scholarly journals Molecular modeling of the Plasmodium falciparum pre-mRNA splicing and nuclear export factor PfU52

Author(s):  
Alain Narcisse Newo Soufo

UAP56/SUB2 is a DExD/H-box RNA helicase that is critically involved in pre-mRNA splicing and mRNA nuclear export. This helicase is broadly conserved and essential in many eukaryotic lineages, including protozoan and metazoan parasites. Previous research suggests that helicases from parasites could be promising drug targets for treating parasitic diseases. Accordingly, characterizing the structure and function of these proteins is of interest for structure-based, de novo design of new lead compounds. Here, we used homology modeling to construct a three-dimensional structure of PfU52 (PMDB ID: PM0079288), the Plasmodium falciparum ortholog of UAP56/SUB2. Comparative in silico analysis revealed that although PfU52 shared many physicochemical, structural and dynamic similarities with its human homolog, it also displayed some unique features that could be exploited for drug design.

2013 ◽  
Author(s):  
Alain Narcisse Newo Soufo

UAP56/SUB2 is a DExD/H-box RNA helicase that is critically involved in pre-mRNA splicing and mRNA nuclear export. This helicase is broadly conserved and essential in many eukaryotic lineages, including protozoan and metazoan parasites. Previous research suggests that helicases from parasites could be promising drug targets for treating parasitic diseases. Accordingly, characterizing the structure and function of these proteins is of interest for structure-based, de novo design of new lead compounds. Here, we used homology modeling to construct a three-dimensional structure of PfU52 (PMDB ID: PM0079288), the Plasmodium falciparum ortholog of UAP56/SUB2. Comparative in silico analysis revealed that although PfU52 shared many physicochemical, structural and dynamic similarities with its human homolog, it also displayed some unique features that could be exploited for drug design.


Author(s):  
Cambyz Irajie ◽  
Milad Mohkam ◽  
Navid Nezafat ◽  
Fatemeh Mohammadi ◽  
Younes Ghasemi

Nattokinase or subtilisin NAT (EC 3.4.21.62) is one of the most remarkable enzymes produced by Bacillus subtilis sp. Natto, which posses direct fibrinolytic activity. The aim of this study is in silico analysis of Nattokinase structure and function. The three-dimensional structure of serine protease Nattokinase from Bacillus subtilis sp. natto was determined using homology modeling performed by Geno3D2 Web Server and refined by ModRefiner. The obtained models were validated via programs such as RAMPAGE, ERRAT, 3D Match and verify 3D for consistency; moreover, functional analysis performed by PFP from Kihara Bioinformatics laboratory. RAMPAGE analysis showed that 96.7% of the residues are located in the favored region, 3.0% in allowed region and 0.4% in outlier region of the Ramachandran plot. The verify 3D value of 0.73 indicates that the environmental sketch of the model is fine. SOPMA and PSIPRED were exploited for computation of the secondary structural properties of serine protease Nattokinase. Active site determination via AADS suggested that this enzyme can be applied as a potent enzyme for cardiovascular therapy. However, these results should be more confirmed by wet lab researches for designing the more active enzyme for better functions on its fibrinolysis activity.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3006-3006
Author(s):  
Joel G Turner ◽  
Thomas C Rowe ◽  
David Ostrov ◽  
Jana L Dawson ◽  
Elizabeth Ciaravino ◽  
...  

Abstract Abstract 3006 Abstract Human multiple myeloma (MM) still remains an incurable disease despite improved treatment regimens that include bortezomib, lenalidomide and thalidomide. New therapeutic targets are needed to further improve treatment outcomes. We have shown that targeting intracellular trafficking of proteins may sensitize cells to antitumor agents (Turner et al. 2009, Cancer Res, 69, 6899-905). We have previously demonstrated that topoisomerase II alpha (topo IIα) trafficking from the nucleus to the cytoplasm in myeloma cells occurs by a CRM1-dependent mechanism and resulting in drug resistance to topo II inhibitors (Engel et al. 2004, Exp Cell Res, 295, 421-31). We have also identified the nuclear export signals (NES) for topo IIα at amino acids 1017-28 (site 1) and 1054-66 (site 2) (Turner et al. 2004, J Cell Sci, 117, 3061-71). Blocking nuclear export of topo IIα with a CRM1 inhibitor or by siRNA has been shown to sensitize MM cells to topo II poisons (Turner et al. 2009, Cancer Res, 69, 6899-905). The NES amino acid sequence of topo IIα at 1017–1028 is a unique site. Even though this site conforms to the hydrophobic amino acid motif for an NES, the amino acid sequence does not occur in any other human protein. In addition, this NES is in a pocket formed by the three-dimensional structure of the topo IIα protein. These factors allow the potential for the development of drugs that will exclusively block the NES of topo IIα and not affect the export of other nuclear proteins, as occurs with other known CRM1 inhibitors. Drug resistance to topo II inhibitors occurs when topo IIα is trafficked from the nucleus to the cytoplasm where it is no longer in contact with the DNA, and thus unable to induce cell death (Valkov et al 2000, Br J Haematol, 108, 331-45, Engel et al. 2004, Exp Cell Res, 295, 421-31). We therefore hypothesize that targeting a specific NES in topo IIα is an innovative treatment approach in MM and may allow a very focused and potent combination with topo II inhibitors, possibly overcoming de novo drug resistance in this malignancy. To date, we know of no agents that target the NES of a specific protein that are being developed to treat cancer. A computer generated hybrid molecule using the known three dimensional structure of yeast topo II and the human NES sequences of topo IIα was produced. Molecules were docked in silico using the NCI small molecule database (140,000 compounds). The molecules with the highest docking scores were obtained from NCI and assayed for IC50 values and synergy with the topo II inhibitor doxorubicin. All NES site 1 molecules tested showed activity, however, none of the NES site 2 molecules exhibited any anti-neoplastic activity with or without a topo II inhibitor. CT blue (Promega) robotic cell viability assays determined that several of the site 1 inhibitors had anti-proliferative activity. The IC50 values obtained from single drug cell viability assays in low density cells revealed two site 1 inhibitors compounds with IC50 values of 4.7 (NCI-36400) and 11.1 μM (NCI-35847). None of the site 1 inhibitors affected the viability of high-density cells (IC50>100 μM). Data from apoptosis assays indicate that three of the site 1 inhibitors (NCI-36400, NCI-35847, NCI-35024) that dock to NES site 1 do significantly (p<0.05) sensitize high density MM cells to doxorubicin. Immunofluorescence microscopy revealed an increase in topo IIα in the cell nucleus of cells treated for 20 hours with the three lead site 1 inhibitors. Nuclear-cytoplasmic fractionation revealed that the NES site 1 docking molecules prevent nuclear export of topo IIα. These compounds may lead to new chemotherapeutic treatments of myeloma. Disclosures: No relevant conflicts of interest to declare.


