DFT and docking studies of designed conjugates of noscapines & repurposing drugs: promising inhibitors of main protease of SARS-CoV-2 and falcipan-2.

abstract：:Temporal order ("chronology") of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis of 60 different criteria each offering certain temporal order. After several steps of filtering the chronology vectors are averaged ...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2004-08-01 00:00:00

abstract：:A new algorithm for the analysis of nonselective proton relaxation data in protein solution is presented. T1 and T2 of protein protons in lysozyme and RNase solutions were measured at three resonance frequencies--11, 27 and 90 MHz. In addition we measured water T1 dispersions in lysozyme solutions over the frequency r...

journal_title：Journal of biomolecular structure & dynamics

authors： Krushelnitsky AG,Fedotov VD

更新日期：1993-08-01 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：:Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues t...

journal_title：Journal of biomolecular structure & dynamics

authors： Pai PP,Mondal S

更新日期：2016-10-01 00:00:00

abstract：:This work aims at characterizing structural transitions within the intrinsically disordered C-terminal domain of the nucleoprotein (NTAIL) from the Nipah and Hendra viruses, two recently emerged pathogens gathered within the Henipavirus genus. To this end, we used site-directed spin labeling combined with electron par...

journal_title：Journal of biomolecular structure & dynamics

authors： Martinho M,Habchi J,El Habre Z,Nesme L,Guigliarelli B,Belle V,Longhi S

更新日期：2013-01-01 00:00:00

abstract：:Visible and near infrared magnetic circular dichroism (MCD) spectra of heme proteins and enzymes as well as those of a protein-free heme bound to 2-methylimidazole were recorded and compared at 4.2 K in unrelaxed metastable and relaxed equilibrium heme stereochemistry. The relaxed and unrelaxed stereochemistries of a ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharonov YuA,Pismensky VF,Yarmola EG

更新日期：1989-08-01 00:00:00

abstract：:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A → G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin → duplex equilibrium corresponding to A → B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K....

journal_title：Journal of biomolecular structure & dynamics

authors： Kaushik M,Kukreti S

更新日期：2015-01-01 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：:Drug re-purposing might be a fast and efficient way of drug development against the novel coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We applied a bioinformatics approach using molecular dynamics and docking to identify FDA-approved drugs that can be re-purposed to ...

journal_title：Journal of biomolecular structure & dynamics

authors： Chandel V,Sharma PP,Raj S,Choudhari R,Rathi B,Kumar D

更新日期：2020-08-24 00:00:00

abstract：:The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhavnani V,Kaviraj S,Panigrahi P,Suresh CG,Yapara S,Pal J

更新日期：2018-08-01 00:00:00

abstract：:Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell-wall thickening. sHSP16.3 is also a promising candidate for vaccine, ser...

journal_title：Journal of biomolecular structure & dynamics

authors： Jee B,Kumar S,Yadav R,Singh Y,Kumar A,Sharma N

更新日期：2018-10-01 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：:Peptide- and protein-protein dockings were carried out on β2-adrenergic receptor (β2AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two β2AR monomers, thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially, a porti...

journal_title：Journal of biomolecular structure & dynamics

authors： Koroglu A,Akten ED

更新日期：2015-01-01 00:00:00

abstract：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Efimov AV

更新日期：2020-02-01 00:00:00

abstract：:The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1...

journal_title：Journal of biomolecular structure & dynamics

authors： Golovanov EuI,Kalambet YuA,Auezova LJ,Alexandrov AA

更新日期：1986-06-01 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：:A number of tandemly repeated DNA sequences have the ability to form hairpin structures by forming non-standard base pairs. When (GCC)15 and (GGC)15 strands are annealed together, the expected duplex is the only product. However, when (GCC)15 is annealed with (GCC)10, depending on the relative concentrations, up to fi...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao Y,Cheng W,Gibb CL,Gupta G,Kallenbach NR

更新日期：1996-10-01 00:00:00

abstract：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Huertas D,Lipps H,Azorín F

更新日期：1994-08-01 00:00:00

abstract：:The drug design and discovery of lipid modulators is very demanding as no new molecule has entered into the market in the last 35 years. Cholesteryl ester transfer protein (CETP) is a promising target as lipid modulators. Inhibition of the CETP enzyme reduces the risk of cardiovascular events. The first CETP inhibitor...

