STUDY OF STRUCTURAL FEATURES OF PROTEINS OF BIOTECHNOLOGICAL INTEREST BY MD SIMULATIONS Anna...
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STUDY OF STRUCTURAL FEATURES OF PROTEINS OF BIOTECHNOLOGICAL INTEREST BY MD SIMULATIONS Anna Marabotti Dept. Chemistry and Biology, University of Salerno, Fisciano (SA), Ita Molecular dynamics simulations are a powerful tool to investigate the structural features of proteins at atomic level, and in particular to introduce flexibility and temporal evolution in the analysis of molecular systems. During these years I have been involved in the study of many different proteins with potential application in biotechnology. The knowledge of their dynamics using a MD approach, coupled to the experimental evaluation of their structural and functional properties, has allowed to gain and integrate information at different levels, with a better comprehension of molecular phenomena associated to physico-chemical perturbations. MD simulations have been performed using the open- source software GROMACS, running in parallel (MPI) on the CRESCO clusters CRESCO1 and 2. The length of simulation was variable between 10 and 100 ns. In general, simulations were run on 96 nodes, obtaining a performance of 15 ns/day (previous benchmarks performed showed that this combination is the best one in terms of scalability of the performances on these systems). At the end of simulations, several analyses were conducted using programs built within GROMACS, and results were visualized and elaborated with the aid of the freely available program Grace. Some examples of simulations and results: e-binding protein (ArgBP) from T. maritima: analysis of its thermostability in different ons. ArgBP, open form ArgBP, close form rant-binding protein (bOBP): analysis of its stability towards pressure stress MD simulations on this protein in different conditions of pH and temperature showed that helices appear to be more unstable than sheets to thermal stress (above). Three b-strands (indicated with red boxes in the picture on the left), that are formed by hydrophobic residues and are completely shielded from solvent in the protein core, appear to be unaltered in any condition and seem to be essential for protein thermostability. Ref.: Scirè A, Marabotti A, Staiano M, Iozzino L, Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S. Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability. Mol Biosyst. 2010;6(4):687-98. bOBP The MD simulations showed that, in native conditions, bOBP has a strong intrinsic resistance to high pressure (up to 600 bar) and keeps its dimeric assembly essentially unaltered, as shown by the conservation of the distance between center of mass of each monomer (picture on the middle). The comparison of the representative structures for each pressure (picture on the right) shows that the differences between them are focused mainly in the loops connecting the strands forming the central b-barrel. Hence, dimerization and substrate binding significantly increase the resistance of the protein to pressure. Ref.: Marchal S, Marabotti A, Staiano M, Varriale A, Domaschke T, Lange R, D'Auria S. Under pressure that splits a family in two. The case of lipocalin family. PLoS One. 2012;7(11):e50489. se binding protein (MalE2) from T. thermophilus: effect of pH on protein's fold MalE2 Ref.: Varriale A, Marabotti A, Mei G, Staiano M, D'Auria S. Correlation spectroscopy and molecular dynamics simulations to study the structural features of proteins. PLoS One 2013; 8(6):e64840. The MD simulations in different pH conditions showed that MalE2 at pH 4 is kinetically more unstable than in the other two pH conditions (7 and 10). The analysis of cluster structures (middle) showed that at pH 7 and 10 there is essentially a unique structure that prevails along the entire simulation, with multiple subpopulations in the case of higher pH. Instead, at acidic pH, MalE2 shows an enhanced instability of its tertiary structure. The representation of free energy landscape of the protein indicates the presence of
STUDY OF STRUCTURAL FEATURES OF PROTEINS OF BIOTECHNOLOGICAL INTEREST BY MD SIMULATIONS Anna Marabotti Dept. Chemistry and Biology, University of Salerno,
STUDY OF STRUCTURAL FEATURES OF PROTEINS OF BIOTECHNOLOGICAL
INTEREST BY MD SIMULATIONS Anna Marabotti Dept. Chemistry and
Biology, University of Salerno, Fisciano (SA), Italy Molecular
dynamics simulations are a powerful tool to investigate the
structural features of proteins at atomic level, and in particular
to introduce flexibility and temporal evolution in the analysis of
molecular systems. During these years I have been involved in the
study of many different proteins with potential application in
biotechnology. The knowledge of their dynamics using a MD approach,
coupled to the experimental evaluation of their structural and
functional properties, has allowed to gain and integrate
information at different levels, with a better comprehension of
molecular phenomena associated to physico-chemical perturbations.
