Abstract:
:Ebola virus (EBOV) is highly lethal due to virally encoded immune antagonists, and the combination of EBOV VP24 with karyopherin alpha (KPNA) will trigger anti-interferon (IFN) signaling. The crystal structure of VP24-KPNA5 has been proposed in recent studies, but the precise binding mechanisms are still unclear. In order to explore the VP24-KPNA5 protein binding micro-mechanisms, Molecular Dynamic (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation are performed. The obtained results show that EBOV VP24 binding to KPNA5 will rigidify their binding-face, and both proteins will be compacted during binding. According to the analyses of binding free energies of WT and the eight mutant systems, MUT3 makes the most effective contributions to the interaction; additionally MUT4, R398A and the double mutant have the second most effective influence. Hydrogen bond analysis demonstrates that inhibitors which can interfere with the formation of hydrogen bonds D480-T138, E483-R137 and D205-R396 will prevent the anti-IFN effect. Meanwhile, by combining the decomposition of binding free energies (DC) with computational alanine scanning (CAS) results, it is shown that VP24 residues R137 and T138 will be potential targets for EBOV VP24 inhibitors, and KPNA5 residues R396, R398, R480, Y477 and F484 will be potential targets to prevent KPNA5 binding to VP24, which will ultimately block anti-IFN signaling. Our investigations provide theoretical data to understand the binding modes of VP24-KPNA5. The precise binding mechanisms of the complex may shed light on the development of potential novel inhibitors against EBOV infection.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Ding JN,Zhang YJ,Zhong H,Ao CC,Li J,Han JGdoi
10.1039/c7mb00136csubject
Has Abstractpub_date
2017-05-02 00:00:00pages
1031-1045issue
5eissn
1742-206Xissn
1742-2051journal_volume
13pub_type
杂志文章abstract::New-type oseltamivir-resistant H1N1 influenza viruses have been a major threat to human health since the 2009 flu pandemic. To resolve the drug resistance issue, we aimed to identify a new type of inhibitors against H1 from traditional Chinese medicine (TCM) by employing the world's largest TCM database () for virtual...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05320e
更新日期:2011-12-01 00:00:00
abstract::RNA interference (RNAi) techniques hold forth great promise for therapeutic silencing of deleterious genes. However, clinical applications of RNAi require the development of safe and efficient methods for intracellular delivery of small interfering RNA (siRNA) oligonucleotides specific to targeted genes. We describe t...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b603229j
更新日期:2006-06-01 00:00:00
abstract::Mirror image phage display is a straightforward approach to identify new potentially therapeutically active D-enantiomeric peptides. Such D-peptides are more resistant to proteolytic degradation compared to L-peptides. In this review, several examples of mirror image phage display derived D-peptides with therapeutical...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b904138a
更新日期:2009-08-01 00:00:00
abstract::Deciphering functional interactions between proteins is one of the great challenges in biology. Sequence-based homology-free encoding schemes have been increasingly applied to develop promising protein-protein interaction (PPI) predictors by means of statistical or machine learning methods. Here we analyze the relatio...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb05427b
更新日期:2012-04-01 00:00:00
abstract::Primarily used for medicinal purposes in the past, biologically active small molecules have been increasingly employed to explore complex biological processes in the era of "chemical genetics". Since the contributions of this small molecule approach to biology have been extensive, we limit the focus of our review to t...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b716221a
更新日期:2008-04-01 00:00:00
abstract::The adaptation of the cellular network to functional changes, timing and patterning of gene expression is regulated by binding of transcription factors to gene regulatory elements, which in turn depends on co-occurring histone modifications. These two layers influence each other, enabling a further level of regulatory...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05363a
更新日期:2012-02-01 00:00:00
abstract::The dairy bacterium Lactococcus lactis has to master a complicated task. It must control its essentially linear glycolytic pathway in such a fashion that, when the substrate, glucose, runs out, it retains enough phosphoenolpyruvate and fructose-1,6-bisphosphate to be able to restart glycolysis as soon as new glucose b...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00726g
更新日期:2016-01-01 00:00:00
abstract::Precise quantification of endogenous protein-protein interactions across live cells would be a major boon to biology. Such precise measurement is theoretically possible with fluorescence lifetime imaging microscopy (FLIM) but requires first properly addressing multiple biological, instrumental, statistical, and photop...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00132e
更新日期:2011-02-01 00:00:00
abstract::Insight into the molecular mechanism of complex diseases is an important topic in the current bio-medical research. However, different from the single-gene disorders, high heterogeneity of many of the complex diseases prevents scientists from the exact understanding of the etiology. In this study, we used Myelodysplas...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05018d
更新日期:2011-06-01 00:00:00
abstract::Intrinsically disordered regions in proteins are known to evolve rapidly while maintaining their function. However, given their lack of structure and sequence conservation, the means through which they stay functional is not clear. Poor sequence conservation also hampers the classification of these regions into functi...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25202c
更新日期:2012-10-30 00:00:00
abstract::The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at th...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25528f
更新日期:2013-03-01 00:00:00
abstract::As a versatile pathogen Staphylococcus aureus can cause various disease patterns, which are influenced by strain specific virulence factor repertoires but also by S. aureus physiological adaptation capacity. Here, we present metabolomic descriptions of S. aureus central metabolic pathways and demonstrate the potential...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00315h
