Onconase dimerization through 3D domain swapping: structural investigations and increase in the apoptotic effect in cancer cells*

2017 ◽  
Vol 474 (22) ◽  
pp. 3767-3781 ◽  
Author(s):  
Andrea Fagagnini ◽  
Andrea Pica ◽  
Sabrina Fasoli ◽  
Riccardo Montioli ◽  
Massimo Donadelli ◽  
...  
Keyword(s):  
Cytotoxic Activity ◽  
Three Dimensional ◽  
Homology Model ◽  
Rnase A ◽  
Domain Swapping ◽  
Structural Investigations ◽  
C Terminus ◽  
Apoptotic Effect ◽  
Bovine Seminal Ribonuclease ◽  
High Cytotoxic Activity

Onconase® (ONC), a protein extracted from the oocytes of the Rana pipiens frog, is a monomeric member of the secretory ‘pancreatic-type’ RNase superfamily. Interestingly, ONC is the only monomeric ribonuclease endowed with a high cytotoxic activity. In contrast with other monomeric RNases, ONC displays a high cytotoxic activity. In this work, we found that ONC spontaneously forms dimeric traces and that the dimer amount increases about four times after lyophilization from acetic acid solutions. Differently from RNase A (bovine pancreatic ribonuclease) and the bovine seminal ribonuclease, which produce N- and C-terminal domain-swapped conformers, ONC forms only one dimer, here named ONC-D. Cross-linking with divinylsulfone reveals that this dimer forms through the three-dimensional domain swapping of its N-termini, being the C-terminus blocked by a disulfide bond. Also, a homology model is proposed for ONC-D, starting from the well-known structure of RNase A N-swapped dimer and taking into account the results obtained from spectroscopic and stability analyses. Finally, we show that ONC is more cytotoxic and exerts a higher apoptotic effect in its dimeric rather than in its monomeric form, either when administered alone or when accompanied by the chemotherapeutic drug gemcitabine. These results suggest new promising implications in cancer treatment.

scholarly journals Structural investigations of CXCR2 receptor antagonists by CoMFA, CoMSIA and flexible docking studies

2012 ◽  
Vol 62 (3) ◽  
pp. 287-304 ◽  
Author(s):  
Shravan Kumar Gunda ◽  
Rohith Kumar Anugolu ◽  
Sri Ramya Tata ◽  
Saikh Mahmood
Keyword(s):  
Standard Error ◽  
Three Dimensional ◽  
3D Qsar ◽  
Homology Model ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Field Analysis ◽  
Structural Investigations ◽  
Qsar Analysis ◽  
Qsar Studies

= Three-dimensional quantitative structure activity relationship (3D QSAR) analysis was carried out on a et of 56 N,N’-diarylsquaramides, N,N’-diarylureas and diaminocyclobutenediones in order to understand their antagonistic activities against CXCR2. The studies included comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Models with good predictive abilities were generated with CoMFA q2 0.709, r2 (non-cross-validated square of correlation coefficient) = 0.951, F value = 139.903, r2 bs = 0.978 with five components, standard error of estimate = 0.144 and the CoMSIA q2 = 0.592, r2 = 0.955, F value = 122.399, r2 bs = 0.973 with six components, standard error of estimate = 0.141. In addition, a homology model of CXCR2 was used for docking based alignment of the compounds. The most active compound then served as a template for alignment of the remaining structures. Further, mapping of contours onto the active site validated each other in terms of residues involved with reference to the respective contours. This integrated molecular docking based alignment followed by 3D QSAR studies provided a further insight to support the structure-based design of CXCR2 antagonistic agents with improved activity profiles. Furthermore, in silico screening was adapted to the QSAR model in order to predict the structures of new, potentially active compounds.

scholarly journals Propensity for C-terminal domain swapping correlates with increased regional flexibility in the C-terminus of RNase A

2011 ◽  
Vol 20 (10) ◽  
pp. 1735-1744 ◽  
Author(s):  
Katherine H. Miller ◽  
Susan Marqusee
Keyword(s):  
Rnase A ◽  
Domain Swapping ◽  
Terminal Domain ◽  
C Terminus

scholarly journals Interactions Crucial for Three-Dimensional Domain Swapping in the HP-RNase Variant PM8

2011 ◽  
Vol 101 (2) ◽  
pp. 459-467 ◽  
Author(s):  
Pere Tubert ◽  
Douglas V. Laurents ◽  
Marc Ribó ◽  
Marta Bruix ◽  
Maria Vilanova ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Domain Swapping ◽  
Dimensional Domain

scholarly journals Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

2020 ◽  
Author(s):  
Lasse Staby ◽  
Katherine R. Kemplen ◽  
Amelie Stein ◽  
Michael Ploug ◽  
Jane Clarke ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Life Time ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Order And Disorder ◽  
C Terminus ◽  
Close Relationship ◽  
Stability Dynamics ◽  
And Function

Abstract Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order–disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.

scholarly journals The Unfolding Story of Three-Dimensional Domain Swapping

Structure ◽  
2003 ◽  
Vol 11 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Frederic Rousseau ◽  
Joost W.H. Schymkowitz ◽  
Laura S. Itzhaki
Keyword(s):  
Three Dimensional ◽  
Domain Swapping ◽  
Dimensional Domain

scholarly journals Lipoprotein-Free Mitotane Exerts High Cytotoxic Activity in Adrenocortical Carcinoma

2015 ◽  
Vol 100 (8) ◽  
pp. 2890-2898 ◽  
Author(s):  
Ségolène Hescot ◽  
Atmane Seck ◽  
Maryse Guerin ◽  
Florence Cockenpot ◽  
Thierry Huby ◽  
...  
Keyword(s):  
Cytotoxic Activity ◽  
Adrenocortical Carcinoma ◽  
High Cytotoxic Activity

scholarly journals Improved scFv Anti-LOX-1 Binding Activity by Fusion with LOX-1-Binding Peptides

