Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations.

abstract：:At high binding densities acridine orange (AO) forms complexes with ds DNA which are insoluble in aqueous media. These complexes are characterized by high red- and minimal green-luminescence, 1:1 (dye/P) stoichiometry and resemble complexes of AO with ss nucleic acids. Formation of these complexes can be conveniently ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kapuscinski J,Darzynkiewicz Z

更新日期：1984-06-01 00:00:00

abstract：:A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibi...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehraban MH,Odooli S,Yousefi R,Roghanian R,Motovali-Bashi M,Moosavi-Movahedi AA,Ghasemi Y

更新日期：2017-07-01 00:00:00

abstract：:The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-t...

journal_title：Journal of biomolecular structure & dynamics

authors： Chandrasekaran R,Giacometti A,Arnott S

更新日期：2000-06-01 00:00:00

abstract：:The thermal denaturation of the synthetic high molecular weight double stranded polynucleotide poly(dA-dT) x poly(dA-dT) has been studied in aqueous buffered solution (Tris 1.0 mM; pH 7.8+/-0.2) in the presence of increasing concentrations of either Ni(2+) (borderline cation) or Cd(2+) (soft cation) at four different ...

journal_title：Journal of biomolecular structure & dynamics

authors： Airoldi M,Gennaro G,Giomini M,Giuliani AM,Giustini M

更新日期：2007-08-01 00:00:00

abstract：:Diabetes is very much known as a wide-spread disorder all around the world with serious complications for the diabetic patient. In order to reduce these complications, inhibition the activity of aldose reductase (AR) and cyclooxygenase-2 (COX-2) enzymes is a proposed pathway. Within this work potency of curcumin (CUR)...

journal_title：Journal of biomolecular structure & dynamics

authors： Mirzaei M,Harismah K,Soleimani M,Mousavi S

更新日期：2020-07-31 00:00:00

abstract：:Two naphthalene-containing compounds, 4-hydroxy-6,7-dimethoxy-1-(4-(trifluoromethyl)phenyl)-2-naphthoic acid (A) and 4-hydroxy-6,7-dimethoxy-1-phenyl-2-naphthoic acid (B), were prepared by several steps. Their bindings to human serum albumin (HSA) were studied by ultraviolet-visible (UV-vis) absorption, fluorescence, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang X,Xing Y,Su J,Wang C,Wang Z,Yu Y,Xu H,Ma D

更新日期：2020-06-12 00:00:00

abstract：:COVID-19 is a novel severe acute respiratory syndrome coronavirus. Currently, there is no effective treatment and vaccines seem to be the solution in the future. Virtual screening of potential drugs against the S protein of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has provided small molecular comp...

journal_title：Journal of biomolecular structure & dynamics

authors： Yepes-Pérez AF,Herrera-Calderon O,Quintero-Saumeth J

更新日期：2020-10-29 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 worldwide expanding increment in cancer pervasiveness is disturbing and this disease ranks among the main causes of mortality in both developing and developed countries. Unfortunately, available treatment options come with serious side effects and do not guarantee complete success. Although numerous models have be...

journal_title：Journal of biomolecular structure & dynamics

authors： Ojo OA,Aruleba RT,Adekiya TA,Sibuyi NRS,Ojo AB,Ajiboye BO,Oyinloye BE,Adeola HA,Fadaka AO

更新日期：2020-09-14 00:00:00

abstract：:The influences of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates, and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kar I,Chattopadhyaya R

更新日期：2017-11-01 00:00:00

abstract：:The AKT isoforms are a group of key kinases that play a critical role in tumorigenesis. These enzymes are overexpressed in different types of cancers, such as breast, colon, prostate, ovarian, and lung. Because of its relevance the AKT isoforms are attractive targets for the design of anticancer molecules. However, it...

journal_title：Journal of biomolecular structure & dynamics

authors： Trejo-Soto PJ,Hernández-Campos A,Romo-Mancillas A,Medina-Franco JL,Castillo R

更新日期：2018-02-01 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：: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：:In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic cont...

journal_title：Journal of biomolecular structure & dynamics

authors： Agudelo D,Bourassa P,Bariyanga J,Tajmir-Riahi HA

更新日期：2018-12-01 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：:The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conserv...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh SK,Saha B,Banerjee R

更新日期：2020-07-08 00:00:00

abstract：:Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...

journal_title：Journal of biomolecular structure & dynamics

authors： Quan Y,Xiong L,Chen J,Zhang HY

更新日期：2017-02-01 00:00:00

abstract：:The object of the present study is the verification of a new approach to the design of the active truncated forms of enzymes. The method is based on a new way of investigating the protein sequences--the ANalysis of Informational Structure (ANIS). The analysis of informational structure allows to determine the hierarch...

