Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A.

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：:Bruton's tyrosine kinase (Btk) is an important enzyme in B-lymphocyte development and differentiation. Furthermore, Btk expression is considered essential for the proliferation and survival of these cells. Btk inhibition has become an attractive strategy for treating autoimmune diseases, B-cell leukemia, and lymphomas...

journal_title：Journal of biomolecular structure & dynamics

authors： Santos-Garcia L,Assis LC,Silva DR,Ramalho TC,da Cunha EF

更新日期：2016-07-01 00:00:00

abstract：:Minidumbbell (MDB) is a newly found non-B DNA structure formed by short single-strand sequences. Up to now, three MDBs have been reported to form at neutral pH by sequences containing two repeats of TTTA, CCTG and CTTG. Among them, the thermodynamically less stable TTTA and CCTG MDBs have been proposed to be the struc...

journal_title：Journal of biomolecular structure & dynamics

authors： Guo P,Lam SL

更新日期：2020-04-01 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：: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：: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：:The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in ...

journal_title：Journal of biomolecular structure & dynamics

authors： Nikulin A,Mikhailina A,Lekontseva N,Balobanov V,Nikonova E,Tishchenko S

更新日期：2017-06-01 00:00:00

abstract：:Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived muta...

journal_title：Journal of biomolecular structure & dynamics

authors： Ramakrishnan C,Subramanian V,Balamurugan K,Velmurugan D

更新日期：2013-01-01 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

authors： Bůzek J,Kuderová A,Pexa T,Stanková V,Lauerová L,Palecek E

更新日期：1999-08-01 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：:Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the dru...

journal_title：Journal of biomolecular structure & dynamics

authors： Thangsunan P,Tateing S,Hannongbua S,Suree N

更新日期：2016-07-01 00:00:00

abstract：:The nucleoprotein (NP) binds the viral RNA genome as oligomers assembled with the polymerase in a ribonucleoprotein complex required for transcription and replication of influenza A virus. Novel antiviral candidates targeting the nucleoprotein either induced higher order oligomers or reduced NP oligomerization by targ...

journal_title：Journal of biomolecular structure & dynamics

authors： Tarus B,Bertrand H,Zedda G,Di Primo C,Quideau S,Slama-Schwok A

更新日期：2015-09-01 00:00:00

abstract：:Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains reg...

journal_title：Journal of biomolecular structure & dynamics

authors： Auerbach T,Pioletti M,Avila H,Anagnostopoulos K,Weinstein S,Franceschi F,Yonath A

更新日期：2000-02-01 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

authors： Chen CY

更新日期：2010-04-01 00:00:00

abstract：:The thermal denaturation of the synthetic high molecular weight double stranded polynucleotide poly(dA-dT) x poly(dA-dT) has been studied in aqueous buffered solution (Tris 1.0 mM; pH 7.8+/-0.2) in the presence of increasing concentrations of either Ni(2+) (borderline cation) or Cd(2+) (soft cation) at four different ...

journal_title：Journal of biomolecular structure & dynamics

authors： Airoldi M,Gennaro G,Giomini M,Giuliani AM,Giustini M

更新日期：2007-08-01 00:00:00

abstract：:The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portio...

journal_title：Journal of biomolecular structure & dynamics

authors： Whitehead TL,Jones LM,Hicks RP

更新日期：2004-02-01 00:00:00

abstract：:SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodoc...

journal_title：Journal of biomolecular structure & dynamics

authors： Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik I

更新日期：2020-11-17 00:00:00

abstract：:The purpose of this study was to investigate the site-selective binding of erlotinib hydrochloride (ET), a targeted anticancer drug, to bovine serum albumin (BSA) through 1H NMR, spectroscopic, thermodynamic, and molecular modeling methods. The fluorescence quenching of BSA by ET was a result of the formation of BSA-E...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu Y,Chen M,Luo Z,Lin J,Song L

更新日期：2013-10-01 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 binding of the anilido aminoacridine derivative amsacrine with the heme proteins, hemoglobin, and myoglobin, was characterized by various spectroscopic and calorimetric methods. The binding affinity to hemoglobin was (1.21 ± .05) × 105 M-1, while that to myoglobin was three times higher (3.59 ± .15) × 105 M-1. The...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhowmik D,Suresh Kumar G

更新日期：2017-05-01 00:00:00

abstract：:We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role...

journal_title：Journal of biomolecular structure & dynamics

authors： Khechinashvili NN,Capital Ka Cyrillicabanov AV,Kondratyev MS,Polozov RV

更新日期：2014-01-01 00:00:00

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 con...

journal_title：Journal of biomolecular structure & dynamics

authors： Ponnuswamy PK,Anukanth A

更新日期：1989-02-01 00:00:00

abstract：:In order to examine whether chiral metal complexes can be used to discriminate between right- and left-handed DNA conformational states we have studied the enantioselective interactions of Fe(phen)3(2+) and Ru(phen)3(2+) (phen = 1,10-phenanthroline) with poly(dGm5dC) under B- and Z-form conditions. With the inversion-...

journal_title：Journal of biomolecular structure & dynamics

authors： Härd T,Hiort C,Nordén B

更新日期：1987-08-01 00:00:00

abstract：:Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of ...

journal_title：Journal of biomolecular structure & dynamics

authors： Murphy MA,Mun S,Horstemeyer MF,Baskes MI,Bakhtiary A,LaPlaca MC,Gwaltney SR,Williams LN,Prabhu RK

更新日期：2019-03-01 00:00:00

abstract：:Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofac...

journal_title：Journal of biomolecular structure & dynamics

authors： Bairagya HR,Mukhopadhyay BP,Sekar K

更新日期：2009-10-01 00:00:00

abstract：:The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and...

journal_title：Journal of biomolecular structure & dynamics

authors： Cao Z,Liu L,Wang J

更新日期：2010-12-01 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：:The polymorphism exhibited by the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G), as a function of the temperature, DNA concentration and ionic strength, was investigated by means of NMR spectroscopy. It is shown that this partly self-complementary DNA fragment, under conditions of low DNA concentration (0.4 mM) and low ...

journal_title：Journal of biomolecular structure & dynamics

authors： Orbons LP,van der Marel GA,van Boom JH,Altona C

更新日期：1987-06-01 00:00:00

abstract：:Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions such as carbon assimilation, pH acid-base homeostasis, respiration and photosynthesis via a zinc-hydroxide mechanism for carbon dioxide hydration. In earlier studies, it was revealed that...

journal_title：Journal of biomolecular structure & dynamics

authors： Yadav PR,Basha SH,Pindi PK

更新日期：2020-12-24 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