Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

abstract：:Molecular modeling and molecular dynamics were performed to investigate the interaction of norfloxacin with the DNA oligonucleotide 5'-d(ATACGTAT)(2). Eight quinolone-DNA binding structures were built by molecular modeling on the basis of experimental results. A 100ps molecular dynamics calculation was carried out on ...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee HM,Kim JK,Kim SK

更新日期：2002-06-01 00:00:00

abstract：:A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy min...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Bhattacharyya D

更新日期：2013-01-01 00:00:00

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

authors： Cao Z,Liu L,Wang J

更新日期：2010-12-01 00:00:00

abstract：:Over 100 variants have been designed and studied, using multiple docking methods such as Autodock Vina, ArgusLab, Molegro Virtual Docker, and Hex-Cuda, to study the effect of alteration in the structure of carbamate-based acetylcholyne esterase (AChE) inhibitors. Sixteen selected systems were then subjected to 14 ns m...

journal_title：Journal of biomolecular structure & dynamics

authors： Mohammadi T,Ghayeb Y

更新日期：2018-01-01 00:00:00

abstract：:Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. o...

journal_title：Journal of biomolecular structure & dynamics

authors： Lei Y,Kang SK,Gao J,Jia XS,Chen LL

更新日期：2013-03-01 00:00:00

abstract：:The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Bashford D,Weaver DL,Karplus M

更新日期：1984-03-01 00:00:00

abstract：:Chlamydia trachomatis (C.t) is a major causative of infectious blindness in world. It is a real challenge to combat Chlamydial infection as it is an intracellular pathogen. Hence, it is essential to determine the most potential targets of C.t in order to inhibit or suppress its virulence during its infectious phase. T...

journal_title：Journal of biomolecular structure & dynamics

authors： Sadhasivam A,Nagarajan H,Umashankar V

更新日期：2020-07-01 00:00:00

abstract：:MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-ter...

journal_title：Journal of biomolecular structure & dynamics

authors： Naz F,Singh P,Islam A,Ahmad F,Imtaiyaz Hassan M

更新日期：2016-06-01 00:00:00

abstract：:Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by in silico experiments. Switches from t...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolomiets IN,Zarudnaya MI,Potyahaylo AL,Hovorun DM

更新日期：2015-01-01 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：:Our earlier study on the nucleosomes containing TBP binding sites (TATA boxes) indicated that generally the same sequence, which harbors the TATA box, encodes simultaneously an alternative rotational setting of the box, so that the TATA element is either exposed (position "minor groove out") or hidden in position "min...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2016-12-01 00:00:00

abstract：:Biomembranes and lipid systems are rich in unsaturated lipid components and are subject to photo-induced lipid peroxidation. The peroxidized lipid products in cellular systems are known to affect the structural organization and function of the biomembrane. We employed molecular dynamics simulations to study the effect...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar S,Rana R,Yadav DK

更新日期：2020-03-05 00:00:00

abstract：:The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting p...

journal_title：Journal of biomolecular structure & dynamics

authors： Stellwagen NC,Stellwagen D

更新日期：1990-12-01 00:00:00

abstract：:Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and...

journal_title：Journal of biomolecular structure & dynamics

authors： Tanneeru K,Balla AR,Guruprasad L

更新日期：2015-01-01 00:00:00

abstract：:Pebrine is a microsporidian disease caused by Nosema bombycis in Bombyx mori (silk worm) which results in brown/black spots. The affected larvae either spin cocoons which are flimsy with low silk content or not spin a cocoon. It has been hypothesised that Serine Protease Inhibitor 106 (SPN106) is responsible for evasi...

journal_title：Journal of biomolecular structure & dynamics

authors： U M S,Karunakar P,Krishnamurthy V

更新日期：2020-10-01 00:00:00

abstract：:Alzheimer's disease (AD) is the most common progressive neurodegenerative brain disorder. It is characterized by the presence of extracellular aggregated fibrillary form of amyloid beta (Aβ) peptide and intraneuronal neurofibrillary tangles caused by the hyperphosphorylation of tau protein. Monomeric form of Aβ peptid...

