Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study.

abstract：:The interaction of calf-thymus DNA with cobalt-hexammine and cobalt-pentammine cations was investigated, in aqueous solution at pH 6-7 with cation/DNA(phosphate) molar ratios r = 1/80, 1/40, 1/20, 1/10, 1/4, 1/2 and 1, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between spectral chang...

journal_title：Journal of biomolecular structure & dynamics

authors： Tajmir-Riahi HA,Naoui M,Ahmad R

更新日期：1993-08-01 00:00:00

abstract：:The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentati...

journal_title：Journal of biomolecular structure & dynamics

authors： Frenkel ZM,Trifonov EN

更新日期：2005-06-01 00:00:00

abstract：:In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, s...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu HL,Wu YC,Zhao JH,Fang HW,Ho Y

更新日期：2006-12-01 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：: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：: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：:Frequently discussed analogy between genetic and human texts is explored by comparison of alternation of polar and non-polar amino-acid residues in proteins and alternation of consonants and vowels in human texts. In human languages, the usage of possible combinations of consonants and vowels is influenced by pronounc...

journal_title：Journal of biomolecular structure & dynamics

authors： Zemková M,Trifonov EN,Zahradník D

更新日期：2014-01-01 00:00:00

abstract：:1, 4 and 5, 8-Positions as well as type of functionalities on these positions at anthraquinone-9, 10-dione are proposed to be significant for anticancer activity. Therefore, keeping this into consideration, a series of 1-substituted anthraquinone-based compounds are designed, synthesized, characterized and biologicall...

journal_title：Journal of biomolecular structure & dynamics

authors： Awasthi P,Vatsal M,Sharma A

更新日期：2019-10-01 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：:Earlier identified strongest nucleosome DNA sequences of A. thaliana, those with visible 10-11 base sequence periodicity, are mapped along chromosomes. Resulting positional distributions reveal distinct maxima, one per chromosome, located in the centromere regions. Sequence-directed nucleosome mapping demonstrates tha...

journal_title：Journal of biomolecular structure & dynamics

authors： Salih B,Trifonov EN

更新日期：2015-01-01 00:00:00

abstract：:In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...

journal_title：Journal of biomolecular structure & dynamics

authors： Sepehri N,Mohammadi-Khanaposhtani M,Asemanipoor N,Hosseini S,Biglar M,Larijani B,Mahdavi M,Hamedifar H,Taslimi P,Sadeghian N,Norizadehtazehkand M,Gulcin I

更新日期：2020-11-23 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：:Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...

journal_title：Journal of biomolecular structure & dynamics

authors： Borkar A,Rout MK,Hosur RV

更新日期：2012-01-01 00:00:00

abstract：:The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting p...

journal_title：Journal of biomolecular structure & dynamics

authors： Stellwagen NC,Stellwagen D

更新日期：1990-12-01 00:00:00

abstract：:Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th ...

journal_title：Journal of biomolecular structure & dynamics

authors： Majumder R,Roy S,Thakur AR

更新日期：2012-01-01 00:00:00

abstract：:Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...

journal_title：Journal of biomolecular structure & dynamics

authors： Dai H,McFarland EW

更新日期：1996-04-01 00:00:00

abstract：:Different kinds of secondary metabolites present in the medicinal plants play an important role to alleviate different human ailments including neurodegenerative disorders such as Parkinson's, Alzheimer's, epilepsy and schizophrenia etc. Recently we have isolated and characterized a novel bioactive compound viz. 3-(3,...

journal_title：Journal of biomolecular structure & dynamics

authors： Venkataramaiah C,Lakshmi Priya B,Rajendra W

更新日期：2020-05-18 00:00:00

abstract：:Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

journal_title：Journal of biomolecular structure & dynamics

authors： Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

更新日期：2020-07-31 00:00:00

abstract：:Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

journal_title：Journal of biomolecular structure & dynamics

authors： Kashyap K,Kakkar R

更新日期：2020-01-01 00:00:00

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：:Abstract Although the recent structural studies on polymerases have brought new insights on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots for polymerase slippage shows that, in the B- form, these sequences share common str...

