Abstract:
:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and many fruit-specific expansins have been identified in a variety of species. A 3D model for VpEXPA2, an α-expansin involved in softening of Vasconcellea pubescens fruit, was built for the first time by comparative modeling strategy. The model was validated and refined by molecular dynamics simulation. The VpEXPA2 model shows a cellulose binding domain with a β-sandwich structure, and a catalytic domain with a similar structure to the catalytic core of endoglucanase V (EGV) from Humicola insolens, formed by six β-strands with interconnected loops. VpEXPA2 protein contains essential structural moieties related to the catalytic mechanism of EGV, such as the conserved HFD motif. Nevertheless, changes in the catalytic environment are observed in the protein model, influencing its mode of action. The lack of catalytic activity of this expansin and its preference for cellulose are discussed in light of the structural information obtained from the VpEXPA2 protein model, regarding the distance between critical amino acid residues. Finally, the VpEXPA2 model improves our understanding on the mechanism of action of α-expansins on plant cell walls during softening of V. pubescens fruit.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MAdoi
10.1007/s00894-015-2656-7subject
Has Abstractpub_date
2015-05-01 00:00:00pages
115issue
5eissn
1610-2940issn
0948-5023journal_volume
21pub_type
杂志文章abstract::The behavior of the carbon monoxide (CO) adsorbed on the external surface of H-capped (6,0) zigzag single-walled aluminum nitride nanotube (AlNNT) was studied using parallel and transverse electric field (strengths 0-140 × 10(-4) a.u.) and density functional calculations. The calculated adsorption energies of the CO/A...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1614-x
更新日期:2013-02-01 00:00:00
abstract::In this work, the effect of the external electric field (EF) on the drug delivery performance of peptide-based metal-organic framework (MPF) for 6-mercaptopurine (6-MP) drug is investigated by means of the molecular dynamics (MD) simulations. It is found that the strength interaction of drug molecule with MPF is decre...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4178-1
更新日期:2019-09-06 00:00:00
abstract::The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by Pr...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1025-4
更新日期:2011-12-01 00:00:00
abstract::Fine-tuning of magnetic states via an understanding of spin injection on the edge of graphene nanoribbons should allow for greater flexibility of the design of graphene-based spintronics. On the basis of calculations, we predict that coupling constants of the exchange interaction in the series of nitroxide-functionali...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-3944-4
更新日期:2019-02-09 00:00:00
abstract::The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05-2X theories using the 6-31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a conce...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3016-y
更新日期:2016-07-01 00:00:00
abstract::Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowe...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3139-1
更新日期:2016-11-01 00:00:00
abstract::Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations,...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1613-y
更新日期:2013-02-01 00:00:00
abstract::Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C(4)H(9)•) with oxygen (O(2)). On the calculated potential energy surface, the addition of O(2) to C(4)H(9)• forms three intermediates barrierlessly, which can undergo subsequent i...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1241-y
更新日期:2012-05-01 00:00:00
abstract::Ionic liquids (ILs) have been extensively studied and are considered green solvents capable of replacing traditional organic solvents. In this study, seven 1,2,3-triazolium derivative ILs have been synthesized. In order to study the effect of the cation nature on the ILs cytotoxicity, their structures were first ident...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3682-z
更新日期:2018-06-14 00:00:00
abstract::Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet-triplet energy gaps, and spin-orbit matrix elements were co...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3727-3
更新日期:2018-06-29 00:00:00
abstract::The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses hav...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3444-3
更新日期:2017-10-02 00:00:00
abstract::Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-4330-y
更新日期:2020-03-07 00:00:00
abstract::The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3428-3
更新日期:2017-08-14 00:00:00
abstract::We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2608-2
更新日期:2015-03-01 00:00:00
abstract::The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4137-x
更新日期:2019-08-19 00:00:00
abstract::The structures and intramolecular interactions of complexes (FeCNT-CO, FeCNT-NO, NiCNT-CO, and NiCNT-NO) formed by the Fe or Ni doped single-wall carbon nanotube (FeCNT or NiCNT) and gas CO or NO were studied using density functional theory, quantum theory of atom in molecule (QTAIM), and natural bond orbital methods....
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2778-y
更新日期:2015-09-01 00:00:00
abstract::G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-007-0254-z
更新日期:2008-02-01 00:00:00
abstract::The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-003-0160-y
更新日期:2004-02-01 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::Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural diff...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-001-0067-4
更新日期:2002-02-01 00:00:00
abstract::The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0443-4
更新日期:2009-08-01 00:00:00
abstract::Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The inte...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1252-8
更新日期:2012-06-01 00:00:00
abstract::The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1483-3
更新日期:2012-11-01 00:00:00
abstract::A theoretical investigation of the adsorption of CO₂ onto ZrO₂ is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to proper...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1486-0
更新日期:2012-11-01 00:00:00
abstract::Understanding the interactions of the cage molecules with a variety of invited molecules is getting very important. But, the hydrogen bonds can also play a crucial role in the interaction phenomenon. In this work, natural population analysis (NPA), chemical shifts, and atom in molecules (AIM) analysis have been used t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4255-5
更新日期:2019-12-13 00:00:00
abstract::Polymer and molecular-based electronic materials incorporating heterocycles like thiophenes and pyrroles are attractive possibilities as substitutes for semimetal materials. Heterocyclic materials are heavily studied in this regard due to the large variations in possible substrates. Herein we evaluated four different ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-021-04676-6
更新日期:2021-01-31 00:00:00
abstract::Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-004-0216-7
更新日期:2004-12-01 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::A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as gamma-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0361-5
更新日期:2009-04-01 00:00:00
abstract::In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1291-1
更新日期:2012-06-01 00:00:00