A note on crystal packing and global helix structure in short A-DNA duplexes.

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：:FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study...

journal_title：Journal of biomolecular structure & dynamics

authors： Tripathy S,Azam MA,Jupudi S,Sahu SK

更新日期：2018-09-01 00:00:00

abstract：:A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecyl...

journal_title：Journal of biomolecular structure & dynamics

authors： Kutyshenko VP,Prokhorov DA,Molochkov NV,Sharapov MG,Kolesnikov I,Uversky VN

更新日期：2014-01-01 00:00:00

abstract：:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A → G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin → duplex equilibrium corresponding to A → B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K....

journal_title：Journal of biomolecular structure & dynamics

authors： Kaushik M,Kukreti S

更新日期：2015-01-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Efimov AV

更新日期：2020-02-01 00:00:00

abstract：:The Transformer2 (Tra2) proteins in humans are homologues of the Drosophila Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh P,Grellscheid SN,Sowdhamini R

更新日期：2016-09-01 00:00:00

abstract：:NMR experiments with a 21412 Redfield observation pulse were carried out on a kappa-carrageenan aqueous solution containing 0.5M LiI. A detected hydrogen-bonded proton resonance at approximately 17.6 ppm, is in accordance with an ordered carrageenan structure in the solution similar to the double, parallel-stranded he...

journal_title：Journal of biomolecular structure & dynamics

authors： Nerdal W,Haugen F,Knutsen S,Grasdalen H

更新日期：1993-04-01 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：:Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning-based AutoQSAR algorithm to generate drug leads for the flaviviruses-Dengue and West Nile. The drug leads generated by the program are fed as programmatic inputs to AutoDock Vina package for...

journal_title：Journal of biomolecular structure & dynamics

authors： Geoffrey B,Sanker A,Madaj R,Tresanco MSV,Upadhyay M,Gracia J

更新日期：2020-12-04 00:00:00

abstract：:Temporal order ("chronology") of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis of 60 different criteria each offering certain temporal order. After several steps of filtering the chronology vectors are averaged ...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2004-08-01 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：:Molecular modeling and molecular dynamics were performed to investigate the interaction of norfloxacin with the DNA oligonucleotide 5'-d(ATACGTAT)(2). Eight quinolone-DNA binding structures were built by molecular modeling on the basis of experimental results. A 100ps molecular dynamics calculation was carried out on ...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee HM,Kim JK,Kim SK

更新日期：2002-06-01 00:00:00

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：: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：:Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...

journal_title：Journal of biomolecular structure & dynamics

authors： Wei Y,Yi Z,Xu J,Yang W,Yang L,Liu H

更新日期：2019-04-01 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：:In present work, we describe a methodology for prediction of an enzymatic reaction for which no experimental data are available except for a gene sequence. As a challenging case, we have developed the method for identifying the putative substrates of monoester phosphatases, commonly known as acid phosphatase enzymes, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Zamani Amirzakaria J,Malboobi MA,Marashi SA,Lohrasebi T

更新日期：2020-07-02 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：:The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four s...

journal_title：Journal of biomolecular structure & dynamics

authors： Fernandes CL,Escouto GB,Verli H

更新日期：2014-01-01 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：:Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with mole...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu F,Ma Z,Sang J,Lu F

更新日期：2020-05-01 00:00:00

abstract：:The conformational changes of poly(d2NH2A-dT) in aqueous solution, induced by increasing the NaCl concentration from 0.1M to 4M, have been monitored by ultraviolet resonance Raman spectroscopy, in using the 222-, 257- and 281 nm excitation wavelengths. These changes have been interpreted in comparing the polymer spect...

journal_title：Journal of biomolecular structure & dynamics

authors： Mojzes P,Chinsky L,Turpin PY,Miskovsky P

更新日期：1992-08-01 00:00:00

abstract：:The amino acid sequences of the Yersinia pseudotuberculosis porin (YPS) and Y. pestis porin (YPT) have recently deduced but their three-dimensional structures were not known. These sequences were analyzed using the servers 3D-PSSM and PredPort. The YPS and YPT porins were shown to have a high degree of identity (above...

journal_title：Journal of biomolecular structure & dynamics

authors： Likhatskaya GN,Solov'eva TF,Novikova OD,Issaeva MP,Gusev KV,Kryzhko IB,Trifonov EV,Nurminski EA

更新日期：2005-10-01 00:00:00

abstract：:The first fully energy-minimized structures for a series of structurally related metal complexes of the important mammalian metal binding protein metallothionein are described. The structures were calculated based on structural information obtained from existing spectroscopic and crystallographic data, and minimized u...

journal_title：Journal of biomolecular structure & dynamics

authors： Fowle DA,Stillman MJ

更新日期：1997-02-01 00:00:00

abstract：:CgtA is an essential ribosome associated GTPase protein of bacteria. It has three domains, viz., Obg, GTPase, and C-terminal domain. It is a multifunctional protein and it is being considered as a potential drug target against bacterial infections. Despite the importance, CgtA's action mechanisms are not well known wh...

journal_title：Journal of biomolecular structure & dynamics

authors： Chatterjee A,Datta PP

更新日期：2017-09-01 00:00:00

abstract：:A simplified multidimensional search was applied to determine the structure of deoxyhexamer CGCGCG in the crystal form belonging to the space group C222(1) (a = 45.6 A, b = 37.3 A, c = 70.3 A). This crystal form contains two Z-DNA duplexes per asymmetric unit in a similar orientation. The search consists of several ma...

journal_title：Journal of biomolecular structure & dynamics

authors： Strokopytov BV,Malinina LV

更新日期：1994-04-01 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：:Protein folding remains an unsolved problem as main-chain, side-chain, and solvent interactions remain entangled and have been hard to resolve. Polyalanines are promising models to analyze protein folding initiation and propagation structurally as well as energetically. In the present work, the effect of chain-length ...

journal_title：Journal of biomolecular structure & dynamics

authors： Goyal B,Kumar A,Srivastava KR,Durani S

更新日期：2017-07-01 00:00:00

abstract：:Acinetobacter baumannii, an important nosocomial pathogen, is increasingly becoming resistant to antibiotics including recent β-lactam like imipenem. Production of different types of β-lactamases is one of the major resistance mechanisms which bacteria adapt. We recently reported the presence of a β-lactamase, OXA-51,...

journal_title：Journal of biomolecular structure & dynamics

authors： Tiwari V,Moganty RR

更新日期：2014-01-01 00:00:00

abstract：:We have analysed by various approaches the structure of cloned synthetic sequences in supercoiled plasmids. Individual inserts were formed by d(C-G)n blocks interrupted by the presence of A.T pairs positioned either in phase or out of phase of pur-pyr alternation. Based on the thermodynamic analysis we obtained result...

journal_title：Journal of biomolecular structure & dynamics

authors： Vlach J,Sponar J

更新日期：1990-04-01 00:00:00