2003 ◽  
Vol 31 (6) ◽  
pp. 1330-1334 ◽  
Author(s):  
G. Schäfer ◽  
S. Kardinahl

Iron and manganese superoxide dismutases are phylogenetically closely related. They are compared by in silico analysis with regard to their metal specificity and their three-dimensional structure. Special attention is given to the structure and properties of superoxide dismutases from archaeal prokaryotes. The mechanism and the extreme thermostability of superoxide dismutase from Sulfolobus acidocaldarius are discussed on the basis of its high-resolution X-ray structure. An alternating-site mechanism and an evolutionary origin of superoxide dismutases under the environmental conditions on the early Earth are proposed.


2018 ◽  
Vol 74 (9) ◽  
pp. 861-876 ◽  
Author(s):  
Eyram Adjogatse ◽  
Peter Erskine ◽  
Stephen A. Wells ◽  
John M. Kelly ◽  
Jonathan D. Wilden ◽  
...  

Two of the world's most neglected tropical diseases, human African trypanosomiasis (HAT) and Chagas disease, are caused by protozoan parasites of the genus Trypanosoma. These organisms possess specialized metabolic pathways, frequently distinct from those in humans, which have potential to be exploited as novel drug targets. This study elucidates the structure and function of L-threonine-3-dehydrogenase (TDH) from T. brucei, the causative pathogen of HAT. TDH is a key enzyme in the metabolism of L-threonine, and an inhibitor of TDH has been shown to have trypanocidal activity in the procyclic form of T. brucei. TDH is a nonfunctional pseudogene in humans, suggesting that it may be possible to rationally design safe and specific therapies for trypanosomiasis by targeting this parasite enzyme. As an initial step, the TDH gene from T. brucei was expressed and the three-dimensional structure of the enzyme was solved by X-ray crystallography. In multiple crystallographic structures, T. brucei TDH is revealed to be a dimeric short-chain dehydrogenase that displays a considerable degree of conformational variation in its ligand-binding regions. Geometric simulations of the structure have provided insight into the dynamic behaviour of this enzyme. Furthermore, structures of TDH bound to its natural substrates and known inhibitors have been determined, giving an indication of the mechanism of catalysis of the enzyme. Collectively, these results provide vital details for future drug design to target TDH or related enzymes.


Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.


Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.


PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0171355 ◽  
Author(s):  
Roshni Bhattacharya ◽  
Peter W. Rose ◽  
Stephen K. Burley ◽  
Andreas Prlić

2021 ◽  
Author(s):  
Miao Guo ◽  
Yucai Chen ◽  
Longlong Lin ◽  
Yilin Wang ◽  
Anqi Wang ◽  
...  

Abstract Background: Lesch-Nyhan disease (LND) is a rare x-linked purine metabolic neurogenetic disease caused by enzyme hypoxanthine-guanine phosphoriribosyltransferase(HGprt) deficiency, also known as self-destructive appearance syndrome. A series of manifestations are caused by abnormal purine metabolism. The typical clinical manifestations are hyperuricemia, growth retardation, mental retardation, short stature, dance-like athetosis, aggressive behavior, and compulsive self-harm.. Results: we identified a point mutation c.151C > T (p. Arg51*) in a pedigree. We analyzed the clinical characteristics of children in a family, and obtained the blood of their parents and siblings for second-generation sequencing. At the same time, we also analyzed and compared the expression of HPRT1 gene and predicted the three-dimensional structure of the protein. And we analyzed the clinical manifestations caused by the defect of the HPRT1 genethe mutation led to the termination of transcription at the 51st arginine, resulting in the production of truncated protein, and the relative expression of HPRT1 gene in patients was significantly lower than other family members and 10 normal individuals. Conclusion: this mutation leads to the early termination of protein translation and the formation of a truncated HPRT protein, which affects the function of the protein and generates corresponding clinical manifestations.


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