An insight to the dynamics of conserved water molecular triad in IMPDH II (human): recognition of cofactor and substrate to catalytic Arg 322.

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

journal_title：Journal of biomolecular structure & dynamics

authors： Kovalchuk MV,Boikova AS,Dyakova YA,Ilina KB,Konarev PV,Kryukova AE,Marchenkova MA,Pisarevsky YV,Timofeev VI

更新日期：2019-08-01 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：:Molecular modeling studies have been carried out to investigate the interactions between substrate sialyloligosaccharide (SOS) fragments bearing different glycosidic linkages and influenza virus N9 neuraminidase, a surface glycoprotein of influenza virus subtype N9. The studies revealed that the allowed orientation fo...

journal_title：Journal of biomolecular structure & dynamics

authors： Veluraja K,Suresh MX,Christlet TH,Rafi ZA

更新日期：2001-08-01 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：:Identification of new potential inhibitors against Hedgehog pathway activator protein Smoothened (SMO) is considered to be of higher importance to improvise the future cancer therapeutics. Different SMO inhibitors/drugs (e.g. Cyclopamine, Vismodegib, Taladegib) used till date are found to be associated with several dr...

journal_title：Journal of biomolecular structure & dynamics

authors： Sinha N,Chowdhury S,Sarkar RR

更新日期：2018-08-01 00:00:00

abstract：:Most β-Glucosidase (B8CYA8) are prone to inhibition by glucose. Experimentally observed specific activity of B8CYA8 on 20 mM, 50 mM, and 100 mM p-nitrophenyl-β-D-glucopyranoside (pNPGlc) substrate concentrations show surprise dependence on the presence of 0-3 M glucose at 335 K. We found that at high substrate concent...

journal_title：Journal of biomolecular structure & dynamics

authors： Konar S,Sinha SK,Datta S,Ghorai PK

更新日期：2020-07-28 00:00:00

abstract：:Room temperature mid-infrared experiments between 500 and 1800 cm(-1) have been performed on crystalline deoxyadenosine as a function of pressure up to about 10 GPa. Discontinuities observed near 2 and 4 GPa indicate that two separate phase transitions occur at these pressures. Changes in the spectra suggest that both...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee SA,Lettress L,Anderson A

更新日期：2007-06-01 00:00:00

abstract：:The preferred conformation of orexin-B, an orphan G-protein coupled receptor agonist (the human sequence is RSGPPGLQGRLQRLLQASGNHAAGILTM-NH(2)) has been determined by (1)H and (13)C 2D NMR spectroscopy and molecular modeling. Orexin-B has been implicated in sleep-wakefulness and feeding regulation. The membrane mimeti...

journal_title：Journal of biomolecular structure & dynamics

authors： Miskolzie M,Lucyk S,Kotovych G

更新日期：2003-12-01 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：: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：:Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked ...

journal_title：Journal of biomolecular structure & dynamics

authors： van Buuren BN,Schleucher J,Wijmenga SS

更新日期：2000-01-01 00:00:00

abstract：:Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distributio...

journal_title：Journal of biomolecular structure & dynamics

authors： Beveridge DL,Maye PV,Jayaram B,Ravishanker G,Mezei M

更新日期：1984-10-01 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：:Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosid...

journal_title：Journal of biomolecular structure & dynamics

authors： Mondragon-Sanchez JA,Liquier J,Shafer RH,Taillandier E

更新日期：2004-12-01 00:00:00

abstract：:The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial di...

journal_title：Journal of biomolecular structure & dynamics

authors： Uberbacher EC,Bunick GJ

更新日期：1989-08-01 00:00:00

abstract：:The interaction of 6-Thioguanine molecule, an antitumor drug with carbon nanotube and boron nitride nanotube (BNNT) is investigated using molecular dynamics simulations. Based on the obtained results, the strongest negative van der Waals interaction is found between 6-TG and BNNT among the studied nanotubes, which ind...

journal_title：Journal of biomolecular structure & dynamics

authors： Hasanzade Z,Raissi H

更新日期：2020-02-01 00:00:00

abstract：:A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Treatment efforts have been severely impeded due to the lack of specific effective antiviral drugs for the treatment of COVID-associated pathologies. In the pre...

journal_title：Journal of biomolecular structure & dynamics

authors： Naidoo D,Roy A,Kar P,Mutanda T,Anandraj A

更新日期：2020-07-21 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

abstract：:Identifying and predicting the structural characteristics of novel repeats throughout the genome can lend insight into biological function. Specific repeats are believed to have biological significance as a function of their distribution patterns. We have developed 'GenomeMark,' a computer program that detects and sta...

journal_title：Journal of biomolecular structure & dynamics

authors： Fadiel A,Eichenbaum KD,Hamza A

更新日期：2006-02-01 00:00:00

abstract：:We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: d(ATGCAT)2 complex. A comparison of NOE measurements and 1/R6 weighted proton-proton distances confirm the general correctness of the Actinomycin D-DNA model proposed by Sobell. There are, howeve...

journal_title：Journal of biomolecular structure & dynamics

authors： Creighton S,Rudolph B,Lybrand T,Singh UC,Shafer R,Brown S,Kollman P,Case DA,Andrea T

更新日期：1989-04-01 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：:The conformation of a complex of a 41 mer/31 mer DNA fragment and the Klenow fragment of DNA polymerase I of Escherichia coli was studied by scanning tunnelling microscopy (STM). The results shows that near two turns of double helix of this DNA fragment was outside of enzyme while another part containing more than one...

journal_title：Journal of biomolecular structure & dynamics

authors： Lu CD,Li MQ,Qui MY,Yao XW,Xu YL,Gu MM,Hu J

更新日期：1991-10-01 00:00:00

abstract：:The molecular electrostatic potential (MEP) and the molecular electrostatic field (MEF) are associated with significantly different patterns of distribution in the nucleic acids and their constituents. In particular, a) while the values of the minimal potentials at the reactive sites of the bases or at the phosphates ...

journal_title：Journal of biomolecular structure & dynamics

authors： Pullman B

更新日期：1983-12-01 00:00:00

abstract：:The effect of spermine binding on the electrostatic potential of DNA is evaluated. The calculations are performed for the essential reactive sites, atoms N7 and O6 of guanine, N3 and N7 of adenine, of the nucleic acid and for its surface envelope. An important weakening of the potential is found affecting all the impo...

journal_title：Journal of biomolecular structure & dynamics

authors： Zakrzewska K,Pullman B

更新日期：1985-12-01 00:00:00

abstract：:The insertion of viral DNA into the host chromosome is an essential step in the replication of HIV-1, and is carried out by an enzyme, HIV-1 integrase (IN). Since the latter has no human cellular counterpart, it is an attractive target for antiviral drug design. Several IN inhibitors having activities in the micromola...

journal_title：Journal of biomolecular structure & dynamics

authors： Rao GS,Bhatnagar S,Ahuja V

更新日期：2002-08-01 00:00:00

abstract：:The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24...

journal_title：Journal of biomolecular structure & dynamics

authors： Andrianov AM

更新日期：1999-02-01 00:00:00

abstract：:Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled...

journal_title：Journal of biomolecular structure & dynamics

authors： Rather MA,Dutta S,Guttula PK,Dhandare BC,Yusufzai SI,Zafar MI

更新日期：2020-05-01 00:00:00

abstract：:Thorough quantitative study of nucleosome repeat length (NRL) distributions, conducted in 1992 by J. Widom, resulted in a striking observation that the linker lengths between the nucleosomes are quantized. Comparison of the NRL average values with the MNase cut distances predicted from the hypothetical columnar struct...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2016-06-01 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