Binding of Folate-G4-PAMAM dendrimer conjugate with indomethacin via ligand diffusion MD simulations.

abstract：:Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that t...

journal_title：Journal of biomolecular structure & dynamics

authors： Premraj BJ,Yathindra N

更新日期：1998-10-01 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：: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：:This article describes, for the first time, the effect of three different sizes of silver nanoparticles on the binding of curcumin to lysozyme as examined by spectroscopic and zeta potential techniques at physiological conditions. The binding constants of curcumin to lysozyme in the presence of silver nanoparticles we...

journal_title：Journal of biomolecular structure & dynamics

authors： Kamshad M,Jahanshah Talab M,Beigoli S,Sharifirad A,Chamani J

更新日期：2019-05-01 00:00:00

abstract：:The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH3O)2(POS)]-, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calc...

journal_title：Journal of biomolecular structure & dynamics

authors： Steinke CA,Reeves KK,Powell JW,Lee SA,Chen YZ,Wyrzykiewicz T,Griffey RH,Mohan V

更新日期：1997-02-01 00:00:00

abstract：:A family of covalent complexes between oligonucleotides and derivatives of the intercalating agent 9-amino acridine has been synthesized (Asseline, U., Thuong, N.T. and Helene, C. (1983) C.R.Acad. Sci. (Paris) 297 (III), 369-372) and studied (Lancelot, G., Asseline, U., Thuong, N.T., and Helene, C. (1985) Biochemistry...

journal_title：Journal of biomolecular structure & dynamics

authors： Cieplak P,Rao SN,Hélène C,Montenay-Garestier T,Kollman PA

更新日期：1987-10-01 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：:The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Bashford D,Weaver DL,Karplus M

更新日期：1984-03-01 00:00:00

abstract：:An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To ...

journal_title：Journal of biomolecular structure & dynamics

authors： Godwin RC,Gmeiner WH,Salsbury FR Jr

更新日期：2018-08-01 00:00:00

abstract：:Cell-division protein kinases (CDKs) are gorgeous examples of targets for the helpful treatment of cancer by using multi-target inhibitors. Specifically, targeting cell-division protein kinase1/cyclin B (CDK1/Cyclin B), cell-division protein kinase 2/cyclin A (CDK2/Cyclin A) and cell-division protein kinase 4/cyclin D...

journal_title：Journal of biomolecular structure & dynamics

authors： Al-Khafaji K,Taskin Tok T

更新日期：2020-03-24 00:00:00

abstract：:Abstract The forces that direct protein folding lead naturally to native proteins and protein domains that are typically, to a first approximation, globular-spherical and compact, with a relatively clear distinction between the hydrophobic inside and polar outside. The near-universality of these features of protein ...

journal_title：Journal of biomolecular structure & dynamics

authors： Carey J

更新日期：2000-01-01 00:00:00

abstract：:Despite the intensive research efforts towards antiviral drug against COVID-19, no potential drug or vaccines has not yet discovered. Initially, the binding site of COVID-19 main protease was predicted which located between regions 2 and 3. Structure-based virtual screening was performed through a hierarchal mode of e...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra SS,Ranjan S,Sharma CS,Singh HP,Kalra S,Kumar N

更新日期：2020-07-15 00:00:00

abstract：:The selective recognition of the aminoterminal binding pharmacophore Tyr-D-Xaa-Phe of the opioid heptapeptide dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2 (DRM)1, and of dermenkephalin, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2 (DREK), by the mu-opioid receptor and delta-opioid receptor, respectively, depends upon the consti...

journal_title：Journal of biomolecular structure & dynamics

authors： Riand J,Baron D,Nicolas P,Benajiba A,Teng Y,Naim M

更新日期：1999-12-01 00:00:00

abstract：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Huertas D,Lipps H,Azorín F