journal_title：Journal of biomolecular structure & dynamics

authors： Nekrasov AN,Radchenko VV,Shuvaeva TM,Novoselov VI,Fesenko EE,Lipkin VM

更新日期：2007-04-01 00:00:00

abstract：:Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undec...

journal_title：Journal of biomolecular structure & dynamics

authors： Laberge M,Vreugdenhil AJ,Vanderkooi JM,Butler IS

更新日期：1998-06-01 00:00:00

abstract：:Two novel, neutral and water soluble Pd(II) complexes of formula [Pd(Gly)(Ala)] (1) and [Pd(Gly)(Val)] (2) (Gly, Ala, and Val are anionic forms of glycine, alanine, and valine amino acids, respectively) have been synthesized and characterized by FT-IR, UV-Vis, 1H-NMR, elemental analysis, and molar conductivity measure...

journal_title：Journal of biomolecular structure & dynamics

authors： Mansouri-Torshizi H,Zareian-Jahromi S,Abdi K,Saeidifar M

更新日期：2019-08-01 00:00:00

abstract：:Phospholipase A(2) belongs to a super family of enzymes that is massively over expressed in a variety of severe inflammatory diseases, which degrades membrane phospholipids. It has also been reported that this activity leads to loss of tissue, organ integrity and function. This enzyme is an important target for anti-i...

journal_title：Journal of biomolecular structure & dynamics

authors： Ompraba G,Velmurugan D,Louis PA,Rafi ZA

更新日期：2010-02-01 00:00:00

abstract：:Abstract Using high frequency antiphase NMR spectroscopy and computer simulations of the antiphase spectra, we studied the equlibria in the sugar conformations in the DNA duplex 11-mer containing the AAA tract surrounded by cytosines. We demonstrate that at the 3'-end of the A-tract, the sugar switches from the comm...

journal_title：Journal of biomolecular structure & dynamics

authors： Kamath S,Sarma MH,Zhurkin VB,Turner CJ,Sarma RH

更新日期：2000-01-01 00:00:00

abstract：:The 9-aminoacridine-DNA binding curve is analyzed in two ways: with polyelectrolyte effects neglected and with polyelectrolyte effects included. It is found that the analysis which includes polyelectrolyte effects is consistent with the violation of neighbor exclusion displayed by diacridine complexes as observed by A...

journal_title：Journal of biomolecular structure & dynamics

authors： Friedman RA,Shahin M,Zuckerbraun S

更新日期：1991-04-01 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：:SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodoc...

journal_title：Journal of biomolecular structure & dynamics

authors： Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik I

更新日期：2020-11-17 00:00:00

abstract：:A simple statistical approach for the analysis of biological sequences, such as splice-sites, promoter regions, helices and extended structure forming regions or any other sequence dependent functional entities in proteins, is presented. The approach has been proved useful to develop a method for prediction of such en...

journal_title：Journal of biomolecular structure & dynamics

authors： Reddy BV,Pandit MW

更新日期：1995-02-01 00:00:00

abstract：:Proteins are nature's biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for their macro-scaled counterparts, convert (part of) other/various...

journal_title：Journal of biomolecular structure & dynamics

authors： Gur M,Golcuk M,Yilmaz SZ,Taka E

更新日期：2020-02-01 00:00:00

abstract：:Complexes of NaDNA with the bipyridyl-(ethylenediamine)platintum(II) (abbreviated [(bipy)Pt(en)]2+) molecular ion have been studied in solution via ultraviolet absorption experiments at 260 nm between 50 and 90 degrees C. These measurements, performed as a function of the molar ratio of the [(bipy)Pt(en)]2+ complex to...

journal_title：Journal of biomolecular structure & dynamics

authors： Szabó S,Lee SA

更新日期：2008-08-01 00:00:00

abstract：:Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from trad...

journal_title：Journal of biomolecular structure & dynamics

authors： Sun MF,Chang TT,Chang KW,Huang HJ,Chen HY,Tsai FJ,Lin JG,Chen CY

更新日期：2011-06-01 00:00:00

abstract：:The purpose of this study was to investigate the site-selective binding of erlotinib hydrochloride (ET), a targeted anticancer drug, to bovine serum albumin (BSA) through 1H NMR, spectroscopic, thermodynamic, and molecular modeling methods. The fluorescence quenching of BSA by ET was a result of the formation of BSA-E...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu Y,Chen M,Luo Z,Lin J,Song L

更新日期：2013-10-01 00:00:00