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Structural biology

Virus-like particles
vlp Virus-like particles (VLPs) are composed of viral structural proteins that retain the ability to self-assemble without the presence of the encoding viral genome. VLPs and viruses share high versatility, propensity to form arrays and high programmability through genetic engineering. For these reasons they have recently emerged as platforms for synthetic manipulation with a range of applications from materials science to medicine.
  • dr.ssa C. Arcangeli, ENEA
Spermine metabolism and anticancer therapy
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  • prof. F. Polticelli, prof. P. Mariottini, Univ. of Rome Tre
Actin-actinin complex in mechanosensing
Actine Actinin is a microfilament protein. Alpha-Actinin is a cross-linking protein necessary for the attachment of actin filaments to the Z-lines in skeletal muscle cells, and to the dense bodies in smooth muscle cells. The functional protein is an anti-parallel dimer, which cross-links the thin filaments in adjacent sarcomeres, and therefore coordinated contractions between sarcomeres in the horizontal axis. Both ends of the alpha-Actinin terminals are composed of two calmodulin (CH1 CH2) attached to one monomer, and an EF-domain attached to the antiparallel monomer. We investigate, by means of combined rigid-docking and molecular mechanics, the complex structure of alpha-actinin attached to actin filaments. For the first model we obtained rigidly docked structures of the closed CH1-CH2 conformation to an actin monomer, which was then relaxed in physiologic water. The second and third models consists of an actin trimer or pentamer, representing a fragment of an actin filament in the Holmes configuration. We performed rigid docking of the alpha-actinin CH1-CH2 terminal on the actin fragments, and studied the differential adhesion free energy. The image shows the terminal fragment of alpha-Actinin (pink ribbons) interacting with the actin trimer (white). ATP molecules are also shown in the DB site of each actin monomer.
  • prof. F. Cleri, Univ. Lille, France
Protein-protein interaction:
Molecular docking is a fundamental process in biological environment. Among the others we can characterize the action of external agents on immune system. Celiac desease is produced by the strong interaction of a certain class of proteins. Understanding how they interact and how to modify them could give indications for new medical treatments.
  • prof. L. Cavallo, Univ. Salerno
Study of conformational properties of GALT enzyme
The enzyme galactose-1-phosphate uridyltransferase (GALT) is involved in galactose metabolism. The genetic disorder called "classical galactosemia" is linked to the impairment of this enzyme caused by more than 200 sequence variations in the GALT gene, with effect on protein structure and function. People affected by this genetic disease must avoid galactose assumption, but dietary restrictions not necessarily ensure normal physical growth and cognitive development. The molecular effect of all mutations at protein level has been clarified only for few mutants. The aim of our research is to analyze the impact of each mutation not only from a static, but also from a dynamic point of view. Molecular dynamics simulations on the wild-type and mutant proteins for an appropriate timescale, using GROMACS software, can allow to identify the conformational properties of the enzyme and to analyze variations linked to mutations.
  • dr.ssa A. Marabotti, CNR-ISA, Avellino
Study of peptides with biological activity
Bioactive peptides arouse great interest in biomedical and food field for the variety of the physiological effects they can exert. Until now, a great number of studied bioactive peptides can be attributed to milk proteins; in particular, casocidin-I, as described in literature, is the first antimicrobial peptide isolated from the hydrolysis of bovine S2-casein. Among the features that affect antimicrobial property and specificity, the conformation of the peptides plays an important role, and the study of structure-function-dynamics relationships is of fundamental importance to plan the synthesis of new peptides derived from the biologic ones but with improved biostability, bioavailability and activity. The aim of this research is to evaluate the structural and dynamics features of new synthetic peptides derived from S2-casein using molecular dynamics simulations in addition to classical biochemical and biological techniques, in order to understand structure-function relationships and, if possible, to retrieve information for a future computer-assisted molecular design.
  • dr.ssa A. Marabotti, CNR-ISA, Avellino
Study of ligand-binding proteins for biotechnological applications
An exciting goal for biotechnology is the development of biosensors to detect and quantify analytes of different kinds, with many potential applications (medicine and health, environmental applications, routine analytical measurements etc.). Biosensors are generally made of a sensitive biological component able to bind the analyte, and of a physicochemical detector to transduce the biologic signal into a physical one. The choice of the appropriate biologic component is of fundamental importance, and it is necessary not only to know its binding properties, but also its resistance to physicochemical stress, due e.g. to processes to create the biosensor itself and to its use in particular environmental conditions. We are characterizing several amino acid- and sugar-binding proteins from thermophilic organisms in order to understand their resistance to several stresses such as high temperature, pressure and non-physiological pH, in order. Molecular dynamics simulations help us in showing a "molecular portrait" of the effects of these extreme conditions on the proteins, to understand their limits and to evaluate their potential application for the development of biosensors.
  • dr.ssa A. Marabotti, CNR-ISA, Avellino