Deciphering the interaction of puerarin with cancer macromolecules: An in silico investigation.

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：:Cromolyn sodium (CS), an anti-inflammatory drug is used in the treatment of allergic disorders. Bovine serum albumin (BSA) a blood plasma protein is used as a model protein for studying protein folding and ligand binding mechanism as it is the main transporter protein which decides the disposition and pharmacodynamics...

journal_title：Journal of biomolecular structure & dynamics

authors： Yasmeen S,Riyazuddeen,Khatun S,Abul Qais F

更新日期：2020-02-01 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：:Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

journal_title：Journal of biomolecular structure & dynamics

authors： Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

更新日期：1994-08-01 00:00:00

abstract：:Preceding experimental findings revealed that the release of indomethacin decreased when a folate conjugate G4-PAMAM (folate-G4-PAMAM) dendrimer was used compared with its unconjugated dendrimer (G4-PAMAM). Further, better encapsulation of the conjugated dendrimer was achieved, information useful for elucidating the s...

journal_title：Journal of biomolecular structure & dynamics

authors： Martínez-Muñoz A,Correa-Basurto J,Bello M

更新日期：2020-12-21 00:00:00

abstract：:In order to examine whether chiral metal complexes can be used to discriminate between right- and left-handed DNA conformational states we have studied the enantioselective interactions of Fe(phen)3(2+) and Ru(phen)3(2+) (phen = 1,10-phenanthroline) with poly(dGm5dC) under B- and Z-form conditions. With the inversion-...

journal_title：Journal of biomolecular structure & dynamics

authors： Härd T,Hiort C,Nordén B

更新日期：1987-08-01 00:00:00

abstract：:Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both th...

journal_title：Journal of biomolecular structure & dynamics

authors： Bracht F,de Alencastro RB

更新日期：2016-01-01 00:00:00

abstract：:Stereochemical effects of methylphosphonate (MP) in B-DNA and Z-DNA duplexes are studied through molecular mechanics approach. Duplexes of different lengths, tetramers, hexamers, dodecamers are examined to assess the interstrand and intrastrand electrostatic effects due to MPs vis-a-vis phosphates. A variety of models...

journal_title：Journal of biomolecular structure & dynamics

authors： Swarnalatha Y,Yathindra N

更新日期：1993-06-01 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：:The binding of the anilido aminoacridine derivative amsacrine with the heme proteins, hemoglobin, and myoglobin, was characterized by various spectroscopic and calorimetric methods. The binding affinity to hemoglobin was (1.21 ± .05) × 105 M-1, while that to myoglobin was three times higher (3.59 ± .15) × 105 M-1. The...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhowmik D,Suresh Kumar G

更新日期：2017-05-01 00:00:00

abstract：:The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Barton JK

更新日期：1983-12-01 00:00:00

abstract：:The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mech...

journal_title：Journal of biomolecular structure & dynamics

authors： Tian H,Tao P

更新日期：2020-08-04 00:00:00

abstract：:Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Fo...

journal_title：Journal of biomolecular structure & dynamics

authors： Bathaie SZ,Ajloo D,Daraie M,Ghadamgahi M

更新日期：2015-01-01 00:00:00

abstract：:An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy prefe...

journal_title：Journal of biomolecular structure & dynamics

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

更新日期：1999-04-01 00:00:00

abstract：:Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and ca...

journal_title：Journal of biomolecular structure & dynamics

authors： Varughese JF,Chalovich JM,Li Y

更新日期：2010-10-01 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：:The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portio...

journal_title：Journal of biomolecular structure & dynamics

authors： Whitehead TL,Jones LM,Hicks RP

更新日期：2004-02-01 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：:Traditionally biased usage of synonymous codons renders selective advantage to proteins expressed at high levels with a few exceptions like in Escherichia coli. Proteome-wide characteristics indicative of trends in highly expressed proteins of E. coli is analyzed in this communication. Implications for the nature of i...

journal_title：Journal of biomolecular structure & dynamics

authors： Kahali B,Ghosh TC

更新日期：2013-01-01 00:00:00

abstract：:The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Ebrahimi M,Khayamian T,Hadadzadeh H,Sayed Tabatabaei BE,Jannesari Z,Khaksar G

更新日期：2015-01-01 00:00:00

abstract：:-1 programmed ribosomal frameshifting (PRF) in viruses is often stimulated by a pseudoknot downstream from the slippery sequence. At the PRF junction of HIV-1, transmissible gastroenteritis virus (TGEV), Barmah Forest virus (BFV), Fort Morgan virus (FMV), and Equine arteritis virus (EAV), we identified potential doubl...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang G,Yang Y,Huang X,Du Z

更新日期：2015-01-01 00:00:00

abstract：:Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arnold GE,Manchester JI,Townsend BD,Ornstein RL

更新日期：1994-10-01 00:00:00

abstract：:CLTOAB is an ammonium-based ionic liquid composed of ε-Caprolactam (CL) C6H11NO and tetraoctylammonium bromide (TOAB) (C32H68BrN). In this study, experimental IR and Raman spectra of CLTOAB ionic liquid together with the computational results of the compound have been reported. The optimized geometry, vibrational freq...

journal_title：Journal of biomolecular structure & dynamics

authors： Celik S,Albayrak AT,Akyuz S,E Ozel A

更新日期：2019-07-01 00:00:00

abstract：:Transient interactions between cancer stem cells and components of the tumor microenvironment initiate various signaling pathways crucial for carcinogenesis. Predominant hyaluronan (HA) receptor, CD44 is structurally and functionally one of the most variable cell surface receptors having the potential to generate a di...

journal_title：Journal of biomolecular structure & dynamics

authors： Patel S,Shaikh F,Devaraji V,Radadiya A,Shah K,Shah A,Rawal R

更新日期：2017-02-01 00:00:00

abstract：:The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition patte...

journal_title：Journal of biomolecular structure & dynamics

authors： Florián J,Leszczyński J

更新日期：1995-04-01 00:00:00

abstract：:NMR experiments with a 21412 Redfield observation pulse were carried out on a kappa-carrageenan aqueous solution containing 0.5M LiI. A detected hydrogen-bonded proton resonance at approximately 17.6 ppm, is in accordance with an ordered carrageenan structure in the solution similar to the double, parallel-stranded he...

journal_title：Journal of biomolecular structure & dynamics

authors： Nerdal W,Haugen F,Knutsen S,Grasdalen H

更新日期：1993-04-01 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：:Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...

journal_title：Journal of biomolecular structure & dynamics

authors： Dhal AK,Pani A,Yun SI,Mahapatra RK

更新日期：2020-07-07 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：: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