更新日期：1994-08-01 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

authors： Mitra J,Mundra P,Kulkarni BD,Jayaraman VK

更新日期：2007-12-01 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：: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 NIa protease of Potyviridae is the major viral protease that processes potyviral polyproteins. The NIa protease coding region of Cardamom mosaic virus (CdMV) is amplified from the viral cDNA, cloned and expressed in Escherichia coli. NIa protease forms inclusion bodies in E.coli. The inclusion bodies are solubiliz...

journal_title：Journal of biomolecular structure & dynamics

authors： Jebasingh T,Pandaranayaka EP,Mahalakshmi A,Kasin Yadunandam A,Krishnaswamy S,Usha R

更新日期：2013-01-01 00:00:00

abstract：:COVID-19 is an infectious pandemic caused by the SARS-CoV-2 virus. The critical components of SARS-CoV-2 are the spike protein (S-protein) and the main protease (Mpro). Mpro is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the...

journal_title：Journal of biomolecular structure & dynamics

authors： Mondal P,Natesh J,Abdul Salam AA,Thiyagarajan S,Meeran SM

更新日期：2020-11-05 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：:Peptide- and protein-protein dockings were carried out on β2-adrenergic receptor (β2AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two β2AR monomers, thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially, a porti...

journal_title：Journal of biomolecular structure & dynamics

authors： Koroglu A,Akten ED

更新日期：2015-01-01 00:00:00

abstract：:Catalase is an important antioxidant enzyme that catalyzes the disproportionation of H2O2 into harmless water and molecular oxygen. Due to various applications of the enzyme in different sectors of industry as well as medicine, the enhancement of stability of the enzyme is important. Effect of various classes of compa...

journal_title：Journal of biomolecular structure & dynamics

authors： Sepasi Tehrani H,Moosavi-Movahedi AA,Ghourchian H,Ahmad F,Kiany A,Atri MS,Ariaeenejad Sh,Kavousi K,Saboury AA

更新日期：2013-12-01 00:00:00

abstract：:The present study employed the spectroscopic techniques, i.e. fluorescence, and circular dichroism (CD) and the molecular docking approach to investigate the mechanism of interaction of a potent anticancer glucosinolate, sinigrin (SIN), with bovine serum albumin (BSA). SIN binding to BSA resulted in the quenching of i...

journal_title：Journal of biomolecular structure & dynamics

authors： Awasthi S,Saraswathi NT

更新日期：2016-10-01 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：:SARS-CoV-2 has become a pandemic causing a serious global health concern. The absence of effective drugs for treatment of the disease has caused its rapid spread on a global scale. Similarly to the SARS-CoV, the SARS-CoV-2 is also involved in a complex interplay with the host cells. This infection is characterized by ...

journal_title：Journal of biomolecular structure & dynamics

authors： Gollapalli P,B S S,Rimac H,Patil P,Nalilu SK,Kandagalla S,Shetty P

更新日期：2020-11-04 00:00:00

abstract：:Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L bin...

journal_title：Journal of biomolecular structure & dynamics

authors： Lando DY,Nechipurenko YD

更新日期：2008-10-01 00:00:00

abstract：:Thermodynamic and structural properties of two UNCG tetraloops in very short hairpin octamers, 5'-r(GCUUCGGC)-3' and 5'-r(GCUACGGC)-3', have been studied by means of various physical techniques. Melting profiles of both octamers, obtained from UV absorption spectra taken as a function of temperature, are consistent wi...

journal_title：Journal of biomolecular structure & dynamics

authors： Abdelkafi M,Ghomi M,Turpin PY,Baumruk V,Hervé du Penhoat C,Lampire O,Bouchemal-Chibani N,Goyer P,Namane A,Gouyette C,Huynh-Dinh T,Bednárová L

更新日期：1997-04-01 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

authors： Kiran MR,Bansal M

更新日期：1998-12-01 00:00:00

abstract：:A simple statistical approach for the analysis of biological sequences, such as splice-sites, promoter regions, helices and extended structure forming regions or any other sequence dependent functional entities in proteins, is presented. The approach has been proved useful to develop a method for prediction of such en...

journal_title：Journal of biomolecular structure & dynamics

authors： Reddy BV,Pandit MW

更新日期：1995-02-01 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