Abstract:
:Most fibrous polynucleotides of general sequence exhibit secondary structures that are described adequately by regular helices with a repeated motif of only one nucleotide. Such helices exploit the fact that A:T, T:A, G:C, and C:G pairs are essentially isomorphous and have dyadically-related glycosylic bonds. Polynucleotides with regularly repeated base-sequences sometimes assume secondary structures with larger repeated motifs which reflect these base-sequences. The dinucleotide units of the Z-like forms of poly d(As4T):poly d(As4T), poly d(AC):poly d(GT) and poly d(GC):poly d(GC) are dramatic instances of this phenomenon. The wrinkled B and D forms of poly d(GC):poly d(GC) and poly d(AT):poly d(AT) are just as significant but more subtle examples. It is possible also to trap more exotic secondary structures in which the molecular asymmetric unit is even larger. There is, for example, a tetragonal form of poly d(AT):poly d(AT) which has unit cell dimensions a = b = 1.71nm, c = 7.40nm, gamma = 90 degrees. The c dimension corresponds to the pitch of a molecular helix which accommodates 24 successive nucleotide pairs arranged as a 4(3) helix of hexanucleotide duplexes. The great variety of nucleotide conformations which occur in these large asymmetric units has prompted us to describe them as pleiomeric, a term used in botany to describe whorls having more than the usual number of structures. Pleiomeric DNAs need not contain nucleotide conformations that are very different from one another. On the other hand, DNAs carrying nucleotides of very different conformation must be pleiomeric. This is because 4 nucleotides of different conformation are needed to join patches of secondary structure which are as different as A or B or Z. Differences in nucleotide structures may occur also between chains rather than within chains. In poly d(A):poly d(T), the purine nucleotides all contain C3'-endo furanose rings and the pyrimidine nucleotides C2'-endo rings. Analogous heteronomous structures may exist in DNA-RNA hybrids although these duplexes are also found to have symmetrical A-type conformations.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Arnott S,Chandrasekaran R,Banerjee AK,He R,Walker JKdoi
10.1080/07391102.1983.10507453subject
Has Abstractpub_date
1983-10-01 00:00:00pages
437-52issue
2eissn
0739-1102issn
1538-0254journal_volume
1pub_type
杂志文章abstract::Pertussis, caused by Bordetella pertussis is still one of the controversial diseases worldwide due to its high prevalence in both the developed and the developing countries, especially among young children. As currently approved vaccines are not protective enough and provide Th2-type immune responses, there is an urge...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1794966
更新日期:2020-07-21 00:00:00
abstract::Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506574
更新日期:2000-04-01 00:00:00
abstract::The insertion of viral DNA into the host chromosome is an essential step in the replication of HIV-1, and is carried out by an enzyme, HIV-1 integrase (IN). Since the latter has no human cellular counterpart, it is an attractive target for antiviral drug design. Several IN inhibitors having activities in the micromola...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506820
更新日期:2002-08-01 00:00:00
abstract::Complexes of NaDNA with the bipyridyl-(ethylenediamine)platintum(II) (abbreviated [(bipy)Pt(en)]2+) molecular ion have been studied in solution via ultraviolet absorption experiments at 260 nm between 50 and 90 degrees C. These measurements, performed as a function of the molar ratio of the [(bipy)Pt(en)]2+ complex to...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2008.10507227
更新日期:2008-08-01 00:00:00
abstract::The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subs...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508888
更新日期:1996-04-01 00:00:00
abstract::A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508232
更新日期:1998-08-01 00:00:00
abstract::To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure-activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity-descriptors relationship accuracy of 94% referred by regression coefficient (r2 = .9...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1355846
更新日期:2018-07-01 00:00:00
abstract::The assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10506379
更新日期:1987-08-01 00:00:00
abstract::Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1737233
更新日期:2020-03-11 00:00:00
abstract::The conjugation of trypsin (try) and trypsin inhibitor (tryi) with poly(ethylene glycol) (PEG) and methoxypoly(ethylene glycol) anthracene (mPEG-anthracene) was investigated in aqueous solution, using multiple spectroscopic methods, thermodynamic analysis, and molecular modeling. Thermodynamic parameters ΔS, ΔH, and Δ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1214621
更新日期:2017-08-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1989.10507737
更新日期:1989-02-01 00:00:00
