NDLI: QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein

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QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein

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QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein

Content Provider	Springer Nature Link
Author	González Díaz, Humberto Dea Ayuela, María A. Pérez Montoto, Lázaro G. Prado Prado, Francisco J. Agüero Chapín, Guillermín Bolas Fernández, Francisco Vazquez Padrón, Roberto I. Ubeira, Florencio M.
Copyright Year	2009
Abstract	The toxicity and low success of current treatments for Leishmaniosis determines the search of new peptide drugs and/or molecular targets in Leishmania pathogen species (L. infantum and L. major). For example, Ribonucleases (RNases) are enzymes relevant to several biologic processes; then, theoretical and experimental study of the molecular diversity of Peptide Mass Fingerprints (PMFs) of RNases is useful for drug design. This study introduces a methodology that combines QSAR models, 2D-Electrophoresis (2D-E), MALDI-TOF Mass Spectroscopy (MS), BLAST alignment, and Molecular Dynamics (MD) to explore PMFs of RNases. We illustrate this approach by investigating for the first time the PMFs of a new protein of L. infantum. Here we report and compare new versus old predictive models for RNases based on Topological Indices (TIs) of Markov Pseudo-Folding Lattices. These group of indices called Pseudo-folding Lattice 2D-TIs include: Spectral moments π $_{k}$(x,y), Mean Electrostatic potentials ξ $_{k}$(x,y), and Entropy measures θ $_{k}$(x,y). The accuracy of the models (training/cross-validation) was as follows: ξ $_{k}$(x,y)-model (96.0%/91.7%)>π $_{k}$(x,y)-model (84.7/83.3) > θ $_{k}$(x,y)-model (66.0/66.7). We also carried out a 2D-E analysis of biological samples of L. infantum promastigotes focusing on a 2D-E gel spot of one unknown protein with M<20, 100 and pI <7. MASCOT search identified 20 proteins with Mowse score >30, but not one >52 (threshold value), the higher value of 42 was for a probable DNA-directed RNA polymerase. However, we determined experimentally the sequence of more than 140 peptides. We used QSAR models to predict RNase scores for these peptides and BLAST alignment to confirm some results. We also calculated 3D-folding TIs based on MD experiments and compared 2D versus 3D-TIs on molecular phylogenetic analysis of the molecular diversity of these peptides. This combined strategy may be of interest in drug development or target identification.
Starting Page	349
Ending Page	369
Page Count	21
File Format	PDF
ISSN	13811991
Journal	Molecular Diversity
Volume Number	14
Issue Number	2
e-ISSN	1573501X
Language	English
Publisher	Springer Netherlands
Publisher Date	2009-07-04
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	QSAR Topological indices Markov models Protein folding HP Lattice model Ribonucleases Leishmania MALDI-TOF Mass Spectroscopy 2D-Electrophoresis Sequence alignment Molecular dynamics Pharmacy Polymer Sciences Organic Chemistry Biochemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Medicine Drug Discovery Molecular Biology Physical and Theoretical Chemistry Information Systems Catalysis Inorganic Chemistry

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