2-aminopurine fluorescence: discrimination between specific and unspecific ligand binding to the kissing-loop dimer of the HIV-1 RNA.

abstract：:The location, orientation and dynamics of a thiazole-containing analogue of distamycin 1 bound to the decadeoxyribonucleotide d-[CGCAATTGCG]2 have been studied by non-exchangable and imino proton NMR resonances of the 1:1 complex. Using NOE difference, COSY and NOESY experiments, lexitropsin (1) was located in the min...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar S,Bathini Y,Joseph T,Pon RT,Lown JW

更新日期：1991-08-01 00:00:00

abstract：:The rice blast disease caused by the fungus Magnaporthe grisea is one of the most devastating rice diseases, but there is no effective fungicide toward chitinase which is a key enzyme of M. grisea. In this study, we observed that distortion and cell-wall damage of M. grisea hyphae were significantly under the scanning...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu X,Li W,Hu B,Wang M,Wang J,Guan L

更新日期：2019-08-01 00:00:00

abstract：:The interaction between two proton pump inhibitors viz., omeprazole (OME) and esomeprazole (EPZ) with human serum albumin (HSA) was studied by fluorescence, absorption, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), voltammetry, and molecular modeling approaches. The Stern-Volmer quenching c...

journal_title：Journal of biomolecular structure & dynamics

authors： Pawar SK,Punith R,Naik RS,Seetharamappa J

更新日期：2017-11-01 00:00:00

abstract：:Acinetobacter baumannii, an important nosocomial pathogen, is increasingly becoming resistant to antibiotics including recent β-lactam like imipenem. Production of different types of β-lactamases is one of the major resistance mechanisms which bacteria adapt. We recently reported the presence of a β-lactamase, OXA-51,...

journal_title：Journal of biomolecular structure & dynamics

authors： Tiwari V,Moganty RR

更新日期：2014-01-01 00:00:00

abstract：:Triple-negative breast cancers (TNBCs) are one of the most aggressive and complex forms of cancers in women. TNBCs are commonly known for their complex heterogeneity and poor prognosis. The present work aimed to develop a predictive 2D and 3D quantitative structure-activity relationship (QSAR) models against metastati...

journal_title：Journal of biomolecular structure & dynamics

authors： Shukla A,Tyagi R,Meena S,Datta D,Srivastava SK,Khan F

更新日期：2020-01-01 00:00:00

abstract：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Anish Babu A,Karthick K,Subramanian R,Swarnalatha K

更新日期：2020-08-01 00:00:00

abstract：:We attempt to give an alternate point of view of the analysis by Roterman et al. (J. Biolmol. Struct. Dyn. 7,415 (1989]. In particular, we argue for the use of flexible geometry and explicit inclusion of solvent effects in analyzing phi, psi maps of peptides. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kollman PA,Dill KA

更新日期：1991-06-01 00:00:00

abstract：:The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation...

journal_title：Journal of biomolecular structure & dynamics

authors： Pastor N,MacKerell AD Jr,Weinstein H

更新日期：1999-02-01 00:00:00

abstract：:Human β-defensin-3 (HβD-3) is an endogenous antimicrobial peptide with potent and broad killing activity against various microorganisms, and thus, it is an attractive candidate for the development of novel peptide antibiotics, but its antimicrobial mechanism remains elusive. To characterize the mechanism, we used mult...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao X,Yu H,Yang L,Li Q,Huang X

更新日期：2015-01-01 00:00:00

abstract：:Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-gly...

journal_title：Journal of biomolecular structure & dynamics

authors： Mamidi AS,Surolia A

更新日期：2015-01-01 00:00:00

abstract：:NPC1 is a 25-exon gene located on the long arm of chromosome 18q11.2 and encodes NPC1, a transmembrane protein comprising 1278 amino acid residues. Mutations in the NPC1 gene can cause Niemann-Pick disease type C (NP-C), a rare autosomal-recessive neurovisceral disease. We assessed mutant protein folding using compute...

journal_title：Journal of biomolecular structure & dynamics

authors： Martínez-Archundia M,Hernández Mojica TG,Correa-Basurto J,Montaño S,Camacho-Molina A

更新日期：2020-08-01 00:00:00

abstract：:The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subs...

journal_title：Journal of biomolecular structure & dynamics

authors： de Groot BL,Amadei A,van Aalten DM,Berendsen HJ

更新日期：1996-04-01 00:00:00

abstract：:We performed a neuraminidase sequence analysis of thirty-two pediatric patients with influenza B who visited Teikyo University Hospital from January 2016 to March 2017, and found oseltamivir-resistant samples belonging to the Yamagata and Victoria lineages. Comparison with the neuraminidase sequence of oseltamivir-sus...

journal_title：Journal of biomolecular structure & dynamics

authors： Kato Y,Takahashi K,Ito F,Suzuki S,Fukui K,Mimaki M,Suzuki K

更新日期：2020-05-25 00:00:00

abstract：:The so-called CCAAT box is believed to be a major promoter element of higher eukaryotes though it is ill-defined being deduced from very limited sequence data. The comprehensive computer analysis of an unbiased set of 168 promoters presented here removes several of the persisting uncertainties. In particular, it delin...

