Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

abstract：:We performed molecular dynamics simulations for various oligomers with different beta-sheet conformations consisting of alpha-Synuclein 71-82 residues using an all atom force field and explicit water model. Tetramers of antiparallel beta-sheet are shown to be stable, whereas parallel sheets are highly unstable due to ...

journal_title：Journal of biomolecular structure & dynamics

authors： Yoon J,Jang S,Lee K,Shin S

更新日期：2009-12-01 00:00:00

abstract：:An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are mor...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Leszczynski J,Vetterl V,Hobza P

更新日期：1996-02-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Khan S,Somvanshi P,Singh A,Khan M,Mandal RK,Dar SA,Wahid M,Jawed A,Mishra BN,Haque S

更新日期：2020-03-03 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

authors： Elmezayen AD,Yelekçi K

更新日期：2020-07-27 00:00:00

abstract：:A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy min...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Bhattacharyya D

更新日期：2013-01-01 00:00:00

abstract：:Human β-defensin-3 (HβD-3) is an endogenous antimicrobial peptide with potent and broad killing activity against various microorganisms, and thus, it is an attractive candidate for the development of novel peptide antibiotics, but its antimicrobial mechanism remains elusive. To characterize the mechanism, we used mult...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao X,Yu H,Yang L,Li Q,Huang X

更新日期：2015-01-01 00:00:00

abstract：:Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen L,Yang J,Huang T,Kong X,Lu L,Cai YD

更新日期：2016-01-01 00:00:00

abstract：:The hypothetical protection of genes from oxidative damage provided by the G-rich telomeric overhangs located at the end of chromosomes, which consist, in humans, of single strands of TTAGGG sequence repeats, is investigated here. First principle Moller-Plesset perturbation theory calculations reveal that the TTAGGG h...

journal_title：Journal of biomolecular structure & dynamics

authors： Cauët E

更新日期：2011-12-01 00:00:00

abstract：:We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Benedetti G,Morosetti S

更新日期：1991-04-01 00:00:00

abstract：:Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malar...

journal_title：Journal of biomolecular structure & dynamics

authors： Omotuyi IO,Hamada T

更新日期：2015-01-01 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：: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：:Heavy metal pollutants such as Cd, Hg, Pb, As, and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing t...

journal_title：Journal of biomolecular structure & dynamics

authors： Mahnam K,Foruzandeh S,Mirakhorli N,Saffar B

更新日期：2018-06-01 00:00:00

abstract：:To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure-activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity-descriptors relationship accuracy of 94% referred by regression coefficient (r2 = .9...

journal_title：Journal of biomolecular structure & dynamics

authors： Alam S,Khan F

更新日期：2018-07-01 00:00:00

abstract：:Acinetobacter baumannii, an important nosocomial pathogen, is increasingly becoming resistant to antibiotics including recent β-lactam like imipenem. Production of different types of β-lactamases is one of the major resistance mechanisms which bacteria adapt. We recently reported the presence of a β-lactamase, OXA-51,...

journal_title：Journal of biomolecular structure & dynamics

authors： Tiwari V,Moganty RR

更新日期：2014-01-01 00:00:00

abstract：:Drug resistant mutations have severely restricted the success of HIV therapy. These mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lastin...

journal_title：Journal of biomolecular structure & dynamics

authors： Purohit R,Rajendran V,Sethumadhavan R

更新日期：2011-08-01 00:00:00

abstract：:Seven new quinoline-based bioorganic compounds were prepared by solvent-free synthesis and characterized using spectral techniques. The binding of these compounds with human serum albumin (HSA) was investigated by multi-spectroscopic methods. The quenching of Trp fluorescence upon addition of these compounds to HSA co...

journal_title：Journal of biomolecular structure & dynamics

authors： Vennila KN,Elango KP

更新日期：2019-07-01 00:00:00

abstract：:P21-activated kinase 4 (PAK4) is a serine/threonine protein kinase, which is associated with many cancer diseases, and thus being considered as a potential drug target. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations wer...

