Microperoxidase-11: molecular dynamics and Q-band excited resonance Raman of the oxidized, reduced and carbonyl forms.


:Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undecapeptides are consistent with a six-coordinate, low spin iron in both oxidation states. Porphyrin core size correlations yield a porphyrin-centre to pyrrole-nitrogen distance of 2.00 A for MP11, suggestive of a six-coordinate species in a distorted heme environment. Molecular dynamics results show that the non-planarity of the heme of the parent cytochrome is conserved in the microperoxidase and its carbonmonoxy analog.


J Biomol Struct Dyn


Laberge M,Vreugdenhil AJ,Vanderkooi JM,Butler IS




Has Abstract


1998-06-01 00:00:00












  • Protein-nucleic acid recognition: simulation of base and "model" amino acids complexes in DMSO by the Monte Carlo method.

    abstract::A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH+), acetic acid in neutral (AcOH) and deprotonated (AcO-) forms, G-AcO-, C-AcOH, and CH(+)-AcO- complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetic...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Danilov VI,Slyusarchuk ON,Poltev VI,Alderfer JL

    更新日期:1997-10-01 00:00:00

  • Raman and infrared studies of nucleosides at high pressures: I. Adenosine.

    abstract::Room temperature Raman and infrared (IR) spectra of crystalline adenosine at pressures between 1 atm and 10 GPa are reported. Vibrational modes were identified through assignments in the literature. Many modes were found to increase in frequency with pressure; however, some irregularities were observed. Discontinuitie...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Martin KC,Pinnick DA,Lee SA,Anderson A,Smith W,Griffey RH,Mohan V

    更新日期:1999-06-01 00:00:00

  • General acid-base catalysis in nucleobase amino proton exchange: cytidine.

    abstract::A useful property of DMSO solvent has been exploited to reveal a new catalytic route for cytidine amino proton exchange, relevant to exchange in the macromolecular state, but hidden in aqueous solution. Additional exchange mechanisms in aqueous monomeric cytidine (and adenosine) are obscured by the formation of a fast...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: McConnell B

    更新日期:1986-12-01 00:00:00

  • Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics.

    abstract::Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Abhinand PA,Shaikh F,Bhakat S,Radadiya A,Bhaskar LV,Shah A,Ragunath PK

    更新日期:2016-01-01 00:00:00

  • Novel aryl β-aminocarbonyl derivatives as inhibitors of Trypanosoma cruzi trypanothione reductase: binding mode revised by docking and GRIND2-based 3D-QSAR procedures.

    abstract::Trypanothione reductase has long been investigated as a promising target for chemotherapeutic intervention in Chagas disease, since it is an enzyme of a unique metabolic pathway that is exclusively present in the pathogen but not in the human host, which has the analog Glutathione reductase. In spite of the present da...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: de Paula da Silva CH,Bernardes LS,da Silva VB,Zani CL,Carvalho I

    更新日期:2012-01-01 00:00:00

  • DNA duplexes containing photoactive derivatives of 2'-deoxyuridine as photocrosslinking probes for EcoRII DNA methyltransferase-substrate interaction.

    abstract::EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive 5-iodo-2'-deoxyuridine (i(5)dU) or 5-[4-(3-(trifl...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Koudan EV,Subach OM,Korshunova GA,Romanova EA,Eritja R,Gromova ES

    更新日期:2002-12-01 00:00:00

  • Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions.

    abstract::An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are mor...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Sponer J,Leszczynski J,Vetterl V,Hobza P

    更新日期:1996-02-01 00:00:00

  • Prediction of potential inhibitors against SARS-CoV-2 endoribonuclease: RNA immunity sensing.

    abstract::The World Health Organization has classified the COVID-19 outbreak a pandemic which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and declared it a global health emergency. Repurposing drugs with minimum side effects are one approach to quickly respond in attempt to prevent the spread of CO...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Al-Rashedi NAM,Munahi MG,Ah ALObaidi L

    更新日期:2020-12-27 00:00:00

  • Characterization of polyion counterion interactions in cartilage by 23Na NMR relaxation.

    abstract::Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Dai H,McFarland EW

    更新日期:1996-04-01 00:00:00

  • Pharmacophore model and atom-based 3D quantitative structure activity relationship (QSAR) of human immunodeficiency virus-1 (HIV-1) capsid assembly inhibitors.

