CCAAT box revisited: bidirectionality, location and context.

abstract：:The 9-aminoacridine-DNA binding curve is analyzed in two ways: with polyelectrolyte effects neglected and with polyelectrolyte effects included. It is found that the analysis which includes polyelectrolyte effects is consistent with the violation of neighbor exclusion displayed by diacridine complexes as observed by A...

journal_title：Journal of biomolecular structure & dynamics

authors： Friedman RA,Shahin M,Zuckerbraun S

更新日期：1991-04-01 00:00:00

abstract：:Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease...

journal_title：Journal of biomolecular structure & dynamics

authors： Mandour YM,Zlotos DP,Alaraby Salem M

更新日期：2020-10-23 00:00:00

abstract：:Nanoporous iron oxide (Fe3O4) nanoparticles (NIONPs) have been widely used as promising agents in biomedical applications. Herein, the NIONPs were synthesized by one-step hydrothermal method and well-characterized by FESEM and TEM investigations. Afterwards, their interaction with human serum albumin (HSA) was studied...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehrabi M,Ghasemi MF,Rasti B,Falahati M,Mirzaie A,Hasan A

更新日期：2020-04-15 00:00:00

abstract：:The conformation of the colicin fragment of E. coli 16S rRNA was probed with various nucleases and with the adenosine-specific reagent diethylpyrocarbonate (DEP). The results confirm the presence of a stable central hairpin in the colicin fragment and a weaker additional secondary structure involving the regions 5' an...

journal_title：Journal of biomolecular structure & dynamics

authors： Heus HA,van Knippenberg PH

更新日期：1988-02-01 00:00:00

abstract：:An investigation of the self-association behavior of 2'-deoxy[5'-phosphate-guanylyl-(3'-5')-guanosine] (d(pGpG)) in the presence of Na+ and K+ ions has been carried out by 1H and 31P NMR and FTIR spectroscopy. A comparison has been made of the self- association behavior of d(pGpG) with that of the related dinucleotide...

journal_title：Journal of biomolecular structure & dynamics

authors： Kawasaki MM,Walmsley JA

更新日期：1999-12-01 00:00:00

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

authors： Lee SA,Lettress L,Anderson A

更新日期：2007-06-01 00:00:00

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

authors： Poltev VI,Teplukhin AV,Chuprina VP

更新日期：1988-12-01 00:00:00

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

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

更新日期：2000-01-01 00:00:00

abstract：:The object of the present study is the verification of a new approach to the design of the active truncated forms of enzymes. The method is based on a new way of investigating the protein sequences--the ANalysis of Informational Structure (ANIS). The analysis of informational structure allows to determine the hierarch...

journal_title：Journal of biomolecular structure & dynamics

authors： Nekrasov AN,Radchenko VV,Shuvaeva TM,Novoselov VI,Fesenko EE,Lipkin VM

更新日期：2007-04-01 00:00:00

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

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

更新日期：2017-08-01 00:00:00

abstract：:Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

journal_title：Journal of biomolecular structure & dynamics

authors： Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

更新日期：1994-02-01 00:00:00

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

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

更新日期：2019-04-01 00:00:00

abstract：:The effect of ligand interacting with native DNA by two types on the parameters of helix-coil transition in homopolymers is considered using the most probable distribution method (Yu.S. Lazurkin et al., Biopolymers 1970). It is shown that at a small relative concentration of ligand the melting enthalpy (delta H) of DN...

journal_title：Journal of biomolecular structure & dynamics

authors： Karapetian AT,Vardevanian PO,Tarzikian GA,Frank-Kamenetskii MD

更新日期：1990-08-01 00:00:00

abstract：:Visible and near infrared magnetic circular dichroism (MCD) spectra of heme proteins and enzymes as well as those of a protein-free heme bound to 2-methylimidazole were recorded and compared at 4.2 K in unrelaxed metastable and relaxed equilibrium heme stereochemistry. The relaxed and unrelaxed stereochemistries of a ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharonov YuA,Pismensky VF,Yarmola EG

更新日期：1989-08-01 00:00:00

abstract：:Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharmila DJ,Veluraja K

更新日期：2006-06-01 00:00:00

abstract：:Based on Fourier transform infrared (FTIR) microspectroscopy, the conformation of rhEGF under the influence of pH, heat treatment, chaotropic salts, concentration of salt and protein structure perturbants was studied. The FTIR spectrum of rhEGF showed that major secondary structures from amide I bands composed of 40.6...