journal_title：Journal of biomolecular structure & dynamics

authors： Gao Y,Wang H,Wang J,Cheng M

更新日期：2020-09-01 00:00:00

abstract：:The N-terminal receiver domain of NtrC is the molecular switch in the two-component signal transduction. It is the first protein where structures of both the active (phosphyroylated) and inactive (unphosphyroylated) states are determined experimentally. Phosphorylation of the NtrC at the active site induces large stru...

journal_title：Journal of biomolecular structure & dynamics

authors： Hu X,Wang Y

更新日期：2006-04-01 00:00:00

abstract：:Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of fre...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen C,Huang Y,Xiao Y

更新日期：2013-01-01 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：:Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...

journal_title：Journal of biomolecular structure & dynamics

authors： Malkhed V,Mustyala KK,Potlapally SR,Vuruputuri U

更新日期：2014-12-01 00:00:00

abstract：:Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear r...

journal_title：Journal of biomolecular structure & dynamics

authors： Pyshnyi DV,Goldberg EL,Ivanova EM

更新日期：2003-12-01 00:00:00

abstract：:The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of comple...

journal_title：Journal of biomolecular structure & dynamics

authors： Shamsi A,Ahmed A,Bano B

更新日期：2018-05-01 00:00:00

abstract：:Triple helices with G*G.C and A*A.T base triplets with third GA strands either parallel or antiparallel with respect to the homologous duplex strand have been formed in presence of Na (+) or Mg(2+) counterions. Antiparallel triplexes are more stable and can be obtained even in presence of only monovalent Na(+) counter...

journal_title：Journal of biomolecular structure & dynamics

authors： Liquier J,Geinguenaud F,Huynh-Dinh T,Gouyette C,Khomyakova E,Taillandier E

更新日期：2001-12-01 00:00:00

abstract：:Glycation and oxidation induce structural alterations in the proteins in an interdependent manner with consequent pathological implications. The published literature presents wide range of modifications in conformational characteristics of proteins by glycation and oxidation; however, there is little data that could e...

journal_title：Journal of biomolecular structure & dynamics

authors： Islam S,Moinuddin,Mir AR,Raghav A,Habib S,Alam K,Ali A

更新日期：2018-08-01 00:00:00

abstract：:Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...

journal_title：Journal of biomolecular structure & dynamics

authors： Wei Y,Yi Z,Xu J,Yang W,Yang L,Liu H

更新日期：2019-04-01 00:00:00

abstract：:Tau-tubulin kinase 1 inhibitors inhibit tau protein phosphorylation on Ser198, Ser199, Ser202, Ser422, and also in paired helical filaments. We developed receptor-based pharmacophore models by exploiting three TTBK1 protein structures, i.e., 4NFN, 4BTM, and 4BTK. The integrated e-pharmacophore based virtual screening ...

journal_title：Journal of biomolecular structure & dynamics

authors： Jana S,Singh SK

更新日期：2020-02-01 00:00:00

abstract：:In view of the low toxicity of NNRTIs in comparison to NRTIs, a new series of diarylpyrimidine derivatives has been designed as NNRTIs against HIV-1. In silico studies using DS 3.0 software have shown that these compounds behaved as NNRTIs while interacting at the allosteric site of HIV-RT. The designed compounds have...

journal_title：Journal of biomolecular structure & dynamics

authors： Singh VK,Srivastava R,Gupta PSS,Naaz F,Chaurasia H,Mishra R,Rana MK,Singh RK

更新日期：2020-04-11 00:00:00

abstract：:The studies on protein-dye interactions are important in biological process and it is regarded as vital step in rational drug design. The interaction of thionine (TH) with human serum albumin (HSA) was analyzed using isothermal titration calorimetry (ITC), spectroscopic, and molecular docking technique. The emission s...

journal_title：Journal of biomolecular structure & dynamics

authors： Manivel P,Paulpandi M,Murugan K,Benelli G,Ilanchelian M

更新日期：2017-11-01 00:00:00