Disorderness in Escherichia coli proteome: perception of folding fidelity and protein-protein interactions.

abstract：:P-glycoprotein (P-gp) is a main factor contributing to multidrug resistance. The effect of this transporter protein on limiting the effectiveness of chemotherapy has been shown by various studies. In a previous report, we synthesized some 14-dihydropyridine (DHP) derivatives as inhibitors of human P-gp. In the present...

journal_title：Journal of biomolecular structure & dynamics

authors： Shahraki O,Zargari F,Edraki N,Khoshneviszadeh M,Firuzi O,Miri R

更新日期：2018-01-01 00:00:00

abstract：:Bruton's tyrosine kinase (Btk) is an important enzyme in B-lymphocyte development and differentiation. Furthermore, Btk expression is considered essential for the proliferation and survival of these cells. Btk inhibition has become an attractive strategy for treating autoimmune diseases, B-cell leukemia, and lymphomas...

journal_title：Journal of biomolecular structure & dynamics

authors： Santos-Garcia L,Assis LC,Silva DR,Ramalho TC,da Cunha EF

更新日期：2016-07-01 00:00:00

abstract：:Vibrio cholerae hemolysin (HlyA) is a 65 kDa pore-forming toxin which causes lysis of target eukaryotic cells by forming heptameric channels in the plasma membrane. Deletion of the 15 kDa C-terminus β-prism carbohydrate-binding domain generates a 50 kDa truncated variant (HlyA50) with 1000-fold-reduced pore-forming ac...

journal_title：Journal of biomolecular structure & dynamics

authors： Dutta S,Banerjee KK,Ghosh AN

更新日期：2014-01-01 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：:Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...

journal_title：Journal of biomolecular structure & dynamics

authors： Pan Z,Wang Y,Gu X,Wang J,Cheng M

更新日期：2020-10-01 00:00:00

abstract：:The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...

journal_title：Journal of biomolecular structure & dynamics

authors： Almeida JSFD,Botelho FD,de Souza FR,Dos Santos MC,Goncalves ADS,Rodrigues RLB,Cardozo M,Kitagawa DAS,Vieira LA,Silva RSF,Cavalcante SFA,Bastos LDC,Nogueira MOT,de Santana PIR,Brum JOC,Nepovimova E,Kuca K,LaPlante SR,G

更新日期：2021-01-08 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 conformational space available to GnRH and lGnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calcu...

journal_title：Journal of biomolecular structure & dynamics

authors： Watts CR,Mezei M,Murphy RF,Lovas S

更新日期：2001-04-01 00:00:00

abstract：:Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-t...

journal_title：Journal of biomolecular structure & dynamics

authors： Boyarshin KS,Priss AE,Rayevskiy AV,Ilchenko MM,Dubey IY,Kriklivyi IA,Yaremchuk AD,Tukalo MA

更新日期：2017-02-01 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：:β-lactoglobulin (β-LG) is a member of lipocalin superfamily of transporters for small hydrophobic molecules such as retinoids. We located the binding sites of retinol and retinoic acid on β-LG in aqueous solution at physiological conditions, using FTIR, CD, fluorescence spectroscopic methods, and molecular modeling. T...

journal_title：Journal of biomolecular structure & dynamics

authors： Belatik A,Kanakis CD,Hotchandani S,Tarantilis PA,Polissiou MG,Tajmir-Riahi HA

更新日期：2012-01-01 00:00:00

abstract：:We performed a neuraminidase sequence analysis of thirty-two pediatric patients with influenza B who visited Teikyo University Hospital from January 2016 to March 2017, and found oseltamivir-resistant samples belonging to the Yamagata and Victoria lineages. Comparison with the neuraminidase sequence of oseltamivir-sus...

journal_title：Journal of biomolecular structure & dynamics

authors： Kato Y,Takahashi K,Ito F,Suzuki S,Fukui K,Mimaki M,Suzuki K

更新日期：2020-05-25 00:00:00

abstract：:Thermodynamic and structural properties of two UNCG tetraloops in very short hairpin octamers, 5'-r(GCUUCGGC)-3' and 5'-r(GCUACGGC)-3', have been studied by means of various physical techniques. Melting profiles of both octamers, obtained from UV absorption spectra taken as a function of temperature, are consistent wi...