abstract::At high binding densities acridine orange (AO) forms complexes with ds DNA which are insoluble in aqueous media. These complexes are characterized by high red- and minimal green-luminescence, 1:1 (dye/P) stoichiometry and resemble complexes of AO with ss nucleic acids. Formation of these complexes can be conveniently ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507532
更新日期:1984-06-01 00:00:00
abstract::Lymphatic filariasis is a debilitating vector borne parasitic disease that infects human lymphatic system by nematode Brugia malayi. Currently available anti-filarial drugs are effective only on the larval stages of parasite. So far, no effective drugs are available for humans to treat filarial infections. In this reg...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1427633
更新日期:2019-02-01 00:00:00
abstract::Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.842185
更新日期:2014-12-01 00:00:00
abstract::The interactions of a homologous series of four anthraquinone (AQ) intercalators with increasing lengths of polyethylene glycol (PEG) side chains with DNA have been studied via molecular dynamics (MD) simulations. The geometry, conformation, interactions, and hydration of the complexes were examined. The geometries of...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/073911012010525031
更新日期:2012-01-01 00:00:00
abstract::NAD(P)H: quinone oxidoreductase 1 (NQO1) inhibitors are proved as promising therapeutic agents against cancer. This study is to determine potent NAD(P)H-dependent NQO1 inhibitors with new scaffold. Pharmacophore-based three-dimensional (3D) QSAR model has been built based on 45 NQO1 inhibitors reported in the literatu...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1585291
更新日期:2020-02-01 00:00:00
abstract::Communicated by Ramaswamy H. Sarma. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 信件
doi:10.1080/07391102.2019.1680436
更新日期:2020-09-01 00:00:00
abstract::In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1847193
更新日期:2020-11-23 00:00:00
abstract::Proton ENDOR has been observed from frozen solutions (ca. 38K degrees) of copper meso-(4-N-tetra-methylpyridyl)porphyrin (CuTMpyP(4)) complexed with Salmon sperm DNA in water and D2O. Lines from exchangeable protons of the DNA bases have been observed in these ENDOR spectra. Analyses of these ENDOR data show that the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507962
更新日期:1992-04-01 00:00:00
abstract::A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy min...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.713780
更新日期:2013-01-01 00:00:00
abstract::Triple-negative breast cancers (TNBCs) are one of the most aggressive and complex forms of cancers in women. TNBCs are commonly known for their complex heterogeneity and poor prognosis. The present work aimed to develop a predictive 2D and 3D quantitative structure-activity relationship (QSAR) models against metastati...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1570868
更新日期:2020-01-01 00:00:00
abstract::The AKT isoforms are a group of key kinases that play a critical role in tumorigenesis. These enzymes are overexpressed in different types of cancers, such as breast, colon, prostate, ovarian, and lung. Because of its relevance the AKT isoforms are attractive targets for the design of anticancer molecules. However, it...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1285724
更新日期:2018-02-01 00:00:00
abstract::Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506995
更新日期:2004-10-01 00:00:00
abstract::Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of re...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2021.1871957
更新日期:2021-01-18 00:00:00
abstract::Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malar...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.924878
更新日期:2015-01-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2015.1100551
更新日期:2016-09-01 00:00:00
abstract::The funnel shaped energy landscape model of the protein folding suggests that progression of folding proceeds through multiple pathways, having the multiple intermediates which leads to multidimensional free-energy surface. Herein, we applied all-atom MD simulation to conduct a comparative study on the structure of β-...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1695669
更新日期:2020-10-01 00:00:00
abstract::The inhibitory efficacy of two substituted coumarin derivatives on the activity of neurodegenerative enzyme acetylcholinesterase (AChE) was assessed in aqueous buffer as well as in the presence of human serum albumin (HSA) and compared against standard cholinergic AD drug, Donepezil (DON). The experimental data reveal...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1465853
更新日期:2019-04-01 00:00:00
abstract::Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.881303
更新日期:2015-01-01 00:00:00
abstract::Haloxyfop was reported to exhibit inhibition effect targeting Mycobacterium tuberculosis and pathogenic parasites. To pave its way for drug development, more research is required to determine the affinities interacting with biological receptors in vivo. In this work, the interactions of Haloxyfop with two model transp...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1552624
更新日期:2019-10-01 00:00:00