On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains.

Abstract:

:The number of fatalities and economic losses caused by the Ebola virus infection across the planet culminated in the havoc that occurred between August and November 2014. However, little is known about the molecular protein profile of this devastating virus. This work represents a thorough bioinformatics analysis of the regularities of charge distribution (polar profiles) in two groups of proteins and their functional domains associated with Ebola virus disease: Ebola virus proteins and Human proteins interacting with Ebola virus. Our analysis reveals that a fragment exists in each of these proteins-one named the "functional domain"-with the polar profile similar to the polar profile of the protein that contains it. Each protein is formed by a group of short sub-sequences, where each fragment has a different and distinctive polar profile and where the polar profile between adjacent short sub-sequences changes orderly and gradually to coincide with the polar profile of the whole protein. When using the charge distribution as a metric, it was observed that it effectively discriminates the proteins from their functional domains. As a counterexample, the same test was applied to a set of synthetic proteins built for that purpose, revealing that any of the regularities reported here for the Ebola virus proteins and human proteins interacting with Ebola virus were not present in the synthetic proteins. Our results indicate that the polar profile of each protein studied and its corresponding functional domain are similar. Thus, when building each protein from its functional domai-adding one amino acid at a time and plotting each time its polar profile-it was observed that the resulting graphs can be divided into groups with similar polar profiles.

journal_name

Cell Biochem Biophys

authors

Polanco C,Samaniego Mendoza JL,Buhse T,Uversky VN,Bañuelos Chao IP,Bañuelos Cedano MA,Tavera FM,Tavera DM,Falconi M,Ponce de León AV

doi

10.1007/s12013-018-0839-4

subject

Has Abstract

pub_date

2018-09-01 00:00:00

pages

411-431

issue

3

eissn

1085-9195

issn

1559-0283

pii

10.1007/s12013-018-0839-4

journal_volume

76

pub_type

杂志文章
  • Quercetin potentiates the antitumor activity of rituximab in diffuse large B-cell lymphoma by inhibiting STAT3 pathway.

    abstract::STAT3 pathway plays an important role in the growth of diffuse large B-cell lymphoma (DLBCL) cells. Here we investigated the antitumor activity of Quercetin, a flavonoid compound, in combination with rituximab in DLBCL cell lines in vitro. We found that Quercetin synergistically enhanced rituximab-induced growth inhib...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-0064-8

    authors: Li X,Wang X,Zhang M,Li A,Sun Z,Yu Q

    更新日期:2014-11-01 00:00:00

  • Simultaneous determination of calycosin-7-O-β-D-glucoside, ononin, calycosin, formononetin, astragaloside IV, and astragaloside II in rat plasma after oral administration of Radix Astragali extraction for their pharmacokinetic studies by ultra-pressure li

    abstract::A sensitive and reliable ultra-pressure liquid chromatography with tandem mass spectrometry (UPLC-MS) was developed and validated for simultaneous quantification of six main bioactive components, i.e., calycosin-7-O-β-D-glucoside, ononin, calycosin, formononetin, astragaloside IV, and astragaloside II in rat plasma af...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-9972-x

    authors: Liu XH,Zhao JB,Guo L,Yang YL,Hu F,Zhu RJ,Feng SL

    更新日期:2014-09-01 00:00:00

  • Construction of small-caliber, polydioxanone cyclohexanone vascular stents.

    abstract::Objective of this article is to construct and characterize a three-layered small-caliber, artificial vascular stent. The outer layer of the stent consisted of small intestine submucosa (SIS), the middle layer was the polydioxanone (PDS) vascular stents, and the inner layer. The SIS and PDS were attached with 8-0 PDS t...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-010-9081-4

    authors: You Q,Wang F,Duan L,Du X,Xiao M,Shen Z

    更新日期:2010-05-01 00:00:00

  • Insight into the oseltamivir resistance R292K mutation in H5N1 influenza virus: a molecular docking and molecular dynamics approach.

