Abstract：
:The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were considered for conformational energy minimization process and scrutinized with reference to properties, such as base-stacking, hydrogen-bonding, internal flexibility and base sequence-phosphate influence. The P-O bond torsions and the phosphate groups were treated with special attention. The results reveal a number of preferred conformational states other than the known helical forms, such as, A-, B-, C-, Z-, and Watson-Crick conformation. Many interesting one-step (change in only one of the dihedral angles or sugar puckers) conformational transitions which involve just about a kcal/mol of energy came to light. The two base sequences CG and GC were noted to differ strikingly in many of their conformational characteristics.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Ponnuswamy PK,Anukanth Adoi
10.1080/07391102.1989.10507737subject
Has Abstractpub_date
1989-02-01 00:00:00pages
781-800issue
4eissn
0739-1102issn
1538-0254journal_volume
6pub_type
杂志文章abstract：:Pebrine is a microsporidian disease caused by Nosema bombycis in Bombyx mori (silk worm) which results in brown/black spots. The affected larvae either spin cocoons which are flimsy with low silk content or not spin a cocoon. It has been hypothesised that Serine Protease Inhibitor 106 (SPN106) is responsible for evasi...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2019.1696704
更新日期：2020-10-01 00:00:00
abstract：:A general method for generation of base-pairs in a curved DNA structure, for any prescribed values of helical parameters--unit rise (h), unit twist (theta), wedge roll (theta R) and wedge tilt (theta T), propeller twist (theta p) and displacement (D) is described. Its application for generation of uniform as well curv...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1988.10506484
更新日期：1988-08-01 00:00:00
abstract：:About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2015.1080629
更新日期：2016-07-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2020.1765872
更新日期：2020-05-25 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
pub_type： 杂志文章
doi：10.1080/07391102.2019.1585951
更新日期：2020-02-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2020.1800513
更新日期：2020-07-31 00:00:00
abstract：:In this work, we integrate a non-linear signal analysis method, recurrence quantification analysis (RQA), with the well-known machine-learning algorithm, support vector machines for the binary classification of protein sequences. Two different classification problems were selected, discriminating between aggregating a...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2007.10507177
更新日期：2007-12-01 00:00:00
abstract：:Poly(dA-dT).poly(dA-dT) can adopt the B- and D- forms in the fibrous state. Theoretical energy calculations and fiber diffraction analyses suggest that there can be three structural models of poly(dA-dT).poly(dA-dT) in each of these two forms viz right and left-handed Watson Crick models and left-handed Hoogsteen--a t...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1983.10507450
更新日期：1983-10-01 00:00:00
abstract：:Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen bonded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To ch...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1998.10508266
更新日期：1998-12-01 00:00:00
abstract：:Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have n...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1798812
更新日期：2020-07-27 00:00:00
abstract：:We determined the binding sites of curcumin (cur), resveratrol (res), and genistein (gen) with milk β-lactoglobulin (β-LG) at physiological conditions. Fourier transform infrared spectroscopy, circular dichroism, and fluorescence spectroscopic methods as well as molecular modeling were used to determine the binding of...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2012.742461
更新日期：2013-12-01 00:00:00
abstract：:Osmium tetroxide complexes with nitrogen ligands (Os,L) have been widely used as probes of the DNA structure. A monoclonal antibody OsBP7H8 against DNA adducts with Os,L was produced in mice. OsBP7H8 does not bind to proteins or total yeast RNA modified with Os,2,2'-bipyridine (bipy) nor to the unmodified nucleic acid...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1999.10508339
更新日期：1999-08-01 00:00:00
abstract：:The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechan...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2015.1077737
更新日期：2015-01-01 00:00:00
abstract：:Fpg protein (formamidopyrimidine or 8-oxoguanine DNA glycosylase) from E. coli catalyzes excision of several damaged purine bases, including 8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine from DNA. In this study the interaction of E. coli Fpg with various specific and nonspecific oligodeoxynucleo...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1999.10508363
更新日期：1999-10-01 00:00:00