journal_title：Journal of biomolecular structure & dynamics

authors： Timsit Y

更新日期：2000-01-01 00:00:00

abstract：:Geometries and interaction energies of unusual UU and AA base pairs with one standard hydrogen bond (H-bond) and additional C-H...O or C-H...N contacts have been determined by quantum-chemical methods taking into account electron correlation. Whereas the C-H bond length in the UU C-H...O contact increases upon complex...

journal_title：Journal of biomolecular structure & dynamics

authors： Brandl M,Meyer M,Sühnel J

更新日期：2001-02-01 00:00:00

abstract：:Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed...

journal_title：Journal of biomolecular structure & dynamics

authors： Etchebest C,Pullman A

更新日期：1985-02-01 00:00:00

abstract：:PPARα and PPARγ play important roles in regulating glucose and lipid metabolism. In recent years, the development of dual PPAR agonists has become a hot topic in the field of anti-diabetic medicinal chemistry. The dual PPARα/γ agonists can both improve metabolism and reduce side effects caused by single drugs, and has...

journal_title：Journal of biomolecular structure & dynamics

authors： Feng XY,Ding TT,Liu YY,Xu WR,Cheng XC

更新日期：2020-04-01 00:00:00

abstract：:Three dimensional models of NB-ARC domains in five different proteins were constructed based on the recently published crystal structure of the apoptotic protease activating factor 1, of which two are for tomato species, one each for flax, Arabidopsis, and nematode. Standard multiple sequence alignment was performed f...

journal_title：Journal of biomolecular structure & dynamics

authors： Chattopadhyaya R,Pal A

更新日期：2008-02-01 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：:We studied the influence of different 2'-OMe-RNA and DNA strand combinations on single strand targeted foldback triplex formation in the Py.Pu:Py motif using ultraviolet (UV) and circular dichroism (CD) spectroscopy, and molecular modeling. The study of eight combinations of triplexes (D.D:D, R*.D:D, D.D:R*, R*.D:R*, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kandimalla ER,Venkataraman G,Sasisekharan V,Agrawal S

更新日期：1997-06-01 00:00:00

abstract：:Microtubule affinity regulating kinase 4 (MARK4) plays essential role in the tau-assisted regulation of microtubule dynamics. Over expression of MARK4 causes early phosphorylation of Ser262 of tau protein which is essential for microtubule binding. Hyperphosphorylation of tau protein causes the formation of paired hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Naqvi AAT,Jairajpuri DS,Noman OMA,Hussain A,Islam A,Ahmad F,Alajmi MF,Hassan MI

更新日期：2020-08-01 00:00:00

abstract：:The interaction between two proton pump inhibitors viz., omeprazole (OME) and esomeprazole (EPZ) with human serum albumin (HSA) was studied by fluorescence, absorption, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), voltammetry, and molecular modeling approaches. The Stern-Volmer quenching c...

journal_title：Journal of biomolecular structure & dynamics

authors： Pawar SK,Punith R,Naik RS,Seetharamappa J

更新日期：2017-11-01 00:00:00

abstract：:The hydration properties of the non-palindromic duplex d(CTACTGCTTTAG). d(CTAAAGCAGTAG) were investigated by NMR spectroscopy. The oligonucleotide possesses a heterogeneous B-DNA structure. The H2(n)-H1'(m+1) distances reflect a minor groove narrowing within the TTT/AAA segment (approximately 3.9A) and a sudden wideni...

journal_title：Journal of biomolecular structure & dynamics

authors： Leporc S,Mauffret O,El Antri S,Convert O,Lescot E,Tevanian G,Fermandjian S

更新日期：1998-12-01 00:00:00