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Stefan.Janecek@savba.sk
phone: ++ 421 2 5930 7420
fax: ++ 421 2 5930 7416 |
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Dubravska cesta 9 SK-84551 |
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Laboratory of Protein Evolution is
engaged in basic research in the field of protein bioinformatics. It is
focused
on the in silico study of proteins at the molecular
level, i.e. to
compare the primary and tertiary protein structures and to draw the
relationships
between the sequence, structure and evolution on one side and function,
specificity and stability of the other side. The main aim is - within a
collaboration with experimental approaches - protein engineering and
design. In
the centre of attention, there are enzymes hydrolyzing starch and
related
oligo- and polysaccharides, mainly from the alpha-amylase families (~30
different enzyme specificities), currently classified in the CAZy system
(Carbohydrate-Active Enzymes) into families of glycoside hydrolases
GH13, GH57,
GH119 and eventually also GH126. The interest is also in functionally
and
evolutionarily related enzymes from families GH70, GH77 and GH31, as
well as in
starch binding domains from the so-called CAZy CBM families.
The Head of the Laboratory, Stefan
Janecek, has
been devoted to the scientific field of the in silico
studying of
proteins for 25 years continuously, 15 last years being giving his
experiences
to students as a university teacher at the University of SS
Cyril and
Methodius in Trnava. Under his supervising, 5 PhD-students have already
finished their studies successfully. He has been the founder and main
organizer
of a series of international symposia about the enzymes from the
alpha-amylase
family - ALAMYs, held
from 2001 traditionally in the Smolenice Castle in Slovakia. In 2016,
he
established the international open-access scientific journal Amylase. He is
also one of curators and co-authors of the web-based encyclopedia for
carbohydrate-active enzymes CAZypedia.
Representative scientific achievements
could be listed as follows:
(i) identification of conserved sequence regions in amylolytic enzyme
families
GH13 and GH57; (ii) definition of subfamilies of oligo-1,6-glucosidases
and
neopullulanase in the alpha-amylase family GH13; (iii) revealing a
remote
homology between the alpha-amylase family GH13 and its related family
of
alpha-glucosidases GH31; (iv) discovery and characterisation of
sequence unique
amylomaltase from the family GH77 from borreliae (namely from Borrelia
burgdorferi); (v) identification of sequence-structural
similarity and
evolutionary homology between the alpha-amylase families GH57 and
GH119; (vi)
describing a close relatedness of family GH13 alpha-amylases from
archaeons and
plants; (vii) elucidation of evolutionary relationships among
individual enzyme
specificities in the alpha-amylase families GH13 and GH57; (viii)
highlighting
the evolutionary history of the mammalian heavy-chain amino acid
transporters
within the alpha-amylase family GH13; (ix) contributing to the
knowledge on
relationships among different families of starch-binding domains from
various
enzymes and proteins; and (x) describing a putative starch-binding
domain of
the family CBM20 typical for microbial amylolytic enzymes in the
mammalian
protein genethonin-1.
==========
Interested in joining the group? Prospective students? Looking for a Bachelor, Master and/or PhD-project...? Feel free to contact at Stefan.Janecek@savba.sk. Write a few lines describing your interest in this type of research work and your motivation. You should be ready to study and work a lot having, however, ambitious scientific aims and, especially, enjoying a highly friendly and generous atmosphere.
==========
Selected publications
Full Papers:
(29) Janickova Z. & Janecek S. (2021) In silico
analysis of fungal and chloride-dependent α-amylases within
the family GH13
with identification of possible secondary surface-binding
sites. Molecules 26: 5704.
(28) Marecek F., Moeller M.S., Svensson B. & Janecek
S. (2021) A putative novel starch-binding domain revealed by in silico
analysis
of the N-terminal domain in bacterial amylomaltases from the family
GH77. 3 Biotech 11: 229.
(27) Kerenyiova L. & Janecek S. (2020) Extension of the taxonomic
coverage of the family GH126 outside Firmicutes and in silico
characterization
of its non-catalytic terminal domains. 3 Biotech 10: 420.
