Sirota Fernanda L.

Isolation and Identification of an Anthracimycin Analogue from Nocardiopsis kunsanensis, a Halophile from a Saltern, by Genomic Mining Strategy

Published date : 21 May 2018

Modern medicine is unthinkable without antibiotics; yet, growing issues with microbial drug resistance require intensified search for new active compounds. Natural products generated by Actinobacteria have been a rich source of candidate antibiotics, for example anthracimycin that, so far, is only known to be produced by Streptomyces species. Based on sequence similarity with the respective biosynthetic cluster, we sifted through available microbial genome data with the goal to find alternative anthracimycin-producing organisms.

type
Journal Paper
journal
Journal of Genomics, Vol. 6, 2018, Pg 63-73, doi:10.7150/jgen.24368
Impact Factor
2.402

The Recipe for Protein-Based Function Predition and its implementation in the ANNOTATOR Software Environment

Published date : 27 Apr 2016

As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction.

type
Book/Book Chapter
journal
Data Mining Techniques for the Life Sciences, Vol. 1415, pg 477-506,2016, ISBN: 978-1-4939-3570-3

Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: to be or not to be exposed for enzyme access

Published date : 02 Jun 2015

Many protein posttranslational modifications (PTMs) are the result of an enzymatic reaction. The modifying enzyme has to recognize the substrate protein’s sequence motif containing the residue(s) to be modified; thus, the enzyme’s catalytic cleft engulfs these residue(s) and the respective sequence environment. This residue accessibility condition principally limits the range where enzymatic PTMs can occur in the protein sequence.

type
Journal Paper
journal
Proteomics, 2015, Jun 2, doi: 10.1002/pmic.201400633
Impact Factor
3.973

Conservation of the extended substrate specificity profiles among homologous granzymes across species

Published date : 20 Jun 2013

Granzymes are structurally related serine proteases involved in cell death and immunity. To date four out of five human granzymes have assigned orthologues in mice; however for granzyme H, no murine orthologue has been suggested and its role in cytotoxicity remains controversial. Here, we demonstrate that, as is the case for granzyme C, human granzyme H is an inefficient cytotoxin which together with their similar pattern of GrB divergence and functional similarity strongly hint to their orthologous relationship.

type
Journal Paper
journal
Molecular & Cellular Proteomics 2013, 20 Jun, doi: 10.1074/mcp.M113.028670

Protein Sequence-Structure-Function-Network Links Discovered with the ANNOTATOR Software Suite: Application to ELYS/Mel-28

Published date : 19 Sep 2012

While very little genomic sequence is interpretable in terms of biological mechanism directly, the chances are much better for protein-coding genes that can be translated into protein sequences. This review considers the different concepts applicable to sequence analysis and function prediction of globular and non-globular protein segments. The publicly accessible ANNOTATOR software environment integrates most of the reliable protein sequence-based function prediction methods, protein domain databases and pathway, and protein–protein interaction collections developed in academia.

type
Book/Book Chapter
journal
Computational Medicine - Tools and Challenges, 2012, pg 111-143, ISBN 978-3-7091-0946-5

Beware Of Moving Targets: Reference Proteome Content Fluctuates Substantially Over The Years

Published date : 09 Aug 2012

Reference proteomes are generated by increasingly sophisticated annotation pipelines as part of regular genome build releases; yet, the corresponding changes in reference proteomes' content are dramatic. In the history of the NCBI-curated human proteome, the total number of entries has remained roughly constant but approximately half of the proteins from the 2003 build 33 are no longer represented by entries in current releases, while about the same number of new proteins have been added (for sequence identity thresholds 50-90%).

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 10, No. 6 (2012), doi: 10.1142/S0219720012500205

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

Published date : 23 Apr 2012

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic.

type
Journal Paper
journal
Bioinformatics 2012, June 15, Vol 28, Issue 12, Pg 1645-1646