    abstract::H5N1 is a subtype of the influenza A virus that can cause disease in humans and many other animal species. Oseltamivir (Tamiflu) is a potent and selective antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase (NA), a flu protein responsible for the release and spread of the...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-013-9709-2

    authors: Karthick V,Ramanathan K

    更新日期:2014-03-01 00:00:00

  • Ecto-mesenchymal stem cells from facial process: potential for muscle regeneration.

    abstract::Ecto-mesenchymal stem cells (EMSCs) originate from the cranial neural crest and participate in the formation of tooth, salivary, and muscle in early development stage. The transplantation of EMSCs, a potential source of myoblast stem cell, might improve muscle regeneration. The purpose of this study was to explore whe...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-9964-x

    authors: Nie X,Xing Y,Deng M,Gang L,Liu R,Zhang Y,Wen X

    更新日期:2014-09-01 00:00:00

  • Chemical-physical changes in cell membrane microdomains of breast cancer cells after omega-3 PUFA incorporation.

    abstract::Epidemiologic and experimental studies suggest that dietary fatty acids influence the development and progression of breast cancer. However, no clear data are present in literature that could demonstrate how n - 3 PUFA can interfere with breast cancer growth. It is suggested that these fatty acids might change the str...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-012-9365-y

    authors: Corsetto PA,Cremona A,Montorfano G,Jovenitti IE,Orsini F,Arosio P,Rizzo AM

    更新日期:2012-09-01 00:00:00

  • Extremely high frequency electromagnetic radiation enforces bacterial effects of inhibitors and antibiotics.

    abstract::The coherent electromagnetic radiation (EMR) of the frequency of 51.8 and 53 GHz with low intensity (the power flux density of 0.06 mW/cm(2)) affected the growth of Escherichia coli K12(lambda) under fermentation conditions: the lowering of the growth specific rate was considerably (approximately 2-fold) increased wit...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-008-9020-9

    authors: Tadevosyan H,Kalantaryan V,Trchounian A

    更新日期:2008-01-01 00:00:00

  • The protein-binding potential of C2H2 zinc finger domains.

    abstract::There are over 10,000 C2H2-type zinc finger (ZF) domains distributed among more than 1,000 ZF proteins in the human genome. These domains are frequently observed to be involved in sequence-specific DNA binding, and uncharacterized domains are typically assumed to facilitate DNA interactions. However, some ZFs also fac...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-008-9007-6

    authors: Brayer KJ,Kulshreshtha S,Segal DJ

    更新日期:2008-01-01 00:00:00

  • Contribution of hydrogenase 2 to stationary phase H2 production by Escherichia coli during fermentation of glycerol.

    abstract::Escherichia coli has four hydrogenases (Hyd), three genes of which are encoded by the hya, hyb, and hyc operons. The proton-reducing and hydrogen-oxidizing activities of Hyd-2 (hyb) were analyzed in whole cells grown to stationary phase and cell extracts, respectively, during glycerol fermentation using novel double m...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-012-9458-7

    authors: Trchounian K,Soboh B,Sawers RG,Trchounian A

    更新日期:2013-05-01 00:00:00

  • Tirofiban Combined with Fondaparinux for Post-PCI Treatment of Patients with Acute Coronary Syndrome and Mild Renal Insufficiency.

    abstract::Proper administration of antithrombotic and antiplatelet drugs after percutaneous coronary intervention (PCI) in patients with acute coronary syndrome (ACS) and renal insufficiency is a challenging task. In this study, we utilized Fondaparinux and Tirofiban (either separately or combined) to treat post-PCI patients wi...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章,随机对照试验

    doi:10.1007/s12013-015-0580-1

    authors: Changjiang H,Jian Q,Yuan Z,Liang Y,Puqing L,Xiaolong G

    更新日期:2015-12-01 00:00:00

  • Non-steroidal anti-inflammatory drugs and hypertension.