    abstract::A potential anti-Human Immunodeficiency Virus (HIV) agent with novel mode of action is urgently needed to fight against drug resistance HIV. The HIV capsid protein is important for both late and early stages of the viral replication cycle and emerged as a promising target for the developing of small molecule inhibitor...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Bhole RP,Bonde CG,Bonde SC,Chikhale RV,Wavhale RD

    更新日期:2021-02-01 00:00:00

  • Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities.

    abstract::Flavonoids correspond to a major class of polyphenolic phytochemicals with flavone as major parent scaffold. This class of compounds is attributed with very rich nutritional as well as therapeutic values. The present study focuses on a panel of 16 flavonoid molecules that are demonstrated to exhibit various bioactivit...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Meshram RJ,Bagul KT,Pawnikar SP,Barage SH,Kolte BS,Gacche RN

    更新日期:2020-03-01 00:00:00

  • Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation.

    abstract::A molecular dynamics simulation of the Sm binding site from human U4 snRNA was undertaken to determine the conformational flexibility of this region and to identify RNA conformations that were important for binding of the Sm proteins. The RNA was fully-solvated (>9,000 water molecules) and charge neutralized by inclus...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Guo J,Daizadeh I,Gmeiner WH

    更新日期:2000-12-01 00:00:00

  • Quantum-chemical analysis of C-H...O and C-H...N interactions in RNA base pairs--H-bond versus anti-H-bond pattern.

    abstract::Geometries and interaction energies of unusual UU and AA base pairs with one standard hydrogen bond (H-bond) and additional C-H...O or C-H...N contacts have been determined by quantum-chemical methods taking into account electron correlation. Whereas the C-H bond length in the UU C-H...O contact increases upon complex...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Brandl M,Meyer M,Sühnel J

    更新日期:2001-02-01 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


    authors: Sehailia M,Chemat S

    更新日期:2020-07-22 00:00:00

  • QSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives.

    abstract::Sirtuin 2 is a key enzyme in gene expression regulation that is often associated with tumor proliferation control and therefore is a relevant anticancer drug target. Anilinobenzamide derivatives have been discussed as selective sirtuin 2 inhibitors and can be developed further. In the present study, hologram and three...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Ferreira GM,Magalhães JG,Maltarollo VG,Kronenberger T,Ganesan A,Emery FDS,Trossini GHG

    更新日期:2020-02-01 00:00:00

  • DNA bending and sugar switching.

    abstract::Abstract Using high frequency antiphase NMR spectroscopy and computer simulations of the antiphase spectra, we studied the equlibria in the sugar conformations in the DNA duplex 11-mer containing the AAA tract surrounded by cytosines. We demonstrate that at the 3'-end of the A-tract, the sugar switches from the comm...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Kamath S,Sarma MH,Zhurkin VB,Turner CJ,Sarma RH

    更新日期:2000-01-01 00:00:00

  • 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 mechan...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Brovarets' OO,Hovorun DM

    更新日期:2015-01-01 00:00:00

  • Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

    abstract::The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of comple...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Shamsi A,Ahmed A,Bano B

    更新日期:2018-05-01 00:00:00

  • Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy.

    abstract::Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosid...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Mondragon-Sanchez JA,Liquier J,Shafer RH,Taillandier E

    更新日期:2004-12-01 00:00:00

  • Edaravone inhibits the conformational transition of amyloid-β42: insights from molecular dynamics simulations.

    abstract::Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with mole...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Liu F,Ma Z,Sang J,Lu F

    更新日期:2020-05-01 00:00:00

  • Monte-Carlo simulation of DNA duplex hydration. B and B' conformations of poly(dA).poly(dT) have different hydration shells.

    abstract::Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Poltev VI,Teplukhin AV,Chuprina VP

    更新日期:1988-12-01 00:00:00

  • Predictive models for designing potent tyrosine kinase inhibitors in chronic myeloid leukemia for understanding its molecular mechanism of resistance by molecular docking and dynamics simulations.

    abstract::BCR-ABL fusion protein drives chronic myeloid leukemia (CML) which constitutively activates tyrosine kinase involved in the initiation and maintenance of CML phenotype. Ponatinib, an oral drug, was discovered as an efficient BCR-ABL inhibitor by addressing imatinib drug resistance arising due to the point mutations at...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Melge AR,Kumar LG,K P,Nair SV,K M,C GM

    更新日期:2019-11-01 00:00:00

  • Interaction of purine nucleotides with inert paramagnetic Cr(III) probes evaluated by NMR relaxation effects. Molecular mechanics calculations on Cr(III) and Co(III) polyphosphate complexes.

