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-characterized electrostatically-stabilized external binding site, but rather is seen to be a covalently bound complex which is stabilized by two hydrogen bonds between the ethidium ligand and guanine in the double stranded (ds) B-form DNA. This site [(1), R. Monaco, F. Hasheer. J Biomol Struct Dyn 10, 675 (1993)] can only exist at very low occupancy ratios. The existence of this binding site leads directly to the expectation that there will exist particular mechanistic steps along the pathway of interaction between ethidium and ds B-DNA at low and high ligand concentrations that involve this binding mode. This would not only explain observations published recently [for example, see (2-6), W. Wilson, I. Lopp. Biopolymers 18, 3025 (1979); L. Wakelin, M. Waring. J Mol Biol 144, 183-214 (1980); A. Karpetyan, N. Mehrabian, G. Terzikian, A. Antonian, P. Vardevanian, M. Frank-Kamenetshii. Proceedings of the 10th Conversation, SUNY Albany, 275 (1998); P. Vardevanyan, A. Antonyan, G. Manukyan, A. Karapetyan. Experimental and Molecular Medicine 33, 205 (2001); P. Vardevanyan, A. Antonyan, L. Minasbekan, A. Karapetyan. Proceedings of the 2002 Miami Nature Biotechnology Winter Symposium, 2(S1), 144 (2002)] but also give insight into discrepancies reported in the literature over the years by different workers studying the mechanism of interaction between ethidium and DNA. In this paper this novel binding interaction is discussed, and it is shown how the elucidation of this interaction led to the proposal of two distinct mechanisms of intercalation between ds B-DNA and ethidium cation for high and low concentrations of ligand. Modeling studies show the stability, configuration, and relative energies of this outside binding site. It is expected that this externally bound complex between ethidium cation and ds B-form DNA will be experimentally detectable using fluorescent polarization and/or linear and circular dichroism spectroscopic studies [(7, 8) E. Tuite, U. Sehlstedt, P. Hagmar, B. Norden, M. Takahashi. Euro J Biochem 243, 482-492 (1997); T. Hard. Biopolymers 26, 613-618 (1987)].
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Monaco RRdoi
10.1080/07391102.2007.10507160subject
Has Abstractpub_date
2007-10-01 00:00:00pages
119-25issue
2eissn
0739-1102issn
1538-0254pii
d=3028&c=4239&p=16112&do=detailjournal_volume
25pub_type
杂志文章abstract::In the present study, the impact of chromium(III) complexes ([Cr(salen)(H2O)2](+) (1), [Cr(en)3]3+ (2) and [Cr(EDTA)(H2O)]- (3)) on the biophysical properties of mucin like specific viscosity, zeta potential and particle size has been investigated. It is evident from the present investigation that the nature of the co...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506958
更新日期:2004-04-01 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::Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508090
更新日期:1994-08-01 00:00:00
abstract::Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of h...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1163294
更新日期:2017-03-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1991.10507920
更新日期:1991-10-01 00:00:00
abstract::With a view to understanding the structural requirement for tyrosine phosphorylation, we have examined the free and Ca(2+)-bound conformations of the synthetic peptide tBoc-Leu-Pro-Tyr-Ala-NHCH3, a substrate for a protein tyrosine kinase, using circular dichroism (CD), 1H and 13C nuclear magnetic resonance (NMR) and m...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1993.10508012
更新日期:1993-12-01 00:00:00
abstract::Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506627
更新日期:2000-01-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2005.10507018
更新日期:2005-02-01 00:00:00
abstract::Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1157037
更新日期:2017-02-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1995.10508776
更新日期:1995-02-01 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::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
pub_type: 杂志文章
doi:10.1080/07391102.2016.1224732
更新日期:2017-09-01 00:00:00
abstract::Conversion of the rod-like tobacco mosaic virus (TMV) virions into "ball-like particles" by thermal denaturation at 90-98 °C had been described by R.G. Hart in 1956. We have reported recently that spherical particles (SPs) generated by thermal denaturation of TMV at 94-98 °C were highly stable, RNA-free, and water-ins...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.788983
更新日期:2014-01-01 00:00:00
abstract::Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked whic...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1064831
更新日期:2016-05-01 00:00:00
abstract::Repetitive basic polypeptides containing lysine or arginine as every third amino acid were shown to cause DNA condensation at physiological salt concentration connected with selective DNA binding with respect to DNA composition and sequence. This selectivity is very similar to that existing in the case of histone H1 a...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508912
更新日期:1996-06-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2006.10507089
更新日期:2006-06-01 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::Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenox...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10508509
更新日期:1989-12-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2012.706078
更新日期:2013-01-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508751
更新日期:1994-10-01 00:00:00
abstract::Cardiovascular diseases are the world's leading cause of death. Hypertension is an important risk factor for cardiovascular and renal diseases. Angiotensin-converting enzyme (ACE) can be a possible therapeutic target for managing angiotensin I conversion to angiotensin II and ultimately controlling hypertension. Indol...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1827038
更新日期:2020-10-05 00:00:00
abstract::A theoretical study is presented of the energetic and structural properties of covalent adducts of benzo[a]pyrene and a DNA fragment. Energy optimisation is performed with the use of minimiser with constraints and an advanced semiempirical energy formula. Three types of adducts are studied: an external complex with th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10507682
更新日期:1987-04-01 00:00:00
abstract::Pre-mRNA splicing is one of the most complex and intricate processes in eukaryotic cell biology. Over the past decade, my laboratory has been interested in determining the structures of RNA components of the spliceosome, and in investigating how the structure, stability and dynamics of these RNA components are perturb...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506789
更新日期:2002-04-01 00:00:00
abstract::A conceptually new idea in quantitative structure-activity relationships (QSAR) which makes use of ensembles from molecular dynamics (MD) trajectories and information retrieved from enzyme-inhibitor binding thermodynamics is presented in this study. This new methodology, termed ensemble comparative residue interaction...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.909744
更新日期:2015-01-01 00:00:00
abstract::The With-No-Lysine (WNK) kinase family plays a significant role in regulating cation-chloride cotransporters, blood pressure and body fluid homeostasis. Mutations in the gene of WNK family, especially in WNK1 and WNK4 are responsible for pseudohypoaldosteronism type II (PHAII), characterized by hypertension. The selec...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1602079
更新日期:2020-03-01 00:00:00
abstract::Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508898
更新日期:1996-04-01 00:00:00
abstract::Understanding, at the molecular level, the effect of AMPs on biological membranes is of crucial importance given the increasing number of multidrug-resistant bacteria. Being part of an ancient type of innate immunity system, AMPs have emerged as a potential solution for which bacteria have not developed resistance. Tr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1867640
更新日期:2021-01-05 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::Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1106978
更新日期:2016-10-01 00:00:00
abstract::Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1633407
更新日期:2020-05-01 00:00:00