    abstract::Non-steroidal anti-inflammatory drugs (NSAIDs) are frequently used to alleviate pain of the patients who suffer from inflammatory conditions like rheumatoid arthritis, osteoarthritis, and other painful conditions like gout. This class of drugs works by blocking cyclooxgenases which in turn block the prostaglandin prod...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章,评审

    doi:10.1007/s12013-013-9791-5

    authors: Zheng L,Du X

    更新日期:2014-06-01 00:00:00

  • Glycogen debranching enzyme 6 (AGL), enolase 1 (ENOSF1), ectonucleotide pyrophosphatase 2 (ENPP2_1), glutathione S-transferase 3 (GSTM3_3) and mannosidase (MAN2B2) metabolism computational network analysis between chimpanzee and human left cerebrum.

    abstract::We identified significantly higher expression of the genes glycogen debranching enzyme 6 (AGL), enolase 1 (ENOSF1), ectonucleotide pyrophosphatase 2 (ENPP2_1), glutathione S-transferase 3 (GSTM3_3) and mannosidase (MAN2B2) from human left cerebrums versus chimpanzees. Yet the distinct low- and high-expression AGL, ENO...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-011-9232-2

    authors: Sun L,Wang L,Jiang M,Huang J,Lin H

    更新日期:2011-12-01 00:00:00

  • Expression of Treg subsets on intestinal T cell immunity and endotoxin translocation in porcine sepsis after severe burns.

    abstract::In the present study, the changes of the regulatory T cells (Treg) expression, endotoxin translocation, and the relationships in intestinal lymph nodes were investigated in porcine sepsis induced by severe burns. Flow cytometry, western blot, and Tachypleus amebocyte lysate were applied to study after the burn injury ...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-0116-0

    authors: Zu H,Li Q,Huang P

    更新日期:2014-12-01 00:00:00

  • Expression and functional significance of ezrin in human brain astrocytoma.

    abstract::Ezrin is overexpressed in a variety of neoplastic cells and is involved in the later stages of tumor progression and metastasis. The present study investigated the expression and functional significance of ezrin in human brain astrocytoma. Ezrin expression was examined in specimens from healthy human brains (10 autops...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-013-9653-1

    authors: Mao J,Yuan XR,Xu SS,Jiang XC,Zhao XT

    更新日期:2013-01-01 00:00:00

  • Resveratrol induces pro-oxidant effects and time-dependent resistance to cytotoxicity in activated hepatic stellate cells.

    abstract::Resveratrol (RSV) is known for its antioxidant properties; however, this compound has been proposed to have cytotoxic and pro-oxidant effects depending on its concentration and time of exposure. We previously reported the cell cycle arrest effect of low doses of RSV in GRX cells, an activated hepatic stellate cell mod...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-013-9703-8

    authors: Martins LA,Coelho BP,Behr G,Pettenuzzo LF,Souza IC,Moreira JC,Borojevic R,Gottfried C,Guma FC

    更新日期:2014-03-01 00:00:00

  • Correlations between CT perfusion parameters and vascular endothelial growth factor expression and microvessel density in implanted VX2 lung tumors.

    abstract::To evaluate the correlation between CT perfusion parameters and tumor angiogenesis, expression of VEGF is implanted in VX2 lung tumor. VX2 tumor cells were injected in 15 healthy New Zealand rabbits. After 20 days, tumors with diameter over 7 mm were scanned with 16 row spiral CT. Using Software Perfusion 3, blood flo...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-9966-8

    authors: Ling S,Deng D,Mo Y,Zhang X,Guan X,Wei Q

    更新日期:2014-09-01 00:00:00

  • Simultaneous Determination of Human Erythrocyte Deformability and Adhesion Energy: A Novel Approach Using a Microfluidic Chamber and the "Glass Effect".

    abstract::The simultaneous determination of adhesion and deformability parameters of erythrocytes was carried out through a microfluidic device, which uses an inverted optical microscope with new image acquisition and analysis technologies. Also, an update of the models describing erythrocyte adhesion and deformation was propos...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-020-00956-9

    authors: Londero CM,Riquelme BD

    更新日期:2020-11-07 00:00:00

  • Therapeutical effects and mechanism of salubrinal combined with ulinastatin on treating paraquat poisoning.