更新日期:2011-04-01 00:00:00
abstract::The multidrug resistance (MDR) system actively pumps antibiotics out of cells causing serious health problems. During the pumping, AcrB (one of the key components of MDR) undergoes a series of large-scale and proton-motive conformational changes. Capturing the conformational changes through all-atom simulations is cha...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00276a
更新日期:2017-09-26 00:00:00
abstract::The neuroscientific community rapidly adopted RNA interference techniques as an experimental tool for the dissection of gene function in vitro and in animal models of neurological disease in vivo. Here, we discuss recent advances in the biotechnical implementation of siRNA/shRNA-mediated gene silencing focusing on iss...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b701169e
更新日期:2007-11-01 00:00:00
abstract::Protein-protein interactions play an essential role in the regulation of various cellular processes. Understanding the recognition mechanism of protein-protein complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding si...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/B904161N
更新日期:2009-12-01 00:00:00
abstract::During the preclinical drug discovery process it remains a challenge to enable early elimination of candidate molecules that may have non-specific, off-target activities. Here, we use whole zebrafish embryo assays coupled with genetic analysis to address this issue. PLK1 (Polo-like kinase 1) is one of the key regulato...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b919743e
更新日期:2010-08-01 00:00:00
abstract::Dynamic physical interactions between proteins underpin all key cellular processes and are a highly attractive area for the development of research tools and medicines. Protein-protein interactions frequently involve α-helical structures, but peptides matching the sequences of these structures usually do not fold corr...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70246d
更新日期:2013-11-01 00:00:00
abstract::The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally impor...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00246f
更新日期:2014-07-01 00:00:00
abstract::As the usage of fluorescence microscopy as a tool to study biological systems continues to grow, so does the need for additional tools that permit the selective detection of proteins of interest. Existing selective and well-characterized kinase inhibitors may be exploited to develop novel small molecule probes useful ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb25099c
更新日期:2012-10-01 00:00:00
abstract::To identify an agent with specific activity against human lens epithelial cells (HLECs), we confirmed the presence of glucocorticoid receptors (GRs) and GR-α genes and evaluated whether GRs have a relationship with the apoptotic process in cultured HLECs. We also determined whether the inhibitor RU486 could rescue the...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05045a
更新日期:2011-06-01 00:00:00
abstract::The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of ATP into AMP and diphosphate. NPP1 is a promising drug target as it plays a role in several disorders...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00095b
更新日期:2017-05-30 00:00:00
abstract::The present study describes for the first time, a metabolic profile reflecting the osteoporosis progression in 364 pre- and postmenopausal Chinese women using GC-MS. In order to accurately evaluate the dynamic changes of metabolites along with estrogen deficiency and osteoporosis progression, we divided these subjects...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00181e
更新日期:2016-06-21 00:00:00
abstract::The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical time-course data can be used to elucidate the structure of the underlying molecular mechanisms, but a central and recurring problem is that many and very different models can be fitted to exp...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00107d
更新日期:2011-05-01 00:00:00
abstract::Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5'-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; D-cycloserine (DCS, also known as Seromycin) is a natural product that is used to treat resistant Mycobacterium tuberculosis infec...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c003743e
更新日期:2010-09-01 00:00:00
abstract::We have investigated the thermodynamics of the interaction between the TATA-box-binding protein from Pyrococcus horikoshii (PhoTBP) and its target DNA (TATA-1). The interaction between PhoTBP and double-stranded DNA (dsDNA) is entropically favorable and enthalpically unfavorable. The thermodynamic parameters for TATA-...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b904200h
更新日期:2009-09-01 00:00:00
abstract::Fabry disease (FD) is an X-linked lysosomal storage disorder caused by a deficiency of the lysosomal hydrolase α-galactosidase A (α-GalA) that leads to the intra-lysosomal accumulation of globotriaosylceramide (Gb3) in various organ systems. As a consequence, a multisystems disorder develops, culminating in stroke, pr...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00707g
更新日期:2015-06-01 00:00:00
abstract::Structural insight into DNA quadruplex structures formed by oligodeoxyribonucleotides 3'TG5'-5'GGGT3' (QS55) and 5'TG3'-3'GGGT5' (QS33) is presented. NMR analysis reveals that QS33 forms a parallel-like four-fold symmetric quadruplex, while QS55 possesses a two-fold symmetry and is characterized by a tetrameric antipa...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b718778e
更新日期:2008-05-01 00:00:00
abstract::Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us t...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/c6mb00639f
更新日期:2016-12-20 00:00:00
abstract::The crystal structure of the versatile CYP109B1 enzyme from Bacillus subtilis has been solved at 1.8 Å resolution. This is the first structure of an enzyme from this CYP family, whose members are prevalent across diverse species of bacteria. In the crystal structure the enzyme has an open conformation with an access c...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00665h
更新日期:2015-03-01 00:00:00
abstract::The knowledge available about the application and generation of induced pluripotent stem cells (iPSC) has grown since their discovery, and new techniques to enhance the reprogramming process have been described. Among the new approaches to induce iPSC that have gained great attention is the use of small molecules for ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70159j
更新日期:2013-11-01 00:00:00