journal_title：Journal of biomolecular structure & dynamics

authors： Amin SA,Adhikari N,Gayen S,Jha T

更新日期：2019-10-01 00:00:00

abstract：:Polar mutations in transmembrane alpha helices may alter the structural details of the hydrophobic sequences and control intermolecular contacts. We have performed molecular dynamics simulations on the transmembrane domain of the proto-oncogenic and the oncogenic forms of the Neu receptor in a fluid DMPC bilayer to te...

journal_title：Journal of biomolecular structure & dynamics

authors： Samna Soumana O,Aller P,Garnier N,Genest M

更新日期：2005-08-01 00:00:00

abstract：:Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of ...

journal_title：Journal of biomolecular structure & dynamics

authors： Murphy MA,Mun S,Horstemeyer MF,Baskes MI,Bakhtiary A,LaPlaca MC,Gwaltney SR,Williams LN,Prabhu RK

更新日期：2019-03-01 00:00:00

abstract：:The aim of this study was to attempt to determine the extent to which the chemical shifts of the nonexchangeable base protons of a DNA helix depend upon the base sequence. We measured the proton NMR spectra of twelve decadeoxynucleotides in order to carry out a "statistical" treatment. In the helices, the chemical shi...

journal_title：Journal of biomolecular structure & dynamics

authors： Shindo H,Okhubo S,Matsumoto U,Giessner-Prettre C,Zon G

更新日期：1988-02-01 00:00:00

abstract：:Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

journal_title：Journal of biomolecular structure & dynamics

authors： Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

更新日期：2020-11-02 00:00:00

abstract：:Interaction of levocabastine with human serum albumin (HSA) is investigated by applying fluorescence spectroscopy, circular dichroism spectroscopy and molecular docking methods. Levocabastine is an important drug in treatment of allergy and currently a target drug for drug repurposing to treat other diseases like vern...

journal_title：Journal of biomolecular structure & dynamics

authors： Almutairi FM,Ajmal MR,Siddiqi MK,Majid N,Al-Alawy AIA,Abdelhameed AS,Khan RH

更新日期：2020-04-20 00:00:00

abstract：:2019 - Novel Coronavirus (2019-nCOV), enclosed large genome positive-sense RNA virus characterized by crown-like spikes that protrude from their surface, and have a distinctive replication strategy. The 2019-nCOV belongs to the Coronaviridae family, principally consists of virulent pathogens showing zoonotic property,...

journal_title：Journal of biomolecular structure & dynamics

authors： Naik VR,Munikumar M,Ramakrishna U,Srujana M,Goudar G,Naresh P,Kumar BN,Hemalatha R

更新日期：2020-06-22 00:00:00

abstract：:The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can...

journal_title：Journal of biomolecular structure & dynamics

authors： Nikolaev VA,Grokhovsky SL,Surovaya AN,Leinsoo TA,Sidorova NYu,Zasedatelev AS,Zhuze AL,Strahan GA,Shafer RH,Gursky GV

更新日期：1996-08-01 00:00:00

abstract：:The availability of a significant number of the structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing structures solved from all the known superfamilies. We have describe...

journal_title：Journal of biomolecular structure & dynamics

authors： Jha AN,Vishveshwara S

更新日期：2009-06-01 00:00:00

abstract：:An investigation of the self-association behavior of 2'-deoxy[5'-phosphate-guanylyl-(3'-5')-guanosine] (d(pGpG)) in the presence of Na+ and K+ ions has been carried out by 1H and 31P NMR and FTIR spectroscopy. A comparison has been made of the self- association behavior of d(pGpG) with that of the related dinucleotide...

journal_title：Journal of biomolecular structure & dynamics

authors： Kawasaki MM,Walmsley JA

更新日期：1999-12-01 00:00:00

abstract：:NAD(P)H: quinone oxidoreductase 1 (NQO1) inhibitors are proved as promising therapeutic agents against cancer. This study is to determine potent NAD(P)H-dependent NQO1 inhibitors with new scaffold. Pharmacophore-based three-dimensional (3D) QSAR model has been built based on 45 NQO1 inhibitors reported in the literatu...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvakumar R,Anantha Krishnan D,Ramakrishnan C,Velmurugan D,Gunasekaran K

更新日期：2020-02-01 00:00:00

abstract：:Two 4-ns molecular dynamics simulations of calcium loaded calmodulin in solution have been performed, using both standard nonbonded cutoffs and Ewald summation to treat electrostatic interactions. Our simulation results are generally consistent with solution experimental studies of calmodulin structure and dynamics, i...

journal_title：Journal of biomolecular structure & dynamics

authors： Yang C,Jas GS,Kuczera K

更新日期：2001-10-01 00:00:00