Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: combined molecular docking and molecular dynamics approaches.

abstract：:Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues t...

journal_title：Journal of biomolecular structure & dynamics

authors： Pai PP,Mondal S

更新日期：2016-10-01 00:00:00

abstract：:The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in ...

journal_title：Journal of biomolecular structure & dynamics

authors： Nikulin A,Mikhailina A,Lekontseva N,Balobanov V,Nikonova E,Tishchenko S

更新日期：2017-06-01 00:00:00

abstract：:Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with mole...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu F,Ma Z,Sang J,Lu F

更新日期：2020-05-01 00:00:00

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

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

更新日期：2012-01-01 00:00:00

abstract：:Ornithine decarboxylase (ODC) is an enzyme that initiates polyamine synthesis in human. Polyamines play key roles in cell-cell adhesion, cell motility and cell cycle regulation. Higher synthesis of polyamines also occurs in rapidly proliferating cancer cells are mediated by ODC. As per earlier studies, di-flouro-methy...

journal_title：Journal of biomolecular structure & dynamics

authors： Sivashanmugam M,K N S,V U

更新日期：2019-02-01 00:00:00

abstract：:Time Correlated Single Photon Counting (TCSPC) was used for the first time to analyze the effect/changes in the mode of intercalation of ethidium bromide (EtBr) and acridine orange (AO) to calf thymus DNA brought about due to interaction of naturally occurring methylxanthines such as theophylline (X1), theobromine (X2...

journal_title：Journal of biomolecular structure & dynamics

authors： Johnson IM,Kumar SG,Malathi R

更新日期：2003-04-01 00:00:00

abstract：:The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-...

journal_title：Journal of biomolecular structure & dynamics

authors： Singh R,Meena NK,Das T,Sharma RD,Prakash A,Lynn AM

更新日期：2020-10-01 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：:The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform...

journal_title：Journal of biomolecular structure & dynamics

authors： Cai Y,He J,Lu L

更新日期：2011-04-01 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：:A simplified multidimensional search was applied to determine the structure of deoxyhexamer CGCGCG in the crystal form belonging to the space group C222(1) (a = 45.6 A, b = 37.3 A, c = 70.3 A). This crystal form contains two Z-DNA duplexes per asymmetric unit in a similar orientation. The search consists of several ma...

journal_title：Journal of biomolecular structure & dynamics

authors： Strokopytov BV,Malinina LV

更新日期：1994-04-01 00:00:00

abstract：:A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH+), acetic acid in neutral (AcOH) and deprotonated (AcO-) forms, G-AcO-, C-AcOH, and CH(+)-AcO- complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetic...

journal_title：Journal of biomolecular structure & dynamics

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

更新日期：1997-10-01 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：: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：:Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, lin...

journal_title：Journal of biomolecular structure & dynamics

authors： Brayer G,McPherson A

更新日期：1984-12-01 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：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Huertas D,Lipps H,Azorín F

更新日期：1994-08-01 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 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：:About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Gogoi P,Chandravanshi M,Mandal SK,Srivastava A,Kanaujia SP

更新日期：2016-07-01 00:00:00

abstract：:The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were con...

journal_title：Journal of biomolecular structure & dynamics

authors： Ponnuswamy PK,Anukanth A

更新日期：1989-02-01 00:00:00

abstract：:The Runt domain proteins are eukaryotic transcription factors that regulate major developmental pathways. All members of this family contain a highly-conserved sequence-specific DNA binding domain: the Runt domain (RD). Structural and biochemical studies have shown that the Runt domain undergoes a conformational trans...

journal_title：Journal of biomolecular structure & dynamics

authors： Suad O,Eyal E,Blumenzweig I,Kessler N,Levanon D,Groner Y,Shakked Z

更新日期：2007-02-01 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：: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：: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：:Abstract The forces that direct protein folding lead naturally to native proteins and protein domains that are typically, to a first approximation, globular-spherical and compact, with a relatively clear distinction between the hydrophobic inside and polar outside. The near-universality of these features of protein ...

journal_title：Journal of biomolecular structure & dynamics

authors： Carey J

更新日期：2000-01-01 00:00:00

abstract：:As the number of available three dimensional coordinates of proteins increases, it is now recognized that proteins from different families and topologies are constructed from independent motifs. Detection of specific structural motifs within proteins aids in understanding their role and the mechanism of their operatio...

journal_title：Journal of biomolecular structure & dynamics

authors： Fischer D,Bachar O,Nussinov R,Wolfson H

更新日期：1992-02-01 00:00:00

abstract：:Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploit...

journal_title：Journal of biomolecular structure & dynamics

authors： Patel A,Tiwari S,Jha PK

更新日期：2019-04-01 00:00:00

abstract：:Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation ...

journal_title：Journal of biomolecular structure & dynamics

authors： Mahmoudi Gomari M,Rostami N,Omidi-Ardali H,Arab SS

更新日期：2021-01-21 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