journal_title：Journal of biomolecular structure & dynamics

authors： Dutta N,Borah P,Mattaparthi VSK

更新日期：2020-03-02 00:00:00

abstract：:The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24...

journal_title：Journal of biomolecular structure & dynamics

authors： Andrianov AM

更新日期：1999-02-01 00:00:00

abstract：:The development of SrtA inhibitors targeting the biothreat organism namely Bacillus anthracis was achieved by the combined approach of pharmacophore modeling, binding interactions, electron transferring capacity, ADME, and Molecular dynamics studies. In this study, experimentally reported Ba-SrtA inhibitors (pyridazin...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvaraj C,Singh SK

更新日期：2014-01-01 00:00:00

abstract：:Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

journal_title：Journal of biomolecular structure & dynamics

authors： Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

更新日期：2020-07-31 00:00:00

abstract：:The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentati...

journal_title：Journal of biomolecular structure & dynamics

authors： Frenkel ZM,Trifonov EN

更新日期：2005-06-01 00:00:00

abstract：:Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen L,Yang J,Huang T,Kong X,Lu L,Cai YD

更新日期：2016-01-01 00:00:00

abstract：:This work aims at characterizing structural transitions within the intrinsically disordered C-terminal domain of the nucleoprotein (NTAIL) from the Nipah and Hendra viruses, two recently emerged pathogens gathered within the Henipavirus genus. To this end, we used site-directed spin labeling combined with electron par...

journal_title：Journal of biomolecular structure & dynamics

authors： Martinho M,Habchi J,El Habre Z,Nesme L,Guigliarelli B,Belle V,Longhi S

更新日期：2013-01-01 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：:Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran-PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of...

journal_title：Journal of biomolecular structure & dynamics

authors： Ferreira LA,Povarova OI,Stepanenko OV,Sulatskaya AI,Madeira PP,Kuznetsova IM,Turoverov KK,Uversky VN,Zaslavsky BY

更新日期：2017-01-01 00:00:00

abstract：:Virtually all mRNA sequences carry a 3-base periodical pattern, presumably involved in the translation frame monitoring mechanism (Trifonov, E.N., J. Mol. Biol. 194, 643-652, 87). The hidden pattern, 5'-(GHN)n-3' (H representing nonG, N any base), is further refined by extensive computational analysis of mRNA sequence...

journal_title：Journal of biomolecular structure & dynamics

authors： Lagunez-Otero J,Trifonov EN

更新日期：1992-12-01 00:00:00

abstract：:Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs co...

journal_title：Journal of biomolecular structure & dynamics

authors： Mani A,Gupta DK

更新日期：2015-01-01 00:00:00

abstract：:In the present work fluctuations of number of ligands adsorbed on macromolecule are investigated. We have taken into account the adsorption and desorption of ligands under the circumstance of some adsorption centers fluctuations affected by medium fluctuation. The correlation function and spectral density of number of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arakelyan VB,Haroutiunian SG,Arakelyan HV,Haroutiunian TS

更新日期：2002-08-01 00:00:00

abstract：:In the present study, the impact of chromium(III) complexes ([Cr(salen)(H2O)2](+) (1), [Cr(en)3]3+ (2) and [Cr(EDTA)(H2O)]- (3)) on the biophysical properties of mucin like specific viscosity, zeta potential and particle size has been investigated. It is evident from the present investigation that the nature of the co...

journal_title：Journal of biomolecular structure & dynamics

authors： Shrivastava HY,Sreeram KJ,Nair BU

更新日期：2004-04-01 00:00:00

abstract：:Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Berger I,Spačková N,Leszczynski J,Hobza P

更新日期：2000-01-01 00:00:00

abstract：:The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhavnani V,Kaviraj S,Panigrahi P,Suresh CG,Yapara S,Pal J

更新日期：2018-08-01 00:00:00