    abstract::To explore therapeutic effects and underlying mechanism of Salubrinal combined with Ulinastatin (UTI) on acute Paraquat (PQ) poisoning. Four hundred rats were randomly allocated into UTI group, SAL group, SAL + UTI and control group according to random number table with 100 rats in each group. Acute PQ poisoning model...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-0095-1

    authors: Guo H,Jiang C,Sun X

    更新日期:2014-12-01 00:00:00

  • Expression and purification of rotavirus proteins NSP5 and NSP6 in Escherichia coli.

    abstract::Rotaviruses are one of the worldwide leading causes of gastroenteritis in children under 5 yr old. The rotavirus nonstructural NSP5 is a phosphoprotein implicated in viroplasms formation, whereas NSP6 could have a possible regulatory role of NSP5. It has been reported that N- and C-termini of NSP5 are important for th...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1385/CBB:44:3:336

    authors: Samaniego-Hernández M,De León-Rodriguez A,Aparicio-Fabre R,Arias-Ortiz C,Barba de la Rosa AP

    更新日期:2006-01-01 00:00:00

  • Modelling the role of intrinsic electric fields in microtubules as an additional control mechanism of bi-directional intracellular transport.

    abstract::Active transport is essential for cellular function, while impaired transport has been linked to diseases such as neuronal degeneration. Much long distance transport in cells uses opposite polarity molecular motors of the kinesin and dynein families to move cargos along microtubules. It is clear that many types of car...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-008-9028-1

    authors: Sataric MV,Budinski-Petkovic L,Loncarevic I,Tuszynski JA

    更新日期:2008-01-01 00:00:00

  • Homocysteine-induced apoptosis in endothelial cells coincides with nuclear NOX2 and peri-nuclear NOX4 activity.

    abstract::Apoptosis of endothelial cells related to homocysteine (Hcy) has been reported in several studies. In this study, we evaluated whether reactive oxygen species (ROS)-producing signaling pathways contribute to Hcy-induced apoptosis induction, with specific emphasis on NADPH oxidases. Human umbilical vein endothelial cel...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-011-9297-y

    authors: Sipkens JA,Hahn N,van den Brand CS,Meischl C,Cillessen SA,Smith DE,Juffermans LJ,Musters RJ,Roos D,Jakobs C,Blom HJ,Smulders YM,Krijnen PA,Stehouwer CD,Rauwerda JA,van Hinsbergh VW,Niessen HW

    更新日期:2013-11-01 00:00:00

  • Evaluation of global longitudinal strain of left ventricle and regional longitudinal strain in the region of left ventricular leads predicts the response to cardiac resynchronization therapy in patients with ischemic heart failure.

    abstract::Myocardium viability in ischemic heart failure (HF) may affect the effect of cardiac resynchronization therapy (CRT). We hypothesized that longitudinal strain of 2D-STE, which reflects myocardium viability, can predict the response to CRT in patients with ischemic HF. 2D-STE was performed in 42 patients with HF, 1 wee...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-9870-2

    authors: Ma CY,Liu S,Yang J,Tang L,Zhang LM,Li N,Yu B

    更新日期:2014-09-01 00:00:00

  • Comparison of Gene Expression Profile Between Tumor Tissue and Adjacent Non-tumor Tissue in Patients with Gastric Gastrointestinal Stromal Tumor (GIST).

    abstract::Gastrointestinal stromal tumors (GISTs) are defined as spindle cell and/or epithelioid tumors originated from interstitial Cajal cells or precursors in the digestive tract. This study was conducted to identify genes differing in expression between the gastric tumors and the adjacent non-cancerous mucosas in patients w...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-0504-5

    authors: Kou Y,Zhao Y,Bao C,Wang Q

    更新日期:2015-06-01 00:00:00

  • One-dimensional migration of olfactory ensheathing cells on synthetic materials: experimental and numerical characterization.