abstract：:The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar virus, SA...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1813202
更新日期：2020-09-02 00:00:00
abstract：:Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conform...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2015.1123190
更新日期：2016-11-01 00:00:00
abstract：:The reproducibility of melting curves for repeated hybridizations of target DNA with generic oligonucleotide microchips is shown experimentally to depend on the character of matching between fragments of target DNA and immobilized oligonucleotides. The reproducibility of melting curves is higher for the perfect match ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2001.10506709
更新日期：2001-06-01 00:00:00
abstract：:The hexachlorocyclotriphosphaze compound (N3P3Cl6, HCCP) was reacted with excess (E)-(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-ones (2-11) to produce hexakis[(1-(4-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes (CP 2-11). The structures of products (CP 2-11) were confirmed using eleme...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1846621
更新日期：2020-11-19 00:00:00
abstract：:Triplex and duplex formation of two deoxyribohexadecamers d-A-(G-A)-G (a) and d-C-(T-C)-T (b) have been studied by UV, CD, fluorescence, and proton NMR spectroscopy. Optical studies of a and b at dilute concentrations (microM range) yielded results similar to those seen for polymers of the same sequence, indicating th...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1991.10507857
更新日期：1991-04-01 00:00:00
abstract：:Complexes of NaDNA with the bipyridyl-(ethylenediamine)platintum(II) (abbreviated [(bipy)Pt(en)]2+) molecular ion have been studied in solution via ultraviolet absorption experiments at 260 nm between 50 and 90 degrees C. These measurements, performed as a function of the molar ratio of the [(bipy)Pt(en)]2+ complex to...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2008.10507227
更新日期：2008-08-01 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
pub_type： 杂志文章
doi：10.1080/07391102.1992.10507972
更新日期：1992-04-01 00:00:00
abstract：:Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buc...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2005.10507018
更新日期：2005-02-01 00:00:00
abstract：:Erectile dysfunction (ED) is a sexual disorder mainly caused by decrease in cellular concentration of cyclic guanosine monophosphate (cGMP), which is degraded by phosphodiesterase type-5 (PDE-5). As a potent therapeutic target, inhibitors such as Viagra , Cialis, and Levitra have already been developed to target PDE-5...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2010.10508577
更新日期：2010-04-01 00:00:00
abstract：:A series of novel carbazole based α-aminophosphonate derivatives were synthesized under solvent-free condition, characterized and evaluated for their cholinesterase inhibition, enzyme kinetic inhibition, in-vitro cell viability using N2a cells, neuroprotective studies against H2O2-induced stress using N2a cells and an...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1861981
更新日期：2020-12-21 00:00:00
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
pub_type： 杂志文章
doi：10.1080/07391102.1993.10508711
更新日期：1993-08-01 00:00:00
abstract：:It is well known that the biological activity of gallated proanthocyanidins (PAs) is highly structure-dependent. Polymerization degree (DP) and linkage types affect their biological activity greatly. Positions and orientations of gallated PAs in lipid bilayer reveal their structure-function activity at the molecular l...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2017.1369163
更新日期：2018-08-01 00:00:00
abstract：:The flavivirus membrane fusion is triggered by the acid pH of the endosomes after virus endocytosis. The proposed mechanism involves changes in the protonation state of conserved histidine residues of the E protein present in the viral surface that undergoes a series of structural rearrangements that result in the fus...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2013.827132
更新日期：2014-01-01 00:00:00
abstract：:We previously reported on a mutant lipase KV1 (Mut-LipKV1) from Acinetobacter haemolyticus which optimal pH was raised from 8.0 to 11.0 after triple substitutions of surface aspartic acid (Asp) with lysine (Lys). Herein, this study further examined the Mut-LipKV1 by molecular docking, molecular dynamics (MD) simulatio...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1743364
更新日期：2020-03-23 00:00:00
abstract：:A simple relation exists between the packing density in crystals of short A-DNA duplexes and their global double-helical structure. The volume per nucleotide pair shows a linear inverse correlation with the mean displacement of base pairs from the best straight helix axis. The mean displacement is a measure of major g...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1991.10507846
更新日期：1991-02-01 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
pub_type： 杂志文章
doi：10.1080/07391102.1995.10508797
更新日期：1995-04-01 00:00:00
