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












  • Molecular structure of peptaibol antibiotics: solution conformation and crystal structure of the octapeptide corresponding to the 2-9 sequence of emerimicins III and IV.

    abstract::The infrared absorption and 1H nuclear magnetic resonance analyses of chloroform solutions of the terminally-blocked segment corresponding to the 2-9 sequence of emerimicins III and IV, -(Aib)3-L-Val-Gly-L-Leu-(Aib)2-, are consistent with the presence of a 3(10)-helical structure of high thermal stability. The crystal...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Toniolo C,Bonora GM,Bavoso A,Benedetti E,di Blasio B,Pavone V,Pedone C

    更新日期:1985-12-01 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


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

    更新日期:2017-08-01 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


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

    更新日期:1987-08-01 00:00:00

  • Proton NMR and optical spectroscopic studies on the DNA triplex formed by d-A-(G-A)7-G and d-C-(T-C)7-T.

    abstract::Triplex and duplex formation of two deoxyribohexadecamers d-A-(G-A)-G (a) and d-C-(T-C)-T (b) have been studied by UV, CD, fluorescence, and proton NMR spectroscopy. Optical studies of a and b at dilute concentrations (microM range) yielded results similar to those seen for polymers of the same sequence, indicating th...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Kan LS,Callahan DE,Trapane TL,Miller PS,Ts'o PO,Huang DH

    更新日期:1991-04-01 00:00:00

  • Modeling the correlation functions of conformational motions in proteins.

    abstract::A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational po...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Sitnitsky AE

    更新日期:2000-02-01 00:00:00

  • Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus.

    abstract::The nucleoprotein (NP) binds the viral RNA genome as oligomers assembled with the polymerase in a ribonucleoprotein complex required for transcription and replication of influenza A virus. Novel antiviral candidates targeting the nucleoprotein either induced higher order oligomers or reduced NP oligomerization by targ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Tarus B,Bertrand H,Zedda G,Di Primo C,Quideau S,Slama-Schwok A

    更新日期:2015-09-01 00:00:00

  • Electrostatics of Polymorphic DNA.

    abstract::The molecular electrostatic potential (MEP) and the molecular electrostatic field (MEF) are associated with significantly different patterns of distribution in the nucleic acids and their constituents. In particular, a) while the values of the minimal potentials at the reactive sites of the bases or at the phosphates ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Pullman B

    更新日期:1983-12-01 00:00:00

  • A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives: Monte Carlo simulation.

    abstract::An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy prefe...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


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

    更新日期:1999-04-01 00:00:00

  • Syringaresinol as a novel androgen receptor antagonist against wild and mutant androgen receptors for the treatment of castration-resistant prostate cancer: molecular docking, in-vitro and molecular dynamics study.

    abstract::Phytoestrogens are dietary estrogens having similar structure as of estrogen. Some of these phytoestrogens are androgen receptor (AR) antagonists and exhibit preventive role in the prostate cancer. However, in androgen-independent prostate cancer (AIPC) the ARs were mutated (T877A, W741L, F876L, etc.) and these mutant...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Selvaraj D,Muthu S,Kotha S,Siddamsetty RS,Andavar S,Jayaraman S

    更新日期:2021-02-01 00:00:00

  • A note on crystal packing and global helix structure in short A-DNA duplexes.

    abstract::A simple relation exists between the packing density in crystals of short A-DNA duplexes and their global double-helical structure. The volume per nucleotide pair shows a linear inverse correlation with the mean displacement of base pairs from the best straight helix axis. The mean displacement is a measure of major g...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Heinemann U

    更新日期:1991-02-01 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

  • Theoretical design of a bis-orthopepetide derivative of a tetracationic porphyrin targeted toward a six-base pair sequence of DNA.

    abstract::Tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), is a tetracationic porphyrin that binds to G-C sequences of DNA by means of an intercalative mode. In order to extend its selective sequence recognition capacity for bases beyond the intercalation site, and in the major groove, we have undertaken the theoretical design of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Hui X,Gresh N

    更新日期:1993-10-01 00:00:00

  • SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method.

    abstract::Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residue...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Zhang T,Faraggi E,Xue B,Dunker AK,Uversky VN,Zhou Y

    更新日期:2012-01-01 00:00:00

  • Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing study.

    abstract::The recent COVID-19 pandemic caused by SARS-CoV-2 has recorded a high number of infected people across the globe. The virulent nature of the virus makes it necessary for us to identify promising therapeutic agents in a time-sensitive manner. The current study utilises an in silico based drug repurposing approach to id...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Khan RJ,Jha RK,Singh E,Jain M,Amera GM,Singh RP,Muthukumaran J,Singh AK

