Ab initio simulations of peptide-mineral interactions

We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the a-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN. Keywords: Molecular dynamics; Ab initio; Car-Parrinello; Osteopontin; Calcium oxalate monohydrate; Aspartic acid; Phosphoserin

Lyly and peele

52 p.; 21 cm

The flexible polyelectrolyte hypothesis of protein−biomineral interaction

Biomineralization is characterized by a high degree of control over the location, nature, size, shape, and orientation of the crystals formed. For many years, it has been widely believed that the exquisitely precise nature of crystal formation in biological tissues is the result of stereochemically specific interactions between growing crystals and extracellular matrix proteins. That is, the ability of many mineralized tissue proteins to adsorb to particular faces of biominerals has been attributed to a steric and electrical complementarity between periodic regions of the polypeptide chain and arrays of ions on the crystal face. In recent years, however, evidence has accumulated that many mineral-associated proteins lack periodic structure even when adsorbed to crystals. It also appears that protein-crystal interactions involve a general electrostatic attraction rather than arrays of complementary charges. In the present work, we review these studies and present some relevant new findings involving the mineral-modulating phosphoprotein osteopontin. Using molecular dynamics simulations, we show that the adsorption of osteopontin peptides to hydroxyapatite crystals does not involve a unique conformation of the peptide molecule, and that the adsorbed peptides are not aligned with rows of Ca2+ ions on the crystal face. Further, we show that the interface between osteopontin peptides and calcium oxalate monohydrate crystals consists of peptide regions of high electronegativity and crystal faces of high electropositivity. Collectively, the above-mentioned studies suggest that interactions between mineral-modulating proteins and biologically relevant crystals are primarily electrostatic in nature, and that molecular disorder assists these proteins in forming multiple bonds with cations of the crystal face

The flexible polyelectrolyte hypothesis of protein−biomineral interaction

Biomineralization is characterized by a high degree of control over the location, nature, size, shape, and orientation of the crystals formed. For many years, it has been widely believed that the exquisitely precise nature of crystal formation in biological tissues is the result of stereochemically specific interactions between growing crystals and extracellular matrix proteins. That is, the ability of many mineralized tissue proteins to adsorb to particular faces of biominerals has been attributed to a steric and electrical complementarity between periodic regions of the polypeptide chain and arrays of ions on the crystal face. In recent years, however, evidence has accumulated that many mineral-associated proteins lack periodic structure even when adsorbed to crystals. It also appears that protein-crystal interactions involve a general electrostatic attraction rather than arrays of complementary charges. In the present work, we review these studies and present some relevant new findings involving the mineral-modulating phosphoprotein osteopontin. Using molecular dynamics simulations, we show that the adsorption of osteopontin peptides to hydroxyapatite crystals does not involve a unique conformation of the peptide molecule, and that the adsorbed peptides are not aligned with rows of Ca2+ ions on the crystal face. Further, we show that the interface between osteopontin peptides and calcium oxalate monohydrate crystals consists of peptide regions of high electronegativity and crystal faces of high electropositivity. Collectively, the above-mentioned studies suggest that interactions between mineral-modulating proteins and biologically relevant crystals are primarily electrostatic in nature, and that molecular disorder assists these proteins in forming multiple bonds with cations of the crystal face

Evidence-Based Adjuvant Therapy for Gliomas: Current Concepts and Newer Developments

The incidence of gliomas is increasing worldwide, including India. Of the 18,820 new cases of primary central nervous system (CNS) tumors diagnosed annually in the United States, gliomas account for over 60% with 30-40% of them being glioblastoma multiforme (GBM), 10% being anaplastic astrocytoma (AA), and 10% being low grade gliomas (LGGs). This is in contrast to one study from West Bengal, India, in which only 7.9% of the brain tumors were GBMs, while 46.8% were astrocytomas. Of all adult primary CNS tumors, GBM is the most common and the most malignant with about 7,000 to 8,000 new cases annually in the United States. Given poor outcomes, a number of treatment approaches have been investigated. Common to these approaches is the use of adjuvant radiation therapy, even as surgery alone, with or without chemotherapy, may be the mainstay for some lower grade and low-risk gliomas. Today, treatment typically involves external beam radiation, with concurrent and adjuvant chemotherapy for more aggressive histologies. Although gliomas are relatively uncommon, active research is ongoing. Results of landmark trials along with some of the recently published trials are presented. These trials and management strategies as well as evolving concepts are found by reviewing over 200 articles in the National Library Medical (NLM) database, PubMed, more than 60 of which are refrenced. Specifically, the database is searched using the following keywords, with various combinations: glioma, low-grade, anaplastic, astrocytoma, oligodendroglioma, oligoastrocytoma, glioblastoma multiforme, chemotherapy, radiation, new concepts, phase III, MGMT, CDX-110 (Celldex), temozolomide, 1p/19q deletion, and bevacizumab

Citrate modulates calcium oxalate crystal growth by face-specific interactions

Because of its ability to inhibit the growth of calcium oxalate monohydrate (COM) crystals, citrate plays an important role in preventing the formation of kidney stones. To determine the mechanism of inhibition, we studied the citrate-COM interaction using a combination of microscopic and simulation techniques. Using scanning confocal interference microscopy, we found that addition of citrate preferentially inhibits crystal growth in and, to a lesser extent, directions, suggesting that citrate adsorbs to the faces of COM in the order {100} > {121} > {010}. Scanning electron microscopy showed that the resulting crystals are plate shaped, with large {100} faces and rounded ends. Molecular-dynamics simulations predicted, however, that citrate interacts with the faces of COM in a different order, i.e. {100} > {010} > {121}. Our simulations showed that citrate molecules align with the rows of Ca2+ ions on the {010} face but do not form close contacts, presumably because of electrostatic repulsion by the carboxylate groups that project from the Ca2+-rich plane. We propose that this weak interaction is responsible for citrate’s limited inhibition of COM growth in directions. Overall, these findings indicate that electrostatic interactions with the Ca2+-rich faces of COM crystals are responsible for the growth-modulating properties of citrate