# The Lignin Peroxidase

Lignin Peroxidase (LiP), a hemoprotein isolated from the ligninolytic cultures of the white-rot fungus Phenerochaete Chrysosporium is one of the most important lignin-degrading enzymes. We have investigated the dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant in aqueous solution using MD simulations [1].

# Molecular Machines within us: The human neutrophil collagenase MMP8

Human neutrophil collagenase (HNC, MMP8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S-side of the enzyme active site occupying the S1 primary specificity pocket by their large hydrophobic side-chains. Continue reading

# Molecular Machines within us: The Carbon Monoxide Migration in Sperm Whale Myoglobin

Myoglobin is a small ancient protein of ~150 amino acids specialized in the transport of respiratory gases to muscular tissues and back to the lungs of the superior organisms. Even though, it was one of the first protein having the three-dimensional structure solved using X-ray crystallography, the detail of the transport mechanism of gases in and out the active site is yet not completely understood. More recently, time-resolved x-ray studies have provided clues on the possible pockets in the protein interior where gases can transit but the detail of the migrations dynamics is unclear.

# Molecular Machines within us: The Nucleosome core particle

The nucleosome core particle (NCP) constitutes the basic structural unit of the eukaryotic chromatin. It consists of 147 base-pairs (bp) of DNA wrapped in a left-handed superhelix 1.65 times around a histone octamer. The octamer is formed by two copies of the histone proteins H2A, H2B, H3, and H4. Continue reading

# The β-lactamases TEM-1

β-lactamases are enzymes produced by bacteria (also known as penicillinase) that provide multi-resistance to β-lactam antibiotics such as penicillins, cephamycins, and carbapenems.  Continue reading

# Molecular Machines within us: The Citrate Synthase I

The citrate synthase is a model enzyme for the study of the dynamics of domain motions.  It is a key protein in the metabolic cycle of the cell (Krebs cycle) as it catalyzes the Claisen condensation of acetyl-coenzyme A with oxaloacetate, to form citrate and coenzyme A. The catalytic mechanism is very complex with many unknowns.  In most organisms its structure comprises two identical subunits.  Continue reading

# Molecular Machines within us: The Glutamate Synthase

Glutamate Synthases are key enzymes in the early stages of the assimilation of ammonia in bacteria, yeast, and plants. Azospirillum brasilense glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive transfer of L-glutamine amide group to the (C2) carbon of 2-oxoglutarate(2OG) yielding two molecules of L-glutamate and whose function requires the transfer of ammonia and electrons among distinct catalytic sites. Continue reading

# Molecular Machines within us: Folding/Unfolding Mechanism of the Cytochrome c

The Cytochrome c (Cytc) is a small heme protein of ~100 amino acids. It presents in the mitochondrion of eukaryotic cells and it is loosely associated with their inner membrane. Cytc is highly water-soluble and is an essential component of the electron transport chain in mitochondria where it carries one electron. Continue reading

# Fluorinated solvents models for MD simulations

Experimental studies on peptides and proteins stability and folding in solution are usually made in the presence of membrane mimic nonaqueous solvents. These conditions facilitate the study of hydrophobic stabilization effects. Continue reading

# Secondary structure forming peptides in solution: ß-turns, ß-hairpins and three-stranded peptides

sMy research on peptides is focused on those that are able to form secondary structure elements in solution like $\beta$-turn, $\alpha$-helix and $\beta$-strands. The purpose of these investigations was to establish the stability of this peptide in view of its possible role as a nucleation site for protein folding. Continue reading