Selective binding of synthetic polypeptides to DNA of varying composition and sequence: effect of minor groove binding drugs.

abstract：:Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and ca...

journal_title：Journal of biomolecular structure & dynamics

authors： Varughese JF,Chalovich JM,Li Y

更新日期：2010-10-01 00:00:00

abstract：:A useful property of DMSO solvent has been exploited to reveal a new catalytic route for cytidine amino proton exchange, relevant to exchange in the macromolecular state, but hidden in aqueous solution. Additional exchange mechanisms in aqueous monomeric cytidine (and adenosine) are obscured by the formation of a fast...

journal_title：Journal of biomolecular structure & dynamics

authors： McConnell B

更新日期：1986-12-01 00:00:00

abstract：:The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities...

journal_title：Journal of biomolecular structure & dynamics

authors： Haniford DB,Pulleyblank DE

更新日期：1983-12-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Anish Babu A,Karthick K,Subramanian R,Swarnalatha K

更新日期：2020-08-01 00:00:00

abstract：:The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mech...

journal_title：Journal of biomolecular structure & dynamics

authors： Tian H,Tao P

更新日期：2020-08-04 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

authors： Kan LS,Callahan DE,Trapane TL,Miller PS,Ts'o PO,Huang DH

更新日期：1991-04-01 00:00:00

abstract：:The 1H NMR relaxation effects produced by paramagnetic Cr(III) complexes on nucleoside 5'-mono- and -triphosphates in D2O solution at pH' = 3 were measured. The paramagnetic probes were [Cr(III)(H2O)6]3+, [Cr(III)(H2O)3(HATP)], [Cr(III)(H2O)3(HCTP)] and [Cr(III)(H2O)3(UTP)-, while the matrix nucleotides (0.1 M) were H...

journal_title：Journal of biomolecular structure & dynamics

authors： Cini R,Giorgi G,Laschi F,Rossi C,Marzilli LG

更新日期：1990-02-01 00:00:00

abstract：:With the explosive growth of protein sequences entering into protein data banks in the post-genomic era, it is highly demanded to develop automated methods for rapidly and effectively identifying the protein-protein binding sites (PPBSs) based on the sequence information alone. To address this problem, we proposed a p...

journal_title：Journal of biomolecular structure & dynamics

authors： Jia J,Liu Z,Xiao X,Liu B,Chou KC

更新日期：2016-09-01 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

authors： Heinemann U

更新日期：1991-02-01 00:00:00

abstract：:The EPR study of spin labeled macromolecules has provided insight into structural and dynamical properties of DNA, proteins, and related systems. While spin labeling has been useful, it is experimentally difficult to determine if the spin label significantly alters the conformation of the macromolecule to which it is ...

journal_title：Journal of biomolecular structure & dynamics

authors： Darian E,Gannett PM

更新日期：2005-04-01 00:00:00

abstract：:The SHOM method (Sequencing by Hybridization with Oligonucleotide Matrix) developed in 1988 is a new approach to nucleic acid sequencing by hybridization to an oligonucleotide matrix composed of an array of immobilized oligonucleotides. The original matrix proposed for sequencing by SHOM had to contain at least 65,536...

journal_title：Journal of biomolecular structure & dynamics

authors： Pevzner PA,Lysov YuP,Khrapko KR,Belyavsky AV,Florentiev VL,Mirzabekov AD

更新日期：1991-10-01 00:00:00

abstract：:A recent research has identified chymase, a mast cell-specific protease as an exclusive novel therapeutic target to prevent Japanese encephalitis virus (JEV) induced encephalitis. Interestingly, JEV activates mast cell specific chymase during its penetration through blood brain barrier (BBB) which eventually guide to ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kant K,Rawat R,Bhati V,Bhosale S,Sharma D,Banerjee S,Kumar A

更新日期：2020-02-18 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

authors： Anuar NFSK,Wahab RA,Huyop F,Amran SI,Hamid AAA,Halim KBA,Hood MHM

更新日期：2020-03-23 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：:Flavonoids correspond to a major class of polyphenolic phytochemicals with flavone as major parent scaffold. This class of compounds is attributed with very rich nutritional as well as therapeutic values. The present study focuses on a panel of 16 flavonoid molecules that are demonstrated to exhibit various bioactivit...

journal_title：Journal of biomolecular structure & dynamics

authors： Meshram RJ,Bagul KT,Pawnikar SP,Barage SH,Kolte BS,Gacche RN

更新日期：2020-03-01 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 functional aspect of several mycobacterium proteins annotated as hypothetical are yet to be discovered. In the present investigation, in silico approaches were used to predict the biological function of some of the unknown Mtb proteins, which were further validated by wet lab experiments. After screening thousands...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar A,Sharma A,Kaur G,Makkar P,Kaur J

更新日期：2017-05-01 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：: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：:A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-...

journal_title：Journal of biomolecular structure & dynamics

authors： Monaco RR

更新日期：2007-10-01 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：:Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

journal_title：Journal of biomolecular structure & dynamics

authors： Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

更新日期：1994-08-01 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：:COVID-19 is a novel severe acute respiratory syndrome coronavirus. Currently, there is no effective treatment and vaccines seem to be the solution in the future. Virtual screening of potential drugs against the S protein of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has provided small molecular comp...

journal_title：Journal of biomolecular structure & dynamics

authors： Yepes-Pérez AF,Herrera-Calderon O,Quintero-Saumeth J

更新日期：2020-10-29 00:00:00

abstract：:The conjugation of trypsin (try) and trypsin inhibitor (tryi) with poly(ethylene glycol) (PEG) and methoxypoly(ethylene glycol) anthracene (mPEG-anthracene) was investigated in aqueous solution, using multiple spectroscopic methods, thermodynamic analysis, and molecular modeling. Thermodynamic parameters ΔS, ΔH, and Δ...

journal_title：Journal of biomolecular structure & dynamics

authors： Chanphai P,Agudelo D,Tajmir-Riahi HA

更新日期：2017-08-01 00:00:00

abstract：:Trichoderma spp. are well-known bioagents for the plant growth promotion and pathogen suppression. The beneficial activities of the fungus Trichoderma spp. are attributed to their ability to produce and secrete certain secondary metabolites such as trichodermin that belongs to trichothecene family of molecules. The in...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumari I,Chaudhary N,Sandhu P,Ahmed M,Akhter Y

更新日期：2016-06-01 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

authors： Gupta G,Sarma MH,Dhingra MM,Sarma RH,Rajagopalan M,Sasisekharan V

更新日期：1983-10-01 00:00:00

abstract：:Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium...

journal_title：Journal of biomolecular structure & dynamics

authors： Desai PV,Avery MA

更新日期：2004-06-01 00:00:00

abstract：:The interaction of meso-tetra-(4N-oxyethylpyridyl)porphyrin (TOEPyP4) and its Zn(II)-, Cu(II)-, Mn(III)-derivatives with tRNA from E.Coli at low ionic strength (micro=0.02M) was studied using UV/Vis spectrophotometry and Circular Dichroism (CD) methods. An unusual Induced Circular Dichroism (ICD) spectra profile of th...

journal_title：Journal of biomolecular structure & dynamics

authors： Dalyan Y,Vardanyan I,Chavushyan A,Balayan G

更新日期：2010-08-01 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

authors： Kanakis CD,Tarantilis PA,Polissiou MG,Tajmir-Riahi HA

更新日期：2013-12-01 00:00:00