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Wei Hu ◽  
Qiuhong Xie ◽  
Hongyu Xiang
Keyword(s):  
Targeted Delivery ◽  
Structural Characteristics ◽  
Low Density Lipoprotein ◽  
Three Dimensional ◽  
Density Lipoprotein ◽  
Binding Activity ◽  
Single Chain ◽  
C Terminus ◽  
Density Lipoprotein Receptor ◽  
Therapeutic Molecules

The oxidized low-density lipoprotein receptor-1 (LOX-1) targeted single-chain variable fragment (scFvs) is a promising molecule for the targeted delivery of imaging and therapeutic molecules of atherosclerotic diseases; however, its applications are limited by the inherent low antigen affinity. In this study, the three-dimensional (3D) model of the anti-LOX-1 scFv was constructed and its docking with the LOX-1 protein was developed. To improve the LOX-1-binding activity, the anti-LOX-1 scFv was designed to fuse with one of three LOX-1-binding heptapeptides, LTPATAI, FQTPPQL, and LSIPPKA, at its N-terminus and C-terminus and in the linker region, which have different LOX-1-binding interfaces with the anti-LOX-1 scFv analyzed by an array of computational approaches. These scFv/peptide fusions were constructed, successfully expressed in Brevibacillus choshinensis hosts, and purified by a two-step column purification process. The antigen binding activity, structural characteristics, thermal stability, and stability in serum of these fusion proteins were examined. Results showed that the scFv with N-terminal fusing peptides proteins demonstrated increased LOX-1-binding activity without decrease in stability. These findings will help increase the application efficacy of LOX-1 targeting scFv in LOX-1-based therapy.

scholarly journals Metabolic Profile and Evaluation of Biological Activities of Extracts from the Stems of Cissus trifoliata

2020 ◽  
Vol 21 (3) ◽  
pp. 930
Author(s):  
Luis Fernando Méndez-López ◽  
Elvira Garza-González ◽  
María Yolanda Ríos ◽  
M. Ángeles Ramírez-Cisneros ◽  
Laura Alvarez ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antibacterial Activity ◽  
Cytotoxic Activity ◽  
Metabolic Profile ◽  
Biological Activities ◽  
Cytotoxic Activities ◽  
Aqueous Extracts ◽  
Antitumor Effects ◽  
Anticancer Compounds ◽  
High Cytotoxic Activity

Cissus trifoliata (L.) L belongs to the Vitaceae family and is an important medicinal plant used in Mexico for the management of infectious diseases and tumors. The present study aimed to evaluate the metabolic profile of the stems of C. trifoliata and to correlate the results with their antibacterial and cytotoxic activities. The hexane extract was analyzed using gas chromatography coupled with mass spectrometry (GC-MS) and the CHCl3-MeOH and aqueous extracts by ultraperformance liquid chromatography quadrupole time of fly mass spectrometry (UPLC-QTOF-MS). The antibacterial activity was determined by broth microdilution and the cytotoxicity was evaluated using MTS cell proliferation assay. Forty-six metabolites were putatively identified from the three extracts. Overall, terpenes, flavonoids and stilbenes characterize the metabolic profile. No antibacterial activity was found in any extract against the fifteen bacteria strains tested (MIC >500 µg/mL). However, high cytotoxic activity (IC50 ≤ 30 µg/mL) was found in the hexane and aqueous extracts against hepatocarcinoma and breast cancer cells (Hep3B, HepG2 and MCF7). This is the first report of the bioactive compounds of C. trifoliata stems and their antibacterial and cytotoxic properties. The metabolic profile rich in anticancer compounds correlate with the cytotoxic activity of the extracts from the stems of C. trifoliata. This study shows the antitumor effects of this plant used in the traditional medicine and justifies further research of its anticancer activity.

scholarly journals A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weijun Wang ◽  
Tania Archbold ◽  
Joseph S. Lam ◽  
Matthew S. Kimber ◽  
Ming Z. Fan
Keyword(s):  
Gut Microbiome ◽  
Catalytic Domain ◽  
Hydrolysis Product ◽  
Three Dimensional ◽  
Homology Model ◽  
Industrial Applications ◽  
Glycoside Hydrolase Family ◽  
Expression Library ◽  
Plant Polysaccharides ◽  
Processive Endoglucanase

Abstract Cellulases play important roles in the dietary fibre digestion in pigs, and have multiple industrial applications. The porcine intestinal microbiota display a unique feature in rapid cellulose digestion. Herein, we have expressed a cellulase gene, p4818Cel5_2A, which singly encoded a catalytic domain belonging to glycoside hydrolase family 5 subfamily 2, and was previously identified from a metagenomic expression library constructed from porcine gut microbiome after feeding grower pigs with a cellulose-supplemented diet. The activity of purified p4818Cel5_2A was maximal at pH 6.0 and 50 °C and displayed resistance to trypsin digestion. This enzyme exhibited activities towards a wide variety of plant polysaccharides, including cellulosic substrates of avicel and solka-Floc®, and the hemicelluloses of β-(1 → 4)/(1 → 3)-glucans, xyloglucan, glucomannan and galactomannan. Viscosity, reducing sugar distribution and hydrolysis product analyses further revealed that this enzyme was a processive endo-β-(1 → 4)-glucanase capable of hydrolyzing cellulose into cellobiose and cellotriose as the primary end products. These catalytic features of p4818Cel5_2A were further explored in the context of a three-dimensional homology model. Altogether, results of this study report a microbial processive endoglucanase identified from the porcine gut microbiome, and it may be tailored as an efficient biocatalyst candidate for potential industrial applications.

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