Abstract：
:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employed to study the interaction mechanism of IGFBP4 and IGF-I by molecular dynamics (MD) simulation. In IGF-I, residues Gly7 to Asp12 were found to be the hot spots and they mainly anchored on the N-domain of IGFBP4. The contact area, the shape and size of protein, the surroundings of the binding site, the hydrophobic and electrostatic interaction between the two proteins worked as a complex network to regulate the protein-protein interaction. It was also found that the unfolding of the helix was not inevitable in the mutant, and it could be regulated by careful selection of the substituted amino acid.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Chen X,Zhu S,Duan D,Wu T,Wang Qdoi
10.1007/s00894-013-2020-8subject
Has Abstractpub_date
2013-12-01 00:00:00pages
5257-66issue
12eissn
1610-2940issn
0948-5023journal_volume
19pub_type
杂志文章abstract：:The deregulated breakpoint cluster region (Bcr)-Abelson tyrosine kinase (Abl) fusion protein represents an attractive pharmacological target for the treatment of chronic myeloid leukemia (CML). The high affinity of monobody AS25 was designed to target the Src homology 2 (SH2) domain of Bcr-Abl, leading to allosteric i...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3353-5
更新日期：2017-06-01 00:00:00
abstract：:The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reacti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1908-7
更新日期：2013-09-01 00:00:00
abstract：:Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04663-3
更新日期：2021-01-09 00:00:00
abstract：:The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3440-7
更新日期：2017-08-21 00:00:00
abstract：:The aim of the present work entitled electronic structure of PVA-PEG-Y2O3 (54 atom) is to present a theoretical study based on the hybrid function of three parameters Lee-Yang-Parr B3LYP of the density functional theory "DFT" quantum mechanical approach together with LanL2DZ basis sets for optoelectronics applications...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04479-1
更新日期：2020-07-20 00:00:00
abstract：:Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-005-0048-0
更新日期：2006-07-01 00:00:00
abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1162-9
更新日期：2012-04-01 00:00:00
abstract：:In the present work, conformational analysis of lignin models was accomplished by considering four cross-link types (3-5', β-5', α-O-4 and β-O-4) and three monomer units [guaiacyl (G), p-hydroxyphenyl (H) and syringyl (S)]. Analysis involving the 3-5' and β-5' dimers was conducted following the standard procedure, i.e...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1689-4
更新日期：2013-05-01 00:00:00
abstract：:The substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04378-5
更新日期：2020-04-23 00:00:00
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0324-x
更新日期：2008-09-01 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：:Periodic first-principles calculations have been performed to study the effect of high pressure on the geometric, electronic, and absorption properties of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic pressures of 0-50 GPa. Obvious irregular changes in lattice constants, unit-cell angles, bond le...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1995-5
更新日期：2013-12-01 00:00:00
abstract：:In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (βt) were calculated f...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1644-4
更新日期：2013-05-01 00:00:00
abstract：:The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2471-6
更新日期：2014-10-01 00:00:00
abstract：:Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the d...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-004-0187-8
更新日期：2004-08-01 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：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3881-7
更新日期：2018-11-28 00:00:00
abstract：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2990-4
更新日期：2016-06-01 00:00:00
abstract：:The mechanism of the thermal rearrangement of substituted N-acyl-2,2-dimethylaziridines 1 has been studied using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311++G(2d,2p) level. Relative energies for various stationary points have been determine...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1959-9
更新日期：2013-10-01 00:00:00
abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0133-z
更新日期：2007-01-01 00:00:00
abstract：:Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2621-5
更新日期：2015-04-01 00:00:00
abstract：:Several cellular disorders have been related to the overexpression of the cysteine protease cathepsin B (CatB), such as rheumatic arthritis, muscular dystrophy, osteoporosis, Alzheimer's disease, and tumor metastasis. Therefore, inhibiting CatB may be a way to control unregulated cellular functions and prevent tissue ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2254-0
更新日期：2014-06-01 00:00:00
abstract：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1015-6
更新日期：2011-12-01 00:00:00
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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：:The relationship of Wiener's topochemical index-a distance based topochemical index, molecular connectivity topochemical index-an adjacency based topochemical index and eccentric connectivity topochemical index-an adjacency-cum-distance based topochemical index with sodium channel binding activity has been investigate...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0134-y
更新日期：2007-01-01 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
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1048-x
更新日期：2012-02-01 00:00:00
abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04459-5
更新日期：2020-07-07 00:00:00
abstract：:Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2583-7
更新日期：2015-04-01 00:00:00
abstract：:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3029-6
更新日期：2016-07-01 00:00:00
