Macromolecular design, nucleic acid junctions, and crystal formation.

abstract：:The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomi...

journal_title：Journal of biomolecular structure & dynamics

authors： Chechetkin VR,Lobzin VV

更新日期：2019-06-01 00:00:00

abstract：:The problem that how many protein-coding genes there are in the genome of Aeropyrum pernix K1 has confused many scientists since the sequencing in 1999. In this paper, the protein-coding genes in A. pernix K1 are identified from the original and current NITE annotation by using the Aper_ORFs method. Consequently, 702 ...

journal_title：Journal of biomolecular structure & dynamics

authors： Guo FB,Lin Y

更新日期：2009-02-01 00:00:00

abstract：:A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH+), acetic acid in neutral (AcOH) and deprotonated (AcO-) forms, G-AcO-, C-AcOH, and CH(+)-AcO- complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetic...

journal_title：Journal of biomolecular structure & dynamics

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

更新日期：1997-10-01 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：: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：:Utilizing a new method for modeling furanose pseudorotation (D. A. Pearlman and S.-H. Kim, J. Biomol. Struct. Dyn. 3, 85 (1985)) and the empirical multiple correlations between nucleic acid torsion angles we derived in the previous report (D. A. Pearlman and S.-H. Kim, previous paper in this issue), we have made an en...

journal_title：Journal of biomolecular structure & dynamics

authors： Pearlman DA,Kim SH

更新日期：1986-08-01 00:00:00

abstract：:Two naphthalene-containing compounds, 4-hydroxy-6,7-dimethoxy-1-(4-(trifluoromethyl)phenyl)-2-naphthoic acid (A) and 4-hydroxy-6,7-dimethoxy-1-phenyl-2-naphthoic acid (B), were prepared by several steps. Their bindings to human serum albumin (HSA) were studied by ultraviolet-visible (UV-vis) absorption, fluorescence, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang X,Xing Y,Su J,Wang C,Wang Z,Yu Y,Xu H,Ma D

更新日期：2020-06-12 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：:A potential anti-Human Immunodeficiency Virus (HIV) agent with novel mode of action is urgently needed to fight against drug resistance HIV. The HIV capsid protein is important for both late and early stages of the viral replication cycle and emerged as a promising target for the developing of small molecule inhibitor...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhole RP,Bonde CG,Bonde SC,Chikhale RV,Wavhale RD

更新日期：2021-02-01 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：:Quasi-palindromic sequences (AT) X N12(AT) Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults ...

journal_title：Journal of biomolecular structure & dynamics

authors： Roy K,Mahendru S,Kukreti R,Kukreti S

更新日期：2019-09-01 00:00:00

abstract：:Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undec...

journal_title：Journal of biomolecular structure & dynamics

authors： Laberge M,Vreugdenhil AJ,Vanderkooi JM,Butler IS

更新日期：1998-06-01 00:00:00

abstract：:The development of bacterial resistance toward antibiotics has been led to pay attention to the antimicrobial peptides (AMPs). The common mechanism of AMPs is disrupting the integrity of the bacterial membrane. One of the most accessible targets for α-defensins human neutrophil peptide-1 (HNP-1) is lipid II. In the pr...

journal_title：Journal of biomolecular structure & dynamics

authors： Moazzezy N,Rismani E,Rezaei M,Karam MRA,Rafati S,Bouzari S,Oloomi M

更新日期：2020-09-26 00:00:00

abstract：:Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

journal_title：Journal of biomolecular structure & dynamics

authors： Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

更新日期：2020-07-31 00:00:00

abstract：:This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets' OO,Voiteshenko IS,Pérez-Sánchez H,Hovorun DM

更新日期：2018-05-01 00:00:00

abstract：:P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

journal_title：Journal of biomolecular structure & dynamics

authors： Yellapu NK,Pulaganti M,Pakala SB

更新日期：2017-08-01 00:00:00

abstract：:The SHOM method (Sequencing by Hybridization with Oligonucleotide Matrix) developed in 1988 is a new approach to nucleic acid sequencing by hybridization to an oligonucleotide matrix composed of an array of immobilized oligonucleotides. The original matrix proposed for sequencing by SHOM had to contain at least 65,536...

