07391102.1984.10507565

    authors: Beveridge DL,Maye PV,Jayaram B,Ravishanker G,Mezei M

    更新日期:1984-10-01 00:00:00

  • Investigation on the site-selective binding of bovine serum albumin by erlotinib hydrochloride.

    abstract::The purpose of this study was to investigate the site-selective binding of erlotinib hydrochloride (ET), a targeted anticancer drug, to bovine serum albumin (BSA) through 1H NMR, spectroscopic, thermodynamic, and molecular modeling methods. The fluorescence quenching of BSA by ET was a result of the formation of BSA-E...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2012.726532

    authors: Liu Y,Chen M,Luo Z,Lin J,Song L

    更新日期:2013-10-01 00:00:00

  • In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database.

    abstract::PPARα and PPARγ play important roles in regulating glucose and lipid metabolism. In recent years, the development of dual PPAR agonists has become a hot topic in the field of anti-diabetic medicinal chemistry. The dual PPARα/γ agonists can both improve metabolism and reduce side effects caused by single drugs, and has...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1745279

    authors: Feng XY,Ding TT,Liu YY,Xu WR,Cheng XC

    更新日期:2020-04-01 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

  • Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with TrkA kinase.

    abstract::Tropomyosin receptor kinase A (Trk A) is a receptor tyrosine kinase activated by nerve growth factor (NGF). TrkA plays an important role in pain sensation, which leads to significant interest in the development of small molecule inhibitors of TrkA. However, TrkA and the other two highly homologous isoforms, TrkB and T...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1708798

    authors: Wu X,Li Q,Wan S,Zhang J

    更新日期:2021-01-01 00:00:00

  • Poly(dA-dT).poly(dA-dT) in low salt appears to be a left-handed B-helix combined use of chemical theory, fiber diffraction and NMR spectroscopy.

    abstract::Poly(dA-dT).poly(dA-dT) can adopt the B- and D- forms in the fibrous state. Theoretical energy calculations and fiber diffraction analyses suggest that there can be three structural models of poly(dA-dT).poly(dA-dT) in each of these two forms viz right and left-handed Watson Crick models and left-handed Hoogsteen--a t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1983.10507450

    authors: Gupta G,Sarma MH,Dhingra MM,Sarma RH,Rajagopalan M,Sasisekharan V

    更新日期:1983-10-01 00:00:00