scholarly journals De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

2012 ◽  
Vol 55 (9) ◽  
pp. 4159-4168 ◽  
Author(s):  
Meghan L. Bellows-Peterson ◽  
Ho Ki Fung ◽  
Christodoulos A. Floudas ◽  
Chris A. Kieslich ◽  
Li Zhang ◽  
...  
PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e90095 ◽  
Author(s):  
James Smadbeck ◽  
Meghan B. Peterson ◽  
Barry M. Zee ◽  
Shivani Garapaty ◽  
Aashna Mago ◽  
...  

2005 ◽  
Vol 10 (4) ◽  
pp. 295-304 ◽  
Author(s):  
I. Belda ◽  
X. Llorà ◽  
E. Giralt

2005 ◽  
Vol 19 (8) ◽  
pp. 585-601 ◽  
Author(s):  
Ignasi Belda ◽  
Sergio Madurga ◽  
Xavier Llorà ◽  
Marc Martinell ◽  
Teresa Tarragó ◽  
...  

Author(s):  
Lars G. J. Hammarström ◽  
Ted J. Gauthier ◽  
Robert P. Hammer ◽  
Mark L. McLaughlin

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e10926 ◽  
Author(s):  
E. Besray Unal ◽  
Attila Gursoy ◽  
Burak Erman

Author(s):  
Paul Wrede

Peptides fulfill many tasks in controlling and regulating cellular functions and are key molecules in systems biology. There is a great demand in science and industry for a fast search of innovative peptide structures. In this chapter we introduce a combination of a computer-based guided search of novel peptides in sequence space with their biological experimental validation. The computer-based search uses an evolutionary algorithm that includes artificial neural networks as fitness function and a mutation operator, called the PepHarvester. Optimization occurs during 100 iterations. This system, called DARWINIZER, is applied in the de novo design of neutralizing peptides against autoantibodies from DCM (dilatative cardiomyopathy) patients. Another approach is the optimization of peptide sequences by an ant colony optimization process. This biologically-oriented system identified several novel weak binding T-cell epitopes.


2004 ◽  
Vol 384 (2) ◽  
pp. 429-436 ◽  
Author(s):  
Sundaramurthy VARADHARAJAN ◽  
B. K. Chandrashekar SAGAR ◽  
Pundi N. RANGARAJAN ◽  
Govindarajan PADMANABAN

Our previous studies have demonstrated de novo haem biosynthesis in the malarial parasite (Plasmodium falciparum and P. berghei). It has also been shown that the first enzyme of the pathway is the parasite genome-coded ALA (δ-aminolaevulinate) synthase localized in the parasite mitochondrion, whereas the second enzyme, ALAD (ALA dehydratase), is accounted for by two species: one species imported from the host red blood cell into the parasite cytosol and another parasite genome-coded species in the apicoplast. In the present study, specific antibodies have been raised to PfFC (parasite genome-coded ferrochelatase), the terminal enzyme of the haem-biosynthetic pathway, using recombinant truncated protein. With the use of these antibodies as well as those against the hFC (host red cell ferrochelatase) and other marker proteins, immunofluorescence studies were performed. The results reveal that P. falciparum in culture manifests a broad distribution of hFC and a localized distribution of PfFC in the parasite. However, PfFC is not localized to the parasite mitochondrion. Immunoelectron-microscopy studies reveal that PfFC is indeed localized to the apicoplast, whereas hFC is distributed in the parasite cytoplasm. These results on the localization of PfFC are unexpected and are at variance with theoretical predictions based on leader sequence analysis. Biochemical studies using the parasite cytosolic and organellar fractions reveal that the cytosol containing hFC accounts for 80% of FC enzymic activity, whereas the organellar fraction containing PfFC accounts for the remaining 20%. Interestingly, both the isolated cytosolic and organellar fractions are capable of independent haem synthesis in vitro from [4-14C]ALA, with the cytosol being three times more efficient compared with the organellar fraction. With [2-14C]glycine, most of the haem is synthesized in the organellar fraction. Thus haem is synthesized in two independent compartments: in the cytosol, using the imported host enzymes, and in the organellar fractions, using the parasite genome-coded enzymes.


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