    abstract::Olfactory ensheathing cells (OECs) are of great interest for regenerative purposes since they are believed to aid axonal growth. With the view set on the strategies to achieve reconnection between neuronal structures, it is of great importance to characterize the behaviour of these cells on long thread-like structures...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-012-9399-1

    authors: Pérez-Garnés M,Martínez-Ramos C,Barcia JA,Escobar Ivirico JL,Gómez-Pinedo U,Vallés-Lluch A,Monleón Pradas M

    更新日期:2013-01-01 00:00:00

  • Hepatocellular carcinoma in Budd-Chiari syndrome: enhancement patterns at dynamic gadolinium-enhanced T1-weighted MR imaging.

    abstract::The objective of this study was to analyze the enhancement patterns at dynamic gadolinium-enhanced T1-weighted MR imaging in patients of Hepatocellular Carcinoma (HCC) with associated Budd-Chiari syndrome (BCS). The MR imaging findings in 10 patients of HCC with associated BCS were compared to those of 32 other patien...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-014-9970-z

    authors: Yang C,Xu K,Zheng J,Ma P,Hu C,Li S,Rong Y,Lu X,Zhang Q,Zu M,Hua R,Zhang L

    更新日期:2014-09-01 00:00:00

  • Measuring activity in the ubiquitin-proteasome system: from large scale discoveries to single cells analysis.

    abstract::The ubiquitin-proteasome system (UPS) is the primary pathway responsible for the recognition and degradation of misfolded, damaged, or tightly regulated proteins in addition to performing essential roles in DNA repair, cell cycle regulation, cell migration, and the immune response. While traditional biochemical techni...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章,评审

    doi:10.1007/s12013-013-9621-9

    authors: Melvin AT,Woss GS,Park JH,Waters ML,Allbritton NL

    更新日期:2013-09-01 00:00:00

  • A pH dependence study on the unfolding and refolding of apoazurin: comparison with Zn(II) azurin.

    abstract::Azurin, a small blue copper protein from the bacterial species Pseudomonas aeruginosa, is mostly a beta-sheet protein arranged into a single domain. Previous folding studies have shown that the equilibrium denaturation of the holoprotein follows a two-state process; however, upon removal of the copper, the denaturatio...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1385/cbb:36:1:19

    authors: Hansen JE,McBrayer MK,Robbins M,Suh Y

    更新日期:2002-01-01 00:00:00

  • Theoretical and experimental investigation of calcium-contraction coupling in airway smooth muscle.

    abstract::We investigated theoretically and experimentally the Ca2+-contraction coupling in rat tracheal smooth muscle. [Ca2+]i, isometric contraction and myosin light chain (MLC) phosphorylation were measured in response to 1 mM carbachol. Theoretical modeling consisted in coupling a model of Ca2+-dependent MLC kinase (MLCK) a...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1385/CBB:46:3:233

    authors: Mbikou P,Fajmut A,Brumen M,Roux E

    更新日期:2006-01-01 00:00:00

  • MT2A Promotes Oxaliplatin Resistance in Colorectal Cancer Cells.

    abstract::We aimed to understand the molecular mechanism underlying the incidence of Oxaliplatin resistance in colorectal cancer. The Oxaliplatin-resistant (OR) HT29 colorectal cell line was established by long-term exposure to Oxaliplatin. Cell viability and proliferation were determined by the 3-(4,5-dimethyl thiazol-2-yl)-2,...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-020-00930-5

    authors: Zhao Z,Zhang G,Li W

    更新日期:2020-12-01 00:00:00

  • Clinical application of a dendritic cell vaccine raised against heat-shocked glioblastoma.

    abstract::Establishment of a detection platform for glioblastoma-dendritic cell (DC) vaccine preparation and to determine the efficacy of the vaccine in a clinical trial. Autologous glioblastoma-DC vaccine was prepared from a glioblast specimen procured from surgical resection. The specimen was used to enrich the vaccine with p...

    journal_title:Cell biochemistry and biophysics

    pub_type: 杂志文章

    doi:10.1007/s12013-011-9265-6

    authors: Jie X,Hua L,Jiang W,Feng F,Feng G,Hua Z

    更新日期:2012-01-01 00:00:00