    abstract::The 1H NMR relaxation effects produced by paramagnetic Cr(III) complexes on nucleoside 5'-mono- and -triphosphates in D2O solution at pH' = 3 were measured. The paramagnetic probes were [Cr(III)(H2O)6]3+, [Cr(III)(H2O)3(HATP)], [Cr(III)(H2O)3(HCTP)] and [Cr(III)(H2O)3(UTP)-, while the matrix nucleotides (0.1 M) were H...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Cini R,Giorgi G,Laschi F,Rossi C,Marzilli LG

    更新日期:1990-02-01 00:00:00

  • Selective DNA binding of (N-alkylamine)-substituted naphthalene imides and diimides to G+C-rich DNA.

    abstract::Alkylamine-substituted naphthalene imides and diimides bind DNA by intercalation and have applications as anticancer agents. The unique structures of these imides in which two adjacent carbonyl groups lie coplanar to an extended aromatic ring system allow the possibility of sequence-selective interactions between the ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Liu ZR,Hecker KH,Rill RL

    更新日期:1996-12-01 00:00:00

  • A general procedure for generation of curved DNA molecules.

    abstract::A general method for generation of base-pairs in a curved DNA structure, for any prescribed values of helical parameters--unit rise (h), unit twist (theta), wedge roll (theta R) and wedge tilt (theta T), propeller twist (theta p) and displacement (D) is described. Its application for generation of uniform as well curv...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Bhattacharya D,Bansal M

    更新日期:1988-08-01 00:00:00

  • Novel quinazolin-sulfonamid derivatives: synthesis, characterization, biological evaluation, and molecular docking studies.

    abstract::In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Sepehri N,Mohammadi-Khanaposhtani M,Asemanipoor N,Hosseini S,Biglar M,Larijani B,Mahdavi M,Hamedifar H,Taslimi P,Sadeghian N,Norizadehtazehkand M,Gulcin I

    更新日期:2020-11-23 00:00:00

  • Conformations of complexes derived from the interactions of two stereoisomeric bay-region 5-methylchrysene diol epoxides with DNA.

    abstract::The reaction mechanisms of two isomeric bay-region diol epoxides of 5-methylchrysene (trans-1,2-dihydroxy-anti-3,4-epoxy-1,2,3,4-tetrahydro-5-methylchrysene (DE-I) and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-5-methylchrysene (DE-II) with double-stranded DNA in aqueous solutions were studied utilizing k...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Kim MH,Roche CJ,Geacintov NE,Pope M,Pataki J,Harvey RG

    更新日期:1986-04-01 00:00:00

  • Homology models of the Yersinia pseudotuberculosis and Yersinia pestis general porins and comparative analysis of their functional and antigenic regions.

    abstract::The amino acid sequences of the Yersinia pseudotuberculosis porin (YPS) and Y. pestis porin (YPT) have recently deduced but their three-dimensional structures were not known. These sequences were analyzed using the servers 3D-PSSM and PredPort. The YPS and YPT porins were shown to have a high degree of identity (above...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Likhatskaya GN,Solov'eva TF,Novikova OD,Issaeva MP,Gusev KV,Kryzhko IB,Trifonov EV,Nurminski EA

    更新日期:2005-10-01 00:00:00

  • The size of the topological domain modulates the B-Z transition of a (TG)n containing repeat.

    abstract::Under negative superhelical stress, long (TG)n containing repeats experience a stepwise multiple B-Z transitions. We have investigated the effect of the plasmid size on this transitional behavior. A 66-bp (TG)n containing repeat from the 5'-untranscribed region of mouse ribosomal DNA was inserted in a 3-kb, a 6.5-kb a...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Albert AC,Leng M,Rahmouni AR

    更新日期:1995-08-01 00:00:00

  • Peculiarities of interaction of porphyrins with tRNA at low ionic strength.

    abstract::The interaction of meso-tetra-(4N-oxyethylpyridyl)porphyrin (TOEPyP4) and its Zn(II)-, Cu(II)-, Mn(III)-derivatives with tRNA from E.Coli at low ionic strength (micro=0.02M) was studied using UV/Vis spectrophotometry and Circular Dichroism (CD) methods. An unusual Induced Circular Dichroism (ICD) spectra profile of th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Dalyan Y,Vardanyan I,Chavushyan A,Balayan G

    更新日期:2010-08-01 00:00:00