Anti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: design, synthesis, docking, TOPKAT analysis and molecular dynamics simulations.

abstract：:We have analysed S1 sensitivity of SV40 minichromosomes isolated from the nuclei of infected cells at the late stage of infection. We show that a fraction of purified minichromosomes is sensitive towards double-strand cleavage by S1 nuclease. The pattern of specific cleavage reminiscent of that found for subcloned fra...

journal_title：Journal of biomolecular structure & dynamics

authors： Nedospasov SA,Shakhov AN,Hirt B

更新日期：1989-04-01 00:00:00

abstract：:P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

journal_title：Journal of biomolecular structure & dynamics

authors： Yellapu NK,Pulaganti M,Pakala SB

更新日期：2017-08-01 00:00:00

abstract：:Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs co...

journal_title：Journal of biomolecular structure & dynamics

authors： Mani A,Gupta DK

更新日期：2015-01-01 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：:Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary di...

journal_title：Journal of biomolecular structure & dynamics

authors： Pandey B,Aarthy M,Sharma M,Singh SK,Kumar V

更新日期：2020-06-30 00:00:00

abstract：:Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...

journal_title：Journal of biomolecular structure & dynamics

authors： Petrauskene OV,Yakovleva JN,Alekseev YI,Subach FV,Babkina OV,Gromova ES

更新日期：2000-04-01 00:00:00

abstract：:An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are mor...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Leszczynski J,Vetterl V,Hobza P

更新日期：1996-02-01 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

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：:Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three differ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sutthibutpong T,Rattanarojpong T,Khunrae P

更新日期：2018-11-01 00:00:00

abstract：:Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Patel HM,Shaikh M,Ahmad I,Lokwani D,Surana SJ

更新日期：2020-04-23 00:00:00

abstract：:Repetitive basic polypeptides containing lysine or arginine as every third amino acid were shown to cause DNA condensation at physiological salt concentration connected with selective DNA binding with respect to DNA composition and sequence. This selectivity is very similar to that existing in the case of histone H1 a...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponar J,Votavová H

更新日期：1996-06-01 00:00:00

abstract：:Anisotropic network model (ANM) is used to analyze the collective motions of restriction enzyme EcoRI in free form and in complex with DNA. For comparison, three independent molecular dynamics (MD) simulations, each of 1.5 ns duration, are also performed for the EcoRI-DNA complex in explicit water. Although high mobil...

journal_title：Journal of biomolecular structure & dynamics

authors： Doruker P,Nilsson L,Kurkcuoglu O

更新日期：2006-08-01 00:00:00

abstract：:Two aminobenzoic acid derivatives DAB-0 and DAB-1 showed distinct biological properties on murine bladder cancer (BCa) cell line MB49-I. In contrast to DAB-1, DAB-0 does not possess any anti-inflammatory activity and is less toxic. Furthermore, DAB-0 does not interfere with INFγ-induced STAT1 activation and TNFα-induc...

journal_title：Journal of biomolecular structure & dynamics

authors： Chanphai P,Cloutier F,Oufqir Y,Leclerc MF,Eiján AM,Reyes-Moreno C,Bérubé G,Tajmir-Riahi HA

更新日期：2021-01-01 00:00:00

abstract：:Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

journal_title：Journal of biomolecular structure & dynamics

authors： Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

更新日期：2009-12-01 00:00:00

abstract：:Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in a...

journal_title：Journal of biomolecular structure & dynamics

authors： Gogia S,Puranik M

更新日期：2014-01-01 00:00:00

abstract：:The NIa protease of Potyviridae is the major viral protease that processes potyviral polyproteins. The NIa protease coding region of Cardamom mosaic virus (CdMV) is amplified from the viral cDNA, cloned and expressed in Escherichia coli. NIa protease forms inclusion bodies in E.coli. The inclusion bodies are solubiliz...

journal_title：Journal of biomolecular structure & dynamics

authors： Jebasingh T,Pandaranayaka EP,Mahalakshmi A,Kasin Yadunandam A,Krishnaswamy S,Usha R

更新日期：2013-01-01 00:00:00

abstract：:Virtually all mRNA sequences carry a 3-base periodical pattern, presumably involved in the translation frame monitoring mechanism (Trifonov, E.N., J. Mol. Biol. 194, 643-652, 87). The hidden pattern, 5'-(GHN)n-3' (H representing nonG, N any base), is further refined by extensive computational analysis of mRNA sequence...