    更新日期:2020-09-04 00:00:00

  • An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α.

    abstract::Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

    更新日期:2020-11-02 00:00:00

  • Amino acid/water interactions study: a new amino acid scale.

    abstract::Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrost...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Madeira PP,Bessa A,Álvares-Ribeiro L,Raquel Aires-Barros M,Rodrigues AE,Uversky VN,Zaslavsky BY

    更新日期:2014-01-01 00:00:00

  • Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification.

    abstract::Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Sadhasivam A,Vetrivel U

    更新日期:2018-06-01 00:00:00

  • Structure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors.

    abstract::Mycobacterium tuberculosis remains one of the most successful bacterial pathogens worldwide. The development of drug-resistant strains and the ability of the bacteria to persist in a latent form in the host are major problems for tuberculosis (TB) control. Glyoxylate shunt is a metabolic bypass of the Krebs cycle and ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Shukla R,Shukla H,Tripathi T

    更新日期:2020-04-30 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


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

    更新日期:2001-08-01 00:00:00

  • Computational evidence to inhibition of human acetyl cholinesterase by withanolide a for Alzheimer treatment.

    abstract::Alzheimer's disease (AD), a neurodegenerative disorder, is the most common cause of dementia. So far only five drugs have been approved by US FDA that temporarily slow worsening of symptoms for about six to twelve months. The limited number of therapeutic options for AD drives the exploration of new drugs. Enhancement...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Grover A,Shandilya A,Agrawal V,Bisaria VS,Sundar D

    更新日期:2012-01-01 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


    authors: Awasthi S,Saraswathi NT

    更新日期:2016-10-01 00:00:00

  • Theoretical Design, Chemical Synthesis and Footprinting Analysis of a Novel Peptide Derivative of the Intercalator 7-H Pyridocarbazole Targeted Towards the Major Groove of DNA.

    abstract::Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

    更新日期:1994-08-01 00:00:00

  • Enantioselective light switch effect of Δ- and Λ-[Ru(phenanthroline)2 dipyrido[3,2-a:2', 3'-c]phenazine]2+ bound to G-quadruplex DNA.

    abstract::The interaction of Δ- and Λ-[Ru(phen)2DPPZ]2+ (DPPZ = dipyrido[3,2-a:2', 3'-c]phenazine, phen = phenanthroline) with a G-quadruplex formed from 5'-G2T2G2TGTG2T2G2-3'(15-mer) was investigated. The well-known enhancement of luminescence intensity (the 'light-switch' effect) was observed for the [Ru(phen)2DPPZ]2+ complex...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Park JH,Lee HS,Jang MD,Han SW,Kim SK,Lee YA

    更新日期:2018-06-01 00:00:00

  • Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis.

    abstract::Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simu...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Martínez-Archundia M,Correa-Basurto J,Montaño S,Rosas-Trigueros JL

    更新日期:2019-11-01 00:00:00

  • Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations.

    abstract::Anisotropic network model (ANM) is used to analyze the collective motions of restriction enzyme EcoRI in free form and in complex with DNA. For comparison, three independent molecular dynamics (MD) simulations, each of 1.5 ns duration, are also performed for the EcoRI-DNA complex in explicit water. Although high mobil...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Doruker P,Nilsson L,Kurkcuoglu O

    更新日期:2006-08-01 00:00:00

  • Effects of pH and temperature on the structural and thermodynamic character of alpha-syn12 peptide in aqueous solution.

    abstract::The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Cao Z,Liu L,Wang J

    更新日期:2010-12-01 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


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

    更新日期:2021-01-01 00:00:00

  • Deciphering the interaction of puerarin with cancer macromolecules: An in silico investigation.

    abstract::The worldwide expanding increment in cancer pervasiveness is disturbing and this disease ranks among the main causes of mortality in both developing and developed countries. Unfortunately, available treatment options come with serious side effects and do not guarantee complete success. Although numerous models have be...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Ojo OA,Aruleba RT,Adekiya TA,Sibuyi NRS,Ojo AB,Ajiboye BO,Oyinloye BE,Adeola HA,Fadaka AO

    更新日期:2020-09-14 00:00:00

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

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    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


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

    更新日期:2020-04-01 00:00:00

  • Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

    abstract::Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章


    authors: Jamshidi S,Jalili S,Rafii-Tabar H

    更新日期:2015-01-01 00:00:00