Nanoporous iron oxide nanoparticle: hydrothermal fabrication, human serum albumin interaction and potential antibacterial effects.

abstract：:Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degr...

journal_title：Journal of biomolecular structure & dynamics

authors： Singha DL,Maharana J,Panda D,Dehury B,Modi MK,Singh S

更新日期：2020-05-05 00:00:00

abstract：:Aggregation of amyloid peptide (Aβ) has been shown to be directly related to progression of Alzheimer's disease (AD). Aβ is neurotoxic and its deposition and aggregation ultimately lead to cell death. In our previous work, we reported flavonoid derivative (compound 1) showing promising result in transgenic AD model of...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar A,Srivastava S,Tripathi S,Singh SK,Srikrishna S,Sharma A

更新日期：2016-06-01 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：:Using Fourier transform, we investigate the structural characteristics of genomes for several viruses. The mutual correlations and ordering of the different nucleotides in genomes are compared versus their counterparts from the random sequences with the same nucleotide composition. In order to assess the stastical sig...

journal_title：Journal of biomolecular structure & dynamics

authors： Chechetkin VR,Knizhnikova LA,Turygin AYu

更新日期：1994-10-01 00:00:00

abstract：:The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at...

journal_title：Journal of biomolecular structure & dynamics

authors： Razavi L,Raissi H,Hashemzadeh H,Farzad F

更新日期：2020-06-05 00:00:00

abstract：:Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (sta...

journal_title：Journal of biomolecular structure & dynamics

authors： Arya H,Yadav CS,Lin SY,Syed SB,Charles MRC,Kannadasan S,Hsieh HP,Singh SS,Gajurel PR,Coumar MS

更新日期：2020-08-01 00:00:00

abstract：:Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th ...

journal_title：Journal of biomolecular structure & dynamics

authors： Majumder R,Roy S,Thakur AR

更新日期：2012-01-01 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：:Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buc...

journal_title：Journal of biomolecular structure & dynamics

authors： Danilov VI,Anisimov VM

更新日期：2005-02-01 00:00:00

abstract：:Doublesex and Mab-3-related transcription factor (DMRT) gene family is widely known for its involvement in sex determination and/or differentiation among different phyla. In this study, we identify eight DMRT genes in the cephalochordate amphioxus, a protochordate holding a key phylogenetic position. The eight DMRTs c...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang F,Yu Y,Ji D,Li H

更新日期：2012-01-01 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 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：:Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural t...

journal_title：Journal of biomolecular structure & dynamics

authors： Abhinand PA,Shaikh F,Bhakat S,Radadiya A,Bhaskar LV,Shah A,Ragunath PK

更新日期：2016-01-01 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：:Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...

journal_title：Journal of biomolecular structure & dynamics

authors： Jamshidi S,Jalili S,Rafii-Tabar H

更新日期：2015-01-01 00:00:00

abstract：:Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium...

journal_title：Journal of biomolecular structure & dynamics

authors： Desai PV,Avery MA

更新日期：2004-06-01 00:00:00

abstract：:In this work, we integrate a non-linear signal analysis method, recurrence quantification analysis (RQA), with the well-known machine-learning algorithm, support vector machines for the binary classification of protein sequences. Two different classification problems were selected, discriminating between aggregating a...

journal_title：Journal of biomolecular structure & dynamics

authors： Mitra J,Mundra P,Kulkarni BD,Jayaraman VK

更新日期：2007-12-01 00:00:00

abstract：:Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of re...

journal_title：Journal of biomolecular structure & dynamics

authors： Hernandez R,Facelli JC

更新日期：2021-01-18 00:00:00

abstract：:In this paper, a general method is developed to study site-specific interactions in DNA-protein complexes using heteronuclear NMR spectroscopy and molecular modeling. This method involves two steps: (a) homonuclear 1H NMR and molecular modeling are used to develop a low resolution model and (b) 15N7-guanosine containi...

journal_title：Journal of biomolecular structure & dynamics

authors： Edwards CA,Tung CS,Silks LA,Gatewood JM,Fee JA,Mariappan SV

更新日期：1998-08-01 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：:Human C5a (hC5a), one of the pro-inflammatory glycoproteins of the complement system is known to undergo production hyperdrive in response to stress and infection. hC5a has been associated with the pathogenesis of many chronic and acute diseases, due to its proven ability in triggering the 'cytokine storm', by binding...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra R,Behera LM,Rana S

更新日期：2020-09-15 00:00:00

abstract：:Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolaskar AS,Joshi RR

更新日期：1998-06-01 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：:Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) sim...

journal_title：Journal of biomolecular structure & dynamics

authors： Song W,Guo JT

更新日期：2015-01-01 00:00:00

abstract：:Homologous proteins may fold into similar three-dimensional structures. Spectroscopic evidence suggests this is true for the cereal grain thionins, the mistletoe toxins, and for crambin, three classes of plant proteins. We have combined primary sequence homology and energy minimization to predict the structures alpha ...

journal_title：Journal of biomolecular structure & dynamics

authors： Whitlow M,Teeter MM

更新日期：1985-02-01 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：:Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79...

journal_title：Journal of biomolecular structure & dynamics

authors： Saranya V,Radhika R,Shankar R,Vijayakumar S

更新日期：2020-04-06 00:00:00

abstract：:In this paper, we propose a new method based on the 2-D graphical representation to analyze the similarity of biological sequences and classify the protein secondary structure sequences. Instead of computing some characteristics from the distance matrix, the average area surrounded by the curve and X axis is computed ...

journal_title：Journal of biomolecular structure & dynamics

authors： Huang W,Guo Y,Zhang J

更新日期：2009-04-01 00:00:00

abstract：:A family of covalent complexes between oligonucleotides and derivatives of the intercalating agent 9-amino acridine has been synthesized (Asseline, U., Thuong, N.T. and Helene, C. (1983) C.R.Acad. Sci. (Paris) 297 (III), 369-372) and studied (Lancelot, G., Asseline, U., Thuong, N.T., and Helene, C. (1985) Biochemistry...

journal_title：Journal of biomolecular structure & dynamics

authors： Cieplak P,Rao SN,Hélène C,Montenay-Garestier T,Kollman PA

更新日期：1987-10-01 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