(26)
Kerenyiova L. & Janecek S. (2020) A
detailed in silico analysis of the amylolytic family GH126 and its
possible
relatedness to family GH76. Carbohydr.
Res.
494: 108082.
(25) Janickova Z. & Janecek S. (2020) Fungal
α-amylases from three GH13 subfamilies: their
sequence-structural features and
evolutionary relationships. Int.
J. Biol. Macromol.
159: 763-772.
(24) Janecek S. & Zamocka B. (2020) A new GH13
subfamily represented by the α-amylase from the halophilic
archaeon Haloarcula
hispanica. Extremophiles
24: 207-217.
(23) Zhang X., Leemhuis H., Janecek
S., Martinovicova M., Pijning
T. & van der Maarel M.J.E.C. (2019) Identification of Thermotoga
maritima MSB8 GH57 α-amylase AmyC as a
glycogen-branching enzyme with high
hydrolytic activity. Appl. Microbiol. Biotechnol.
103: 6141-6151.
(22) Martinovicova M. & Janecek S.
(2018) In silico analysis
of the alpha-amylase family GH57: eventual subfamilies reflecting
enzyme
specificities. 3 Biotech 8: 307.
(21) Kuchtova
A., Gentry M.S. & Janecek S. (2018) A
unique evolution of the
carbohydrate-binding module CBM20 in laforin. FEBS
Letters
592: 586-598.
(20)
Janecek S., Majzlova K., Svensson B. & MacGregor E.A. (2017)
The
starch-binding domain family CBM41 – an in silico
analysis of
evolutionary relationships. Proteins Struct. Funct. Bioinform. 85: 1480-1492.
(19) Mieog J.C., Janecek S. & Ral J.P. (2017)
New
insight in cereal starch degradation: identification and structural
characterization of four alpha-amylases in bread wheat. Amylase
1: 35-49.
(18) Sarian F.D., Janecek S., Pijning T.,
Ihsanawati, Nurachman Z., Radjasa O.K., Dijkhuizen L., Natalia D.
& van der
Maarel M.J.E.C. (2017) A new group of glycoside hydrolase family 13
alpha-amylases with an aberrant catalytic triad. Sci.
Rep.
7: 44230.
(17) Kuchtova A. & Janecek S. (2016) Domain
evolution in enzymes of the neopullulanase subfamily. Microbiology 162:
2099-2115.
(16) Kuchtova A. & Janecek S. (2015) In
silico
analysis of family GH77 with focus on amylomaltases from borreliae and
disproportionating enzymes DPE2 from plants and bacteria. Biochim.
Biophys. Acta
1854: 1260-1268.
(15) Janecek S., Kuchtova A. & Petrovicova S.
(2015)
A novel GH13 subfamily of alpha-amylases with a pair of tryptophans in
the
helix alpha3 of the catalytic TIM-barrel, the LPDlx signature in the
conserved
sequence region V and a conserved aromatic motif at the C-terminus. Biologia
70: 1284-1294.
(14) Janecek S. & Kuchtova A. (2012) In silico
identification of catalytic residues and domain fold of the family
GH119
sharing the catalytic machinery with the alpha-amylase family GH57. FEBS
Lett.
586: 3360-3366.
(13) Blesak K. & Janecek S. (2012) Sequence
fingerprints of enzyme specificities from the glycoside hydrolase
family GH57. Extremophiles
16: 497-506.
(12) Janecek S. & Blesak K. (2011)
Sequence-structural features and evolutionary relationships of family
GH57
alpha-amylases and their putative alpha-amylase-like homologues. Protein
J.
30: 429-435.
(11) Gabrisko M. & Janecek S. (2009) Looking
for the
ancestry of the heavy-chain subunits of heteromeric amino acid
transporters
rBAT and 4F2hc within the GH13 alpha-amylase family. FEBS
J.
276: 7265-7278.