journal_title：Journal of biomolecular structure & dynamics

authors： Lagunez-Otero J,Trifonov EN

更新日期：1992-12-01 00:00:00

abstract：:Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L bin...

journal_title：Journal of biomolecular structure & dynamics

authors： Lando DY,Nechipurenko YD

更新日期：2008-10-01 00:00:00

abstract：:Target evaluation is at the centre of rational drug design and biologics development. In order to successfully engineer antibodies, T-cell receptors or small molecules it is necessary to identify and characterise potential binding or contact sites on therapeutically relevant target proteins. Currently, there are numer...

journal_title：Journal of biomolecular structure & dynamics

authors： Kanapeckaitė A,Beaurivage C,Hancock M,Verschueren E

更新日期：2020-12-10 00:00:00

abstract：:A new molecular mechanism of trinucleotide expansion diseases is suggested. The mechanism involves the formation of double-helical RNA hairpins by transcripts carrying (CNG)(n) sequences, which are processed via the RNAi pathway with subsequent RNA silencing of genes containing (CNG)(n) sequences. Depletion of protein...

journal_title：Journal of biomolecular structure & dynamics

authors： Malinina L

更新日期：2005-12-01 00:00:00

abstract：:Calcium/calmodulin-dependent protein kinase IV (CaMKIV) is a multifunctional enzyme which belongs to the Ser/Thr kinase family. CaMKIV plays important role in varieties of biological processes such as gene expression regulation, memory consolidation, bone growth, T-cell maturation, sperm motility, regulation of microt...

journal_title：Journal of biomolecular structure & dynamics

authors： Naz H,Shahbaaz M,Haque MA,Bisetty K,Islam A,Ahmad F,Hassan MI

更新日期：2017-02-01 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：:Acid-induced structural changes of a mouse IgG2a monoclonal antibody (MN12) as indicated by Jiskoot et al. (Eur. J. Biochem. 201,223-232 (1991)) were studied by measuring the transient electric birefringence of MN12 in aqueous solution and in glycerol-water mixtures at different pH conditions. A multi-exponential anal...

journal_title：Journal of biomolecular structure & dynamics

authors： van Haeringen B,Jiskoot W,van Grondelle R,Bloemendal M

更新日期：1992-04-01 00:00:00

abstract：:Proton ENDOR has been observed from frozen solutions (ca. 38K degrees) of copper meso-(4-N-tetra-methylpyridyl)porphyrin (CuTMpyP(4)) complexed with Salmon sperm DNA in water and D2O. Lines from exchangeable protons of the DNA bases have been observed in these ENDOR spectra. Analyses of these ENDOR data show that the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Greiner SP,Kreilick RW,Marzilli LG

更新日期：1992-04-01 00:00:00

abstract：:Crystalline complexes of yeast tRNA(phe) and the oligopeptide antibiotics netropsin and distamycin A were prepared by diffusing drugs into crystals of tRNA. X-ray structure analyses of these complexes reveal a single common binding site for both drugs which is located in the major or deep groove of the tRNA T-stem. Th...

journal_title：Journal of biomolecular structure & dynamics

authors： Rubin J,Sundaralingam M

更新日期：1984-08-01 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：:The fluorescent 2-aminopurine probe (2-AP) incorporated into the loop of 23-mer RNA hairpin of HIV-1 genome dimerization initiation site (DIS) was used for discrimination of specific and unspecific binding of paromomycin and spermine to the kissing loop dimer (KD) formed in solution. While both ligands stabilized the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kaluzhny DN,Beniaminov AD,Minyat EE

更新日期：2008-06-01 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：:By reaction of 1,2-diaminocyclohexane with the 2,3-butanedione monoxime in the presence of ZnCl2, a new Schiff base complex was obtained. This complex was characterized by elemental analyses, FT-IR, 1H NMR, UV-Vis, and conductivity measurements. The reactivity of this complex to human serum albumin (HSA) under simulat...

journal_title：Journal of biomolecular structure & dynamics

authors： Shahraki S,Shiri F,Saeidifar M

更新日期：2018-05-01 00:00:00