journal_title：Journal of biomolecular structure & dynamics

authors： Pevzner PA,Lysov YuP,Khrapko KR,Belyavsky AV,Florentiev VL,Mirzabekov AD

更新日期：1991-10-01 00:00:00

abstract：:Target evaluation is at the centre of rational drug design and biologics development. In order to successfully engineer antibodies, T-cell receptors or small molecules it is necessary to identify and characterise potential binding or contact sites on therapeutically relevant target proteins. Currently, there are numer...

journal_title：Journal of biomolecular structure & dynamics

authors： Kanapeckaitė A,Beaurivage C,Hancock M,Verschueren E

更新日期：2020-12-10 00:00:00

abstract：:In this work, an attempt has been made to study the interaction of four taiwaniaquinoids with fat mass and obesity-associated protein (FTO) by UV-vis absorption, fluorescence spectroscopy, and molecular docking techniques. The results indicated that taiwaniaquinoids effectively quenched the intrinsic fluorescence of F...

journal_title：Journal of biomolecular structure & dynamics

authors： Ren T,Zhang L,Wang J,Song C,Wang R,Chang J

更新日期：2017-11-01 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：: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：:We previously reported on a mutant lipase KV1 (Mut-LipKV1) from Acinetobacter haemolyticus which optimal pH was raised from 8.0 to 11.0 after triple substitutions of surface aspartic acid (Asp) with lysine (Lys). Herein, this study further examined the Mut-LipKV1 by molecular docking, molecular dynamics (MD) simulatio...

journal_title：Journal of biomolecular structure & dynamics

authors： Anuar NFSK,Wahab RA,Huyop F,Amran SI,Hamid AAA,Halim KBA,Hood MHM

更新日期：2020-03-23 00:00:00

abstract：:Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrost...

journal_title：Journal of biomolecular structure & dynamics

authors： Madeira PP,Bessa A,Álvares-Ribeiro L,Raquel Aires-Barros M,Rodrigues AE,Uversky VN,Zaslavsky BY

更新日期：2014-01-01 00:00:00

abstract：:Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries...

journal_title：Journal of biomolecular structure & dynamics

authors： Forde G,Flood A,Salter L,Hill G,Gorb L,Leszczynski J

更新日期：2003-06-01 00:00:00

abstract：:A new molecular mechanism of trinucleotide expansion diseases is suggested. The mechanism involves the formation of double-helical RNA hairpins by transcripts carrying (CNG)(n) sequences, which are processed via the RNAi pathway with subsequent RNA silencing of genes containing (CNG)(n) sequences. Depletion of protein...

journal_title：Journal of biomolecular structure & dynamics

authors： Malinina L

更新日期：2005-12-01 00:00:00

abstract：:A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-...

journal_title：Journal of biomolecular structure & dynamics

authors： Monaco RR

更新日期：2007-10-01 00:00:00

abstract：:Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arnold GE,Manchester JI,Townsend BD,Ornstein RL

更新日期：1994-10-01 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：:We performed a neuraminidase sequence analysis of thirty-two pediatric patients with influenza B who visited Teikyo University Hospital from January 2016 to March 2017, and found oseltamivir-resistant samples belonging to the Yamagata and Victoria lineages. Comparison with the neuraminidase sequence of oseltamivir-sus...

journal_title：Journal of biomolecular structure & dynamics

authors： Kato Y,Takahashi K,Ito F,Suzuki S,Fukui K,Mimaki M,Suzuki K

更新日期：2020-05-25 00:00:00

abstract：:Tropomyosin receptor kinase A (Trk A) is a receptor tyrosine kinase activated by nerve growth factor (NGF). TrkA plays an important role in pain sensation, which leads to significant interest in the development of small molecule inhibitors of TrkA. However, TrkA and the other two highly homologous isoforms, TrkB and T...

journal_title：Journal of biomolecular structure & dynamics

authors： Wu X,Li Q,Wan S,Zhang J

更新日期：2021-01-01 00:00:00