Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity.

abstract：:β-lactoglobulin (β-LG) is a member of lipocalin superfamily of transporters for small hydrophobic molecules such as retinoids. We located the binding sites of retinol and retinoic acid on β-LG in aqueous solution at physiological conditions, using FTIR, CD, fluorescence spectroscopic methods, and molecular modeling. T...

journal_title：Journal of biomolecular structure & dynamics

authors： Belatik A,Kanakis CD,Hotchandani S,Tarantilis PA,Polissiou MG,Tajmir-Riahi HA

更新日期：2012-01-01 00:00:00

abstract：:Polar mutations in transmembrane alpha helices may alter the structural details of the hydrophobic sequences and control intermolecular contacts. We have performed molecular dynamics simulations on the transmembrane domain of the proto-oncogenic and the oncogenic forms of the Neu receptor in a fluid DMPC bilayer to te...

journal_title：Journal of biomolecular structure & dynamics

authors： Samna Soumana O,Aller P,Garnier N,Genest M

更新日期：2005-08-01 00:00:00

abstract：:The infrared absorption and 1H nuclear magnetic resonance analyses of chloroform solutions of the terminally-blocked segment corresponding to the 2-9 sequence of emerimicins III and IV, -(Aib)3-L-Val-Gly-L-Leu-(Aib)2-, are consistent with the presence of a 3(10)-helical structure of high thermal stability. The crystal...

journal_title：Journal of biomolecular structure & dynamics

authors： Toniolo C,Bonora GM,Bavoso A,Benedetti E,di Blasio B,Pavone V,Pedone C

更新日期：1985-12-01 00:00:00

abstract：:Tyrosinase plays an important role in melanin biosynthesis and protects skin against ultraviolet radiations. Functional deficiency of tyrosinase results in serious dermatological diseases. Tyrosinase also participates in neuromelanin formation in the human brain, which leads to neurodegeneration resulting in Parkinson...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghayas S,Ali Masood M,Parveen R,Aquib M,Farooq MA,Banerjee P,Sambhare S,Bavi R

更新日期：2020-07-01 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：:The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density fu...

journal_title：Journal of biomolecular structure & dynamics

authors： Shiri F,Hadidi S,Rahimi-Nasrabadi M,Ahmadi F,Ganjali MR,Ehrlich H

更新日期：2020-03-01 00:00:00

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：: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：:Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF...

journal_title：Journal of biomolecular structure & dynamics

authors： Majumder R,Roy S,Thakur A

更新日期：2011-10-01 00:00:00

abstract：:An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy prefe...

journal_title：Journal of biomolecular structure & dynamics

authors： Alderfer JL,Danilov VI,Poltev VI,Slyusarchuk ON

更新日期：1999-04-01 00:00:00

abstract：:The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, a...

journal_title：Journal of biomolecular structure & dynamics

authors： Usha S,Selvaraj S

更新日期：2014-01-01 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：: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：:Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and d...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets OO,Hovorun DM

更新日期：2014-01-01 00:00:00

abstract：:For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in ...

journal_title：Journal of biomolecular structure & dynamics

authors： Rosandić M,Vlahović I,Glunčić M,Paar V

更新日期：2016-07-01 00:00:00

abstract：:Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

journal_title：Journal of biomolecular structure & dynamics

authors： Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

更新日期：1994-02-01 00:00:00

abstract：:A mononuclear cadmium(II) complex of formula [Cd(5,5'-dmbipy)2(OAc)2]·2H2O (5,5'-dmbipy = 5,5'-dimethyl-2,2'-bipyridine and OAc = acetato ligand) has been synthesized and characterized by FT-IR, UV-Vis, 1H-NMR, elemental analysis and single-crystal X-ray structure analysis. The molecular structure of the complex shows...

journal_title：Journal of biomolecular structure & dynamics

authors： Kondori T,Akbarzadeh-T N,Abdi K,Dušek M,Eigner V

更新日期：2020-01-01 00:00:00

abstract：:Tris-intercalation of an acridine trimer into the self-complementary dodecanucleotide d(CTTCGCGCGAAG) has been studied, in solution, by means of 1H and 31P nuclear magnetic resonance. In a first step all the non-exchangeable protons (except H5', H5"), the imino protons and seven of the eleven phosphorus have been assi...

journal_title：Journal of biomolecular structure & dynamics

authors： Laugaa P,Delepierre M,Dupraz B,Igolen J,Roques BP

更新日期：1988-12-01 00:00:00

abstract：:The effect of ligand interacting with native DNA by two types on the parameters of helix-coil transition in homopolymers is considered using the most probable distribution method (Yu.S. Lazurkin et al., Biopolymers 1970). It is shown that at a small relative concentration of ligand the melting enthalpy (delta H) of DN...

journal_title：Journal of biomolecular structure & dynamics

authors： Karapetian AT,Vardevanian PO,Tarzikian GA,Frank-Kamenetskii MD

更新日期：1990-08-01 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：:DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide ...

journal_title：Journal of biomolecular structure & dynamics

authors： Brukner I,Sánchez R,Suck D,Pongor S

更新日期：1995-10-01 00:00:00

abstract：:Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, lin...

journal_title：Journal of biomolecular structure & dynamics

authors： Brayer G,McPherson A

更新日期：1984-12-01 00:00:00

abstract：:Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions...

journal_title：Journal of biomolecular structure & dynamics

authors： Shchelkanov MYu,Starikov NS,Yaroslavtsev IV,Tsvetkov PO,Yudin AN,Denisov MV,Slavsky AA,Vedenov AA,Karamov EV

更新日期：1998-04-01 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：:Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...

journal_title：Journal of biomolecular structure & dynamics

authors： Jamshidi S,Jalili S,Rafii-Tabar H

更新日期：2015-01-01 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：:We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a prot...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Nithin C,Divakaruni Y,Bahadur RP

更新日期：2019-03-01 00:00:00

abstract：:Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

journal_title：Journal of biomolecular structure & dynamics

authors： Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

更新日期：2009-12-01 00:00:00

abstract：:It is well established that GAA/TTC base triplet expansion is the cause of degenerative disorder in Freidreich's Ataxia. It is also known that these repeat sequences fold back to form the unusual intramolecular triple helix structures in DNA of the type Pyrimidine *Purine *Pyrimidine or Purine *Purine*Pyrimidine. In t...

journal_title：Journal of biomolecular structure & dynamics

authors： Jain A,Rajeswari MR,Ahmed F

更新日期：2002-02-01 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