(10) Godany A., Vidova B. & Janecek S. (2008)
The
unique glycoside hydrolase family 77 amylomaltase from Borrelia
burgdorferi
with only catalytic triad conserved. FEMS
Microbiol. Lett.
284: 84-91.
(9) Machovic
M. & Janecek S. (2006) The evolution of putative
starch-binding domains. FEBS Lett. 580: 6349-6356.
(8) Zona R., Chang-Pi-Hin F., O’Donohue M.J.
&
Janecek S. (2004) Bioinformatics of the family 57 glycoside hydrolases
and
identification of catalytic residues in amylopullulanase from Thermococcus
hydrothermalis. Eur.
J. Biochem.
271: 2863-2872.
(7) Janecek S., Svensson B. & MacGregor E.A.
(2003)
Relation between domain evolution, specificity, and taxonomy of the
alpha-amylase family members containing a C-terminal starch-binding
domain. Eur.
J. Biochem.
270: 635-645.
(6) Oslancova A. & Janecek S. (2002)
Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the
alpha-amylase family defined by the fifth conserved sequence region. Cell.
Mol. Life Sci.
59: 1945-1959.
(5) Janecek S. & Sevcik J. (1999) The
evolution of starch-binding
domain. FEBS Lett. 456: 119-125.
(4) Janecek S., Leveque E., Belarbi A.
& Haye B. (1999) Close evolutionary
relatedness of alpha-amylases from Archaea and plants. J. Mol. Evol. 48: 421-426.
(3) Janecek S., Svensson B. & Henrissat B. (1997) Domain
evolution in the
alpha-amylase family. J. Mol. Evol. 45: 322-331.
(2) Janecek S. (1994) Sequence similarities and evolutionary
relationships of
microbial, plant and animal alpha-amylases. Eur. J. Biochem. 224: 519-524.
(1) Janecek S. (1992) New conserved amino acid region of alpha-amylases
in the
third loop of their (beta/alpha)8-barrel
domains. Biochem. J. 288: 1069-1070.
Review articles:
(10) Janecek S. & Svensson B. (2022) How many
alpha-amylase GH families are there in the CAZy database? Amylase
6: 1-10. An
"Opinion" paper.
(9) Janecek S., Marecek F., Svensson B.
&
MacGregor E.A. (2019) Starch-binding domains as CBM families - history,
occurrence,structure, function and evolution. Biotechnol.
Adv.
37: 107451.
(8) Janecek S. & Gabrisko M. (2016) Remarkable
evolutionary relatedness among the enzymes and proteins from the
alpha-amylase
family. Cell. Mol.
Life Sci.
73: 2707-2725.
(7) Janecek S., Svensson B. & MacGregor E.A.
(2014)
Alpha-amylase - an enzyme specificity found in various families of
glycoside
hydrolases. Cell.
Mol. Life Sci.
71: 1149-1170.
(6) Janecek S., Svensson B. &
MacGregor E.A.
(2011) Structural and evolutionary aspects of two families of
non-catalytic
domains present in starch and glycogen binding proteins from microbes,
plants
and animals. Enzyme
Microb. Technol.
49: 429-440.
(5) Christiansen C., Abou Hachem M., Janecek S.,
Viksoe-Nielsen A., Blennow A. & Svensson B. (2009) The
carbohydrate-binding
module family 20 – diversity, structure, and function. FEBS
J.
276: 5006-5029.
(4) Machovic
M. & Janecek S. (2006) Starch-binding domains in the
post-genome era. Cell. Mol. Life
Sci. 63: 2710-2724.
(3) Janecek
S. (2002) How many conserved sequence regions are there in the
alpha-amylase family? Biologia 57 (Suppl. 11): 29-41.
(2) MacGregor
E.A., Janecek S. & Svensson B. (2001) Relationship of
sequence and structure to specificity in the alpha-amylase family of
enzymes. Biochim. Biophys.
Acta 1546: 1-20.
(1) Janecek S. (1997) Alpha-amylase family:
molecular biology and
evolution. Progr. Biophys.
Mol. Biol. 67: 67-97.