Molecular dynamics simulations are a powerful tool to investigate
the structural features of proteins at atomic level, and in
particular to introduce flexibility and temporal evolution in the
analysis of molecular systems. During these years I have been
involved in the study of many different proteins with potential
application in biotechnology. The knowledge of their dynamics using
a MD approach, coupled to the experimental evaluation of their
structural and functional properties, has allowed to gain and
integrate information at different levels, with a better
comprehension of molecular phenomena associated to physico-chemical
perturbations. MD simulations have been performed using the
open-source software GROMACS, running in parallel (MPI) on the
CRESCO clusters CRESCO1 and 2. The length of simulation was
variable between 10 and 100 ns. In general, simulations were run on
96 nodes, obtaining a performance of 15 ns/day (previous benchmarks
performed showed that this combination is the best one in terms of
scalability of the performances on these systems). At the end of
simulations, several analyses were conducted using programs built
within GROMACS, and results were visualized and elaborated with the
aid of the freely available program Grace. MD simulations have been
performed using the open-source software GROMACS, running in
parallel (MPI) on the CRESCO clusters CRESCO1 and 2. The length of
simulation was variable between 10 and 100 ns. In general,
simulations were run on 96 nodes, obtaining a performance of 15
ns/day (previous benchmarks performed showed that this combination
is the best one in terms of scalability of the performances on
these systems). At the end of simulations, several analyses were
conducted using programs built within GROMACS, and results were
visualized and elaborated with the aid of the freely available
program Grace. Arginine-binding protein (ArgBP) from T. maritima:
analysis of its thermostability in different pH conditions. ArgBP,
open form ArgBP, close form Bovine Odorant-binding protein (bOBP):
analysis of its stability towards pressure stress MD simulations on
this protein in different conditions of pH and temperature showed
that helices appear to be more unstable than sheets to thermal
stress (above). Three -strands (indicated with red boxes in the
picture on the left), that are formed by hydrophobic residues and
are completely shielded from solvent in the protein core, appear to
be unaltered in any condition and seem to be essential for protein
thermostability. Ref.: Scir A, Marabotti A, Staiano M, Iozzino L,
Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S. Amino
acid transport in thermophiles: characterization of an
arginine-binding protein in Thermotoga maritima. 2. Molecular
organization and structural stability. Mol Biosyst.
2010;6(4):687-98. bOBP The MD simulations showed that, in native
conditions, bOBP has a strong intrinsic resistance to high pressure
(up to 600 bar) and keeps its dimeric assembly essentially
unaltered, as shown by the conservation of the distance between
center of mass of each monomer (picture on the middle). The
comparison of the representative structures for each pressure
(picture on the right) shows that the differences between them are
focused mainly in the loops connecting the strands forming the
central -barrel. Hence, dimerization and substrate binding
significantly increase the resistance of the protein to pressure.
Ref.: Marchal S, Marabotti A, Staiano M, Varriale A, Domaschke T,
Lange R, D'Auria S. Under pressure that splits a family in two. The
case of lipocalin family. PLoS One. 2012;7(11):e50489. Maltotriose
binding protein (MalE2) from T. thermophilus: effect of pH on
protein's fold MalE2 Ref.: Varriale A, Marabotti A, Mei G, Staiano
M, D'Auria S. Correlation spectroscopy and molecular dynamics
simulations to study the structural features of proteins. PLoS One
2013; 8(6):e64840. The MD simulations in different pH conditions
showed that MalE2 at pH 4 is kinetically more unstable than in the
other two pH conditions (7 and 10). The analysis of cluster
structures (middle) showed that at pH 7 and 10 there is essentially
a unique structure that prevails along the entire simulation, with
multiple subpopulations in the case of higher pH. Instead, at
acidic pH, MalE2 shows an enhanced instability of its tertiary
structure. The representation of free energy landscape of the
protein indicates the presence of multiple protein conformations at
pH 4 and 10, probably due to the partial unfolding of the MalE2
tertiary structure, as a consequence of the induced perturbation of
native ionic interactions.