The triplet code from first principles.

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 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：: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：: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：: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：:Phytoestrogens are dietary estrogens having similar structure as of estrogen. Some of these phytoestrogens are androgen receptor (AR) antagonists and exhibit preventive role in the prostate cancer. However, in androgen-independent prostate cancer (AIPC) the ARs were mutated (T877A, W741L, F876L, etc.) and these mutant...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvaraj D,Muthu S,Kotha S,Siddamsetty RS,Andavar S,Jayaraman S

更新日期：2021-02-01 00:00:00

abstract：:Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation...

journal_title：Journal of biomolecular structure & dynamics

authors： Sun DR,Zheng QC,Zhang HX

更新日期：2017-03-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

更新日期：2020-11-06 00:00:00

abstract：:The present paper describes design, synthesis, and biological evaluation of a series of some 3-[3-(amino)propoxy]benzenamines as acetylcholinesterase inhibitors using mice as a model and piracetam as a reference drug. The structures of these compounds were confirmed by spectral analysis and compounds were tested for m...

journal_title：Journal of biomolecular structure & dynamics

authors： Malik R,Gupta R,Srivastava S,Choudhary BS,Sharma M

更新日期：2017-08-01 00:00:00

abstract：:The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant...

journal_title：Journal of biomolecular structure & dynamics

authors： Sérgio Alves Bueno P,Carina Biavatti D,Sandro Gularte Chiarello A,Aureliana Fassina V,Aparecida Fernandez M,Augusto Vicente Seixas F

更新日期：2019-09-01 00:00:00

abstract：:The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial di...

journal_title：Journal of biomolecular structure & dynamics

authors： Uberbacher EC,Bunick GJ

更新日期：1989-08-01 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：:The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each...

journal_title：Journal of biomolecular structure & dynamics

authors： Haasnoot CA,Westerink HP,van der Marel GA,van Boom JH

更新日期：1984-10-01 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 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：: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：:Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharmila DJ,Veluraja K

更新日期：2006-06-01 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：:The knowledge of the relationship between the three-dimensional structure of a protein and its biological and stability is one of the most challenging problem in protein chemistry, since offers the possibility of changing both the specific action of a protein and its stability. In this work, we have approached the pro...

journal_title：Journal of biomolecular structure & dynamics

authors： Pedone EM,Bartolucci S,Rossi M,Saviano M

更新日期：1998-10-01 00:00:00

abstract：:In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pat...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets' OO,Hovorun DM

更新日期：2015-01-01 00:00:00

abstract：:The interaction of DNA and RNA with Cu(II), Mg(II), [Co(NH3)6]3+ [Co(NH3)5Cl]2+ chlorides and, cis- and trans-Pt(NH3)2Cl2 (CIS-DDP, trans-DDP) has been studied by Fourier Transform Infrared (FT-IR) spectroscopy and a correlation between metal-base binding and conformational transitions in the sugar pucker has been est...

journal_title：Journal of biomolecular structure & dynamics

authors： Theophanides T,Tajmir-Riahi HA

更新日期：1985-02-01 00:00:00

abstract：:TATA-box binding protein (TBP) in a monomeric form and the complexes it forms with DNA have been elucidated with molecular dynamics simulations. Large TBP domain motions (bend and twist) are detected in the monomer as well as in the DNA complexes; these motions can be important for TBP binding of DNA. TBP interacts wi...

journal_title：Journal of biomolecular structure & dynamics

authors： Miaskiewicz K,Ornstein RL

更新日期：1996-02-01 00:00:00

abstract：:We have performed an 4-ns MD simulation of calmodulin complexed with a target peptide in explicit water, under realistic conditions of constant temperature and pressure, in the presence of a physiological concentration of counterions and using Ewald summation to avoid truncation of long-range electrostatic forces. Dur...

journal_title：Journal of biomolecular structure & dynamics

authors： Yang C,Kuczera K

更新日期：2002-10-01 00:00:00

abstract：:Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buc...

journal_title：Journal of biomolecular structure & dynamics

authors： Danilov VI,Anisimov VM

更新日期：2005-02-01 00:00:00

abstract：:Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(...

journal_title：Journal of biomolecular structure & dynamics

authors： Poltev VI,Teplukhin AV,Chuprina VP

更新日期：1988-12-01 00:00:00

abstract：:The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...

journal_title：Journal of biomolecular structure & dynamics

authors： Fushman D,Ohlenschläger O,Rüterjans H

更新日期：1994-06-01 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：:The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is...

journal_title：Journal of biomolecular structure & dynamics

authors： Vondrásek J,Sponar J,Hobza P

更新日期：1994-02-01 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：:Coumarin molecules have biological activities possessing lipid-controlling activity, anti-hepatitis C activity, anti-diabetic, anti-Parkinson activity, and anti-cancer activity. Here, we have presented an inclusive study on the interaction of 8-substituted-7-hydroxy coumarin derivatives (Umb-1/Umb-2) with α-1-glycopro...

journal_title：Journal of biomolecular structure & dynamics

authors： Yeggoni DP,Manidhar DM,Suresh Reddy C,Subramanyam R

更新日期：2016-09-01 00:00:00