Abstract:
:The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The influence on the stability of the telomeric complex of the presence of 8-oxoguanine (8oxoG) in the central telomeric triad (CTT) was estimated based on trajectories collected during 130 ns MD runs. The data obtained indicate that the system analyzed is highly sensitive to the presence of oxidative damage in the CTT of the B-DNA telomeric sequence. The most important changes were observed in the immediate vicinity of the 8-oxoguanine molecule. The significantly higher mobility of arginine 425 interacting directly with the oxidized guanine molecule has a large influence on the structural, dynamic and energetic properties of neighboring amino acids. Local changes observed for individual hydrogen bonded interactions localized in the major groove of B-DNA also have significant impact on the properties of hydrophobic clusters, which are the second type of force responsible for stability of the studied bio-system. All the changes reported in detail here unambiguously indicate a significant decrease in telomer binding affinity after oxidation.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Czeleń P,Cysewski Pdoi
10.1007/s00894-013-1859-zsubject
Has Abstractpub_date
2013-08-01 00:00:00pages
3339-49issue
8eissn
1610-2940issn
0948-5023journal_volume
19pub_type
杂志文章abstract::Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-2969-1
更新日期:2016-05-01 00:00:00
abstract::This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2101-3
更新日期:2014-02-01 00:00:00
abstract::Quantum chemical calculations were performed for LiNH2-HMgX (X=H, F, Cl, Br, CH3, OH, and NH2) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1538-5
更新日期:2013-01-01 00:00:00
abstract::First principles calculations have been performed for C60@C180 carbon double-layer endofullerenes with up to: three diatomic radioiodine molecules (131I2), two potassium radio-iodide (K131I), and three sodium radio-iodide (Na131I) inside. The plane-wave pseudopotential (PP) method within the general gradient approxima...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3538-y
更新日期:2017-12-04 00:00:00
abstract::The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1205-2
更新日期:2012-05-01 00:00:00
abstract::Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04656-2
更新日期:2021-01-03 00:00:00
abstract::Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3710-z
更新日期:2018-06-23 00:00:00
abstract::Various kinetic studies of the addition of hydrogen halides to alkenes were carried out in the 1930s, 1940s, and 1970s. Since then, there have been theoretical analyses of several aspects of alkene reactivity and regioselectivity during hydrohalogenation. A few works have studied the influence of the hydrogen halide w...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4004-9
更新日期:2019-04-25 00:00:00
abstract::The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4104-6
更新日期:2019-07-02 00:00:00
abstract::The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1694-7
更新日期:2013-07-01 00:00:00
abstract::The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0454-9
更新日期:2009-09-01 00:00:00
abstract::In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04464-8
更新日期:2020-08-01 00:00:00
abstract::CO2 reduction has attracted extensive attentions for its wide applications in chemical engineering and green chemistry. As one of major commercial catalysts, Cu have been widely studied considering its low price and high catalytic efficiency. However, previous studies were mostly focused on the Cu(111) surface, while ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04448-8
更新日期:2020-07-09 00:00:00
abstract::The removal of AsH3 from synthesis gas is crucial to prevent methanol synthesis catalyst from poisoning. In this work, Ti-, Mn-, Fe-, Co-, Ni-, Cu-, and Ag-doped graphene were proposed and their adsorption capabilities for AsH3 and CO were investigated by DFT method. The optimized structures, adsorption energies, elec...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-3991-x
更新日期:2019-05-04 00:00:00
abstract::Understanding the structure and properties at the electrolyte-electrode interface is vital for the rational design of the supercapacitors or other electrochemical devices. In this work, we explored the influence of interlayer spacing of the MoS2 electrode on the interfacial structure and electrical properties of sodiu...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04644-6
更新日期:2021-01-18 00:00:00
abstract::We here report a combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) study on the binding interactions between the α(V)β₃ integrin and eight cyclic arginine-glycine-aspartate (RGD) containing peptides. The initial conformation of each peptide within the binding site of the integrin was det...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1487-z
更新日期:2012-11-01 00:00:00
abstract::A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2295-4
更新日期:2014-07-01 00:00:00
abstract::The Schiff base compound, 2-[(4-Fluorophenylimino)methyl]-3,5-dimethoxyphenol, has been synthesized and characterized by IR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree-Fock (HF)...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0574-2
更新日期:2010-03-01 00:00:00
abstract::A novel mechanism for switching a molecular junction based on a proton transfer reaction triggered by an external electrostatic field is proposed. As a specific example to demonstrate the feasibility of the mechanism, the tautomers [2,5-(4-hydroxypyridine)] and {2,5-[4(1H)-pyridone]} are considered. Employing a combin...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2163-2
更新日期:2014-04-01 00:00:00
abstract::A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1249-3
更新日期:2012-06-01 00:00:00
abstract::Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or d...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3358-0
更新日期:2017-06-01 00:00:00
abstract::Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculati...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1726-3
更新日期:2013-04-01 00:00:00
abstract::Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2598-0
更新日期:2015-04-01 00:00:00
abstract::Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0329-5
更新日期:2008-09-01 00:00:00
abstract::Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3496-4
更新日期:2017-11-09 00:00:00
abstract::Cystic fibrosis (CF), the most common lethal genetic disease among Caucasians, is caused by mutations in cystic fibrosis transmembrane conductance regulator (CFTR). CFTR's main role is to transport chloride ions across epithelial cell membranes. It also regulates many cell functions. However, the exact role of CFTR in...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1029-0
更新日期:2012-01-01 00:00:00
abstract::The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04475-5
更新日期:2020-08-03 00:00:00
abstract::Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts i...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04387-4
更新日期:2020-06-03 00:00:00
abstract::Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2825-8
更新日期:2015-11-01 00:00:00
abstract::Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0785-6
更新日期:2011-04-01 00:00:00