journal_title：Journal of biomolecular structure & dynamics

authors： Yang CH,Wu PC,Huang YB,Tsai YH

更新日期：2004-08-01 00:00:00

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

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

更新日期：2019-04-01 00:00:00

abstract：:Propanidid is an intravenous anesthetic with transient action and rapid recovery features, but it is clinically unacceptable due to its side effects. AZD-3043, an analog of propanidid with the methoxy group substituted by the ethoxy group, has become the focus of recent development efforts. Although propanidid and AZD...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang S,Liu Q,Li X,Zhao X,Qiu L,Lin J

更新日期：2018-11-01 00:00:00

abstract：:The potassium channel Kv1.3 is an important pharmacological target and the Kaliotoxin-type toxins (α-KTX-3 family) are its specific blockers. Here, we study the binding process of two kinds of Kaliotoxin-type toxins:BmKTX and its mutant (BmKTX-D33H) toward to Kv1.3 channel using MD simulation and umbrella sampling sim...

journal_title：Journal of biomolecular structure & dynamics

authors： Zheng Q,Na R,Yang L,Yu H,Zhao X,Huang X

更新日期：2020-05-06 00:00:00

abstract：:Repetitive basic polypeptides containing lysine or arginine as every third amino acid were shown to cause DNA condensation at physiological salt concentration connected with selective DNA binding with respect to DNA composition and sequence. This selectivity is very similar to that existing in the case of histone H1 a...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponar J,Votavová H

更新日期：1996-06-01 00:00:00

abstract：:Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...

journal_title：Journal of biomolecular structure & dynamics

authors： Petrauskene OV,Yakovleva JN,Alekseev YI,Subach FV,Babkina OV,Gromova ES

更新日期：2000-04-01 00:00:00

abstract：:Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conform...

journal_title：Journal of biomolecular structure & dynamics

authors： Malkhasian AY,Howlin BJ

更新日期：2016-11-01 00:00:00

abstract：:The sharp spurt in positive cases of novel coronavirus-19 (SARS-CoV-2) worldwide has created a big threat to human. In view to expedite new drug leads for COVID-19, Main Proteases (Mpro) of novel Coronavirus (SARS-CoV-2) has emerged as a crucial target for this virus. Nitric oxide (NO) inhibits the replication cycle o...

journal_title：Journal of biomolecular structure & dynamics

authors： Al-Sehemi AG,Pannipara M,Parulekar RS,Patil O,Choudhari PB,Bhatia MS,Zubaidha PK,Tamboli Y

更新日期：2020-07-08 00:00:00

abstract：:Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergenc...

journal_title：Journal of biomolecular structure & dynamics

authors： Costa Júnior DB,Araújo JSC,de Mattos Oliveira L,Neri FSM,Moreira POL,Taranto AG,Fonseca AL,de Pilla Varotti F,Leite FHA

更新日期：2020-05-13 00:00:00

abstract：:A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on...

journal_title：Journal of biomolecular structure & dynamics

authors： Grigoriev IV,Rakhmaninova AB,Mironov AA

更新日期：1998-08-01 00:00:00

abstract：:Seven new quinoline-based bioorganic compounds were prepared by solvent-free synthesis and characterized using spectral techniques. The binding of these compounds with human serum albumin (HSA) was investigated by multi-spectroscopic methods. The quenching of Trp fluorescence upon addition of these compounds to HSA co...

journal_title：Journal of biomolecular structure & dynamics

authors： Vennila KN,Elango KP

更新日期：2019-07-01 00:00:00

abstract：:We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Benedetti G,Morosetti S

更新日期：1991-04-01 00:00:00

abstract：:Galantamine (Gnt) is a natural alkaloid inhibitor of acetylcholinesterase and is presently one of the most used drugs in the treatment against Alzheimer's disease during both the initial and intermediate stages. Among several natural Gnt derivatives, sanguinine (Sng) and lycoramine (Lyc) attract attention because of t...

journal_title：Journal of biomolecular structure & dynamics

authors： Rocha REO,Lima LHF

更新日期：2019-04-01 00:00:00

abstract：:We have applied random-search, energy minimization and molecular dynamics simulations to investigate the structural aspects of the interaction of N-acetyl-L-prolyl-D-alanyl-L-alanine-N'-methylamide with Ca2+. Spectral data on related peptides had suggested that the beta-turn conformation might be a prerequisite for th...

journal_title：Journal of biomolecular structure & dynamics

authors： Michel AG,Jeandenans C,Ananthanarayanan VS

更新日期：1992-10-01 00:00:00

abstract：:Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...

journal_title：Journal of biomolecular structure & dynamics

authors： Borkar A,Rout MK,Hosur RV

更新日期：2012-01-01 00:00:00