In Laurea thesis (equivalent to M.Sc. Diploma Thesis, discussed in 1992), I have for the first time investigated and attempted the combination Molecular Dynamics (MD) simulations and theoretical spectra calculation for the interpretation of experimental XANES (X-ray Absorption Near-Edge Spectroscopy) [4]. The method was used to study the aquatrisimidazole copper (II) sulfate complex’s crystal structure, but the results not yet published. The thesis is in Italian, and it is available on request to the interested reader.

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Understanding the mechanisms of the molecular recognition has fundamental impacts in medicine and biotechnology. It plays an important role in discovering new drugs and in developing new biocatalyst. The theoretical study of these mechanisms has boosted the development of approximated but fast methods for screening large compound libraries and protein-protein complexes. Continue reading →

Phytase

1. A. Shivange, U. Schwaneberg, D. Roccatano. Conformational dynamics of active site loop in Escherichia coli phytase. Biopolymers. 93(11), 994–1002, (2010).

Monooxygenase P450 BM3

 Figure.

1. S. Wong, N. Wu, D. Roccatano, M. Zacharias and U. Schwaneberg. Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds. J. Biomol. Screen, 10, 246-252 (2005).
2. Nazor, S. Dannennmann, R. Obeg Adjei, Y. B. Fordjour, T. I. Ghampson, M. Blanusa, D. Roccatano, U. Schwaneberg. Laboratory evolution of P450 BM3 for mediated electron transfer yields and activity-improved & reductase-independent variant. Protein Eng. Des. Sel., 21(1), 29-35, (2008).
3. K. L. Tee, D. Roccatano, S. Stolte, J. Arning, B. Jastorff, U. Schwaneberg. Ionic liquids as cosolvents for biotransformation catalyzed by P450 BM-3. Green Chem., 10, 117-123, (2008).

Chemical environment (pH, salts, co-solvents) plays an important role in the stabilization of secondary structure forming peptides and proteins in solution. The presence of co-solvent in aqueous solution can increase the structural stability as well as to promote denaturation or conformational changes. Continue reading →

The recent progress on time-resolved optical spectroscopy and FRET techniques have opened new exciting perspectives to the understanding the short timescale dynamics of peptides in solution. In fact, experimental data provided by these measurements can be directly compared with the results of computer simulations.

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Danilo Roccatano, Edita Sarukhanyan, and Ronen Zangi. The Journal of Chemical Physics 146, 074703 (2017); doi: http://dx.doi.org/10.1063/1.4975689

Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptake by living cells, and their high surface to volume ratio facilitates the adsorption of molecules of different nature. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutically agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A – Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surface through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalize Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to a loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus, into the interior of the CNT was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.

Citrate Synthase (CS) is an enzyme localized in the mitochondria of our cells where it plays an important role in the aerobic respiration cycle by transforming oxaloacetate molecules (on the right side of the picture) in citrate (on the top left side) with the assistance of the acetyl-coenzyme A (CoA) molecule. Continue reading →

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“To see a World in a Grain of Sand
And a Heaven in a Wild Flower,
Hold Infinity in the palm of your hand
And Eternity in an hour.”

―William Blake, Auguries of Innocence.

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INTRODUCTION

This blog is based on public talks that I have delivered at the University of Lincon, UK and at the Gravity Fields Festival 2016. Here I give a short summary of talk topics.

Nature is an unlimited source of great inspiration (and imitation) for scientist and engineering. In fact, the continuous advance in the knowledge of the complex machinery of life is producing profound impacts in the modern societies. Life, in the form that we know, definitively exploited what we now call “nanotechnology” to emerge. Living cells are crowded with fascinating molecular machines with a large variety of functions not yet completely explored. Nature as a blind and patient engineer builds these machines without a defined blueprint but utilizing the power of the evolution.

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Khadga Jung Karki, Susruta Samanta, and Danilo Roccatano*

J. Phys. Chem. B, August 2016

DOI: 10.1021/acs.jpcb.6b06055

Astaxanthin (AXT) is a reference model of xanthophyll carotenoids, which is used in medicine and food industry, and has potential applications in nanotechnology. Because of its importance, there is a great interest in understanding its molecular properties and aggregation mechanism in water and mixed solvents. In this paper, we report a novel model of AXT for molecular dynamics simulation. Continue reading →