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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), 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.
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
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.
Bovine Odorant-binding protein (bOBP): analysis of its stability towards pressure stress
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.
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.