journal_title：Journal of biomolecular structure & dynamics

authors： Bucher P,Trifonov EN

更新日期：1988-06-01 00:00:00

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

authors： Guo J,Daizadeh I,Gmeiner WH

更新日期：2000-12-01 00:00:00

abstract：:The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (H...

journal_title：Journal of biomolecular structure & dynamics

authors： Bischoff G,Bischoff R,Birch-Hirschfeld E,Gromann U,Lindau S,Meister WV,de A Bambirra S,Bohley C,Hoffmann S

更新日期：1998-10-01 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 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

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

更新日期：1986-04-01 00:00:00

abstract：:In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, s...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu HL,Wu YC,Zhao JH,Fang HW,Ho Y

更新日期：2006-12-01 00:00:00

abstract：:The polymorphism exhibited by the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G), as a function of the temperature, DNA concentration and ionic strength, was investigated by means of NMR spectroscopy. It is shown that this partly self-complementary DNA fragment, under conditions of low DNA concentration (0.4 mM) and low ...

journal_title：Journal of biomolecular structure & dynamics

authors： Orbons LP,van der Marel GA,van Boom JH,Altona C

更新日期：1987-06-01 00:00:00

abstract：:Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from trad...

journal_title：Journal of biomolecular structure & dynamics

authors： Sun MF,Chang TT,Chang KW,Huang HJ,Chen HY,Tsai FJ,Lin JG,Chen CY

更新日期：2011-06-01 00:00:00

abstract：:Non-obstructive azoospermia (NOA) is the most clinical problem in case of infertility. About 70% of NOA patients are idiopathic with uncharacterized molecular mechanisms. This study aimed to analyze the possible pathogenic miRNA-target gene interaction and lncRNA-miRNA association involved in NOA. In the current study...

journal_title：Journal of biomolecular structure & dynamics

authors： Sabetian S,Zarei M,Jahromi BN,Morowvat MH,Tabei SMB,Cava C

更新日期：2021-01-26 00:00:00

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...

journal_title：Journal of biomolecular structure & dynamics

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

更新日期：2018-05-01 00:00:00

abstract：:P21-activated kinase 4 (PAK4) is a serine/threonine protein kinase, which is associated with many cancer diseases, and thus being considered as a potential drug target. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations wer...

journal_title：Journal of biomolecular structure & dynamics

authors： Gao Y,Wang H,Wang J,Cheng M

更新日期：2020-09-01 00:00:00

abstract：:A novel ternary copper(II) complexes, - [Cu(py-phen)(asn)(NO3)(H2O)] (1) and [Cu(py-phen)(trp)(H2O)]NO3 (2)- (py-phen: pyrazino[2,3-f][1,10]phenanthroline, asn: asparagine, trp: tryptophan), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interacti...

journal_title：Journal of biomolecular structure & dynamics

authors： İnci D,Aydın R,Vatan Ö,Zorlu Y

更新日期：2020-08-18 00:00:00

abstract：:Polar mutations in transmembrane alpha helices may alter the structural details of the hydrophobic sequences and control intermolecular contacts. We have performed molecular dynamics simulations on the transmembrane domain of the proto-oncogenic and the oncogenic forms of the Neu receptor in a fluid DMPC bilayer to te...

journal_title：Journal of biomolecular structure & dynamics

authors： Samna Soumana O,Aller P,Garnier N,Genest M

更新日期：2005-08-01 00:00:00

abstract：:P-glycoprotein (P-gp) is a main factor contributing to multidrug resistance. The effect of this transporter protein on limiting the effectiveness of chemotherapy has been shown by various studies. In a previous report, we synthesized some 14-dihydropyridine (DHP) derivatives as inhibitors of human P-gp. In the present...

journal_title：Journal of biomolecular structure & dynamics

authors： Shahraki O,Zargari F,Edraki N,Khoshneviszadeh M,Firuzi O,Miri R

更新日期：2018-01-01 00:00:00

abstract：:Sickle cell disease is caused by the amino acid substitution of glutamic acid to valine, which leads to the polymerization of deoxygenated sickle hemoglobin (HbS) into long strands. These strands are responsible for the sickling of red blood cells (RBCs), making blood hyper-coagulable leading to an increased chance of...

journal_title：Journal of biomolecular structure & dynamics

authors： Yesudasan S,Douglas SA,Platt MO,Wang X,Averett RD

更新日期：2019-03-01 00:00:00

abstract：:Bruton's tyrosine kinase (Btk) is an important enzyme in B-lymphocyte development and differentiation. Furthermore, Btk expression is considered essential for the proliferation and survival of these cells. Btk inhibition has become an attractive strategy for treating autoimmune diseases, B-cell leukemia, and lymphomas...

journal_title：Journal of biomolecular structure & dynamics

authors： Santos-Garcia L,Assis LC,Silva DR,Ramalho TC,da Cunha EF

更新日期：2016-07-01 00:00:00

abstract：:Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

journal_title：Journal of biomolecular structure & dynamics

authors： Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

更新日期：2009-12-01 00:00:00