journal_title：Journal of biomolecular structure & dynamics

authors： Abdelkafi M,Ghomi M,Turpin PY,Baumruk V,Hervé du Penhoat C,Lampire O,Bouchemal-Chibani N,Goyer P,Namane A,Gouyette C,Huynh-Dinh T,Bednárová L

更新日期：1997-04-01 00:00:00

abstract：:The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of α...

journal_title：Journal of biomolecular structure & dynamics

authors： Anwer K,Sonani R,Madamwar D,Singh P,Khan F,Bisetty K,Ahmad F,Hassan MI

更新日期：2015-01-01 00:00:00

abstract：:In present work, we describe a methodology for prediction of an enzymatic reaction for which no experimental data are available except for a gene sequence. As a challenging case, we have developed the method for identifying the putative substrates of monoester phosphatases, commonly known as acid phosphatase enzymes, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Zamani Amirzakaria J,Malboobi MA,Marashi SA,Lohrasebi T

更新日期：2020-07-02 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：: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

abstract：:Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded c...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra M,Singh V,Tellis MB,Joshi RS,Pandey KC,Singh S

更新日期：2020-12-09 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：:A complete three dimensional model (RCSB000408; PDB code 1qaa) for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor is proposed. A model of interaction of the N-terminal operator binding domain 1-72 with the operator was available. We ...

journal_title：Journal of biomolecular structure & dynamics

authors： Chattopadhyaya R,Ghosh K,Namboodiri VM

更新日期：2000-10-01 00:00:00

abstract：:The present paper describes design, synthesis, and biological evaluation of a series of some 3-[3-(amino)propoxy]benzenamines as acetylcholinesterase inhibitors using mice as a model and piracetam as a reference drug. The structures of these compounds were confirmed by spectral analysis and compounds were tested for m...

journal_title：Journal of biomolecular structure & dynamics

authors： Malik R,Gupta R,Srivastava S,Choudhary BS,Sharma M

更新日期：2017-08-01 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 assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kelve M,Aruja A,Kooli K,Männik J,Raukas E

更新日期：1987-08-01 00:00:00

abstract：:Glutamine synthetase (GS) of Mycobacterium tuberculosis (Mtb) is an essential enzyme which is involved in nitrogen metabolism and cell wall synthesis. It is involved in the inhibition of phagosome-lysosome fusion by preventing acidification. Targeting GS can be helpful to control the infection of Mtb. In order to iden...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumari M,Subbarao N

更新日期：2020-10-01 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 interactions of a homologous series of four anthraquinone (AQ) intercalators with increasing lengths of polyethylene glycol (PEG) side chains with DNA have been studied via molecular dynamics (MD) simulations. The geometry, conformation, interactions, and hydration of the complexes were examined. The geometries of...

journal_title：Journal of biomolecular structure & dynamics

authors： Beckford SJ,Dixon DW

更新日期：2012-01-01 00:00:00

abstract：:The studies on protein-dye interactions are important in biological process and it is regarded as vital step in rational drug design. The interaction of thionine (TH) with human serum albumin (HSA) was analyzed using isothermal titration calorimetry (ITC), spectroscopic, and molecular docking technique. The emission s...

journal_title：Journal of biomolecular structure & dynamics

authors： Manivel P,Paulpandi M,Murugan K,Benelli G,Ilanchelian M

更新日期：2017-11-01 00:00:00

abstract：:The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several strategies have been taken by scientists and researchers worldwid...

journal_title：Journal of biomolecular structure & dynamics

authors： Sarkar I,Sen A

更新日期：2020-11-23 00:00:00

abstract：:Pre-mRNA splicing is one of the most complex and intricate processes in eukaryotic cell biology. Over the past decade, my laboratory has been interested in determining the structures of RNA components of the spliceosome, and in investigating how the structure, stability and dynamics of these RNA components are perturb...

journal_title：Journal of biomolecular structure & dynamics

authors： Gmeiner WH

更新日期：2002-04-01 00:00:00

abstract：:The polymorphism exhibited by the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G), as a function of the temperature, DNA concentration and ionic strength, was investigated by means of NMR spectroscopy. It is shown that this partly self-complementary DNA fragment, under conditions of low DNA concentration (0.4 mM) and low ...

journal_title：Journal of biomolecular structure & dynamics

authors： Orbons LP,van der Marel GA,van Boom JH,Altona C

更新日期：1987-06-01 00:00:00