An ultraviolet melting study of the stability of the DNA double helix in the NaDNA-bipyridyl-(ethylenediamine)platintum(II) complex.

abstract：:Quasi-palindromic sequences (AT) X N12(AT) Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults ...

journal_title：Journal of biomolecular structure & dynamics

authors： Roy K,Mahendru S,Kukreti R,Kukreti S

更新日期：2019-09-01 00:00:00

abstract：:Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...

journal_title：Journal of biomolecular structure & dynamics

authors： Malkhed V,Mustyala KK,Potlapally SR,Vuruputuri U

更新日期：2014-12-01 00:00:00

abstract：:The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomi...

journal_title：Journal of biomolecular structure & dynamics

authors： Chechetkin VR,Lobzin VV

更新日期：2019-06-01 00:00:00

abstract：:All major suggestions about the nucleosome positioning sequence pattern(s) are overviewed. Two basic binary periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR and in strong/weak alphabet -SWWWWWSSSSSW. Their merger in four-letter alphabet sequence coincides with first ever complete ...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2010-06-01 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：: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

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

更新日期：2018-06-01 00:00:00

abstract：:Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries...

journal_title：Journal of biomolecular structure & dynamics

authors： Forde G,Flood A,Salter L,Hill G,Gorb L,Leszczynski J

更新日期：2003-06-01 00:00:00

abstract：:Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded c...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra M,Singh V,Tellis MB,Joshi RS,Pandey KC,Singh S

更新日期：2020-12-09 00:00:00

abstract：:In this work, an attempt has been made to study the interaction of four taiwaniaquinoids with fat mass and obesity-associated protein (FTO) by UV-vis absorption, fluorescence spectroscopy, and molecular docking techniques. The results indicated that taiwaniaquinoids effectively quenched the intrinsic fluorescence of F...

journal_title：Journal of biomolecular structure & dynamics

authors： Ren T,Zhang L,Wang J,Song C,Wang R,Chang J

更新日期：2017-11-01 00:00:00

abstract：:Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary di...

journal_title：Journal of biomolecular structure & dynamics

authors： Pandey B,Aarthy M,Sharma M,Singh SK,Kumar V

更新日期：2020-06-30 00:00:00

abstract：:P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

journal_title：Journal of biomolecular structure & dynamics

authors： Yellapu NK,Pulaganti M,Pakala SB

更新日期：2017-08-01 00:00:00

abstract：:Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and d...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets OO,Hovorun DM

更新日期：2014-01-01 00:00:00

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

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

abstract：:We report here two new small-size peptides acting as modulators of the β-site APP cleaving enzyme 1 (BACE1) exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderate but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initi...

journal_title：Journal of biomolecular structure & dynamics

authors： Gutierrez LJ,Angelina E,Gyebrovszki A,Fülöp L,Peruchena N,Baldoni HA,Penke B,Enriz RD

更新日期：2017-02-01 00:00:00

abstract：:RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge ab...

journal_title：Journal of biomolecular structure & dynamics

authors： Fritsch V,Wolf RM

更新日期：1994-06-01 00:00:00

abstract：:The aim of the present study focuses on the molecular docking approach to screen alternative drug that can regulate the hyperglycemia by down-regulating α-glucosidase and α-amylase activity using phenolic compounds: tannic acid (L1), catechin (L2), gallic acid (L3), quercetin (L5) and epicatechin (L6). L1 gives the be...

journal_title：Journal of biomolecular structure & dynamics

authors： Abdelli I,Benariba N,Adjdir S,Fekhikher Z,Daoud I,Terki M,Benramdane H,Ghalem S

更新日期：2020-02-10 00:00:00

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

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

abstract：:To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guano...

journal_title：Journal of biomolecular structure & dynamics

authors： Markova N,Pejov L,Stoyanova N,Enchev V

更新日期：2017-05-01 00:00:00

abstract：:Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three differ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sutthibutpong T,Rattanarojpong T,Khunrae P

更新日期：2018-11-01 00:00:00

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

authors： Chojnacki H,Laskowski Z

更新日期：1985-02-01 00:00:00

abstract：:The interaction of calf-thymus DNA with cobalt-hexammine and cobalt-pentammine cations was investigated, in aqueous solution at pH 6-7 with cation/DNA(phosphate) molar ratios r = 1/80, 1/40, 1/20, 1/10, 1/4, 1/2 and 1, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between spectral chang...

journal_title：Journal of biomolecular structure & dynamics

authors： Tajmir-Riahi HA,Naoui M,Ahmad R

更新日期：1993-08-01 00:00:00

abstract：:Melanoma is a malignant cancer of the skin associated with a high mortality. Early medical diagnosis and surgical intervention are essential for the treatment of melanoma. The use of plant-based compounds is an important strategy for the prevention and treatment of different types of cancers. Curcumin is a promising n...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghazaeian M,Khorsandi K,Hosseinzadeh R,Naderi A,Abrahamse H

更新日期：2020-08-07 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：: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

authors： Seiffert J,Huhle A

更新日期：2008-04-01 00:00:00

abstract：:Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation...

journal_title：Journal of biomolecular structure & dynamics

authors： Sun DR,Zheng QC,Zhang HX

更新日期：2017-03-01 00:00:00

abstract：:Earlier identified strongest nucleosome DNA sequences of A. thaliana, those with visible 10-11 base sequence periodicity, are mapped along chromosomes. Resulting positional distributions reveal distinct maxima, one per chromosome, located in the centromere regions. Sequence-directed nucleosome mapping demonstrates tha...

journal_title：Journal of biomolecular structure & dynamics

authors： Salih B,Trifonov EN

更新日期：2015-01-01 00:00:00

abstract：:Myo-inositol is one of the vital nutritional requirements for the Leishmania parasites' survival and virulence in the mammalian host. . Myo-inositol-1-phosphate synthase (MIPS) is responsible for the synthesis of myo-inositol in Leishmania, which plays a vital role in Leishmania's virulence to mammalian hosts. Earlier...

journal_title：Journal of biomolecular structure & dynamics

authors： Sinha M,Jagadeesan R,Kumar N,Saha S,Kothandan G,Kumar D

更新日期：2020-11-17 00:00:00

abstract：:The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant...

journal_title：Journal of biomolecular structure & dynamics

authors： Sérgio Alves Bueno P,Carina Biavatti D,Sandro Gularte Chiarello A,Aureliana Fassina V,Aparecida Fernandez M,Augusto Vicente Seixas F

更新日期：2019-09-01 00:00:00

abstract：:EhCPADH is a protein complex involved in the virulence of Entamoeba histolytica, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecul...

journal_title：Journal of biomolecular structure & dynamics

authors： Montaño S,Orozco E,Correa-Basurto J,Bello M,Chávez-Munguía B,Betanzos A

更新日期：2017-02-01 00:00:00

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

authors： Doruker P,Nilsson L,Kurkcuoglu O

更新日期：2006-08-01 00:00:00