by Keyword: Molecular biophysics

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Aparicio, C., Salvagni, E., Werner, M., Engel, E., Pegueroles, M., Rodriguez-Cabello, C., Munoz, F., Planell, J. A., Gil, J., (2009). Biomimetic treatments on dental implants for immediate loading applications Journal of Medical Devices , 3, (2), 027555

Summary form only given. Commercially pure titanium (cp Ti) dental implants have been widely and successfully used with high rates of clinical success in normal situations. However, there is still a lack of reliable synthetic materials to be used either a) when immediate loading of the implant is desired or b) when bone presents compromised conditions due to trauma, infection, systemic disease and/or lack of significant bone volume. Our group has aimed the development of biomimetic strategies of surface modification to obtain metallic implants with osteostimulative capabilities. These surface modifications will provide implants with a rapid rate of newly-formed bone growth and with ossecoalescence, i.e., direct chemical contact with the surrounding tissues. Consequently, the biomimetically-modified implants will be reliably used on those more demanding clinical situations, cp Ti surfaces treated to obtain a combination of an optimal random surface topography (in the micro and nanolevels) with a chemical modification of the naturally-formed titania layer have been proved bioactive. These rough and bioactive surfaces nucleate and grow a homogeneous hydroxyapatite layer both in vitro and in vivo. They stimulate the osteoblasts differentiation and trigger a rapid bone formation that mechanically fixes implants under immediate-loading conditions. A simple process using silane chemistry has been proved specific, rapid, and reliable to covalently immobilize biomolecules on cp Ti surfaces. This methodology can be used to develop biofunc- tionalized implant surfaces with different or combined bioactivities. The biofunctional molecules can be biopolymers, proteins, growth factors, and synthetic peptides specifically designed to be attached to the surface. The bioactive properties of the molecules designed and used can be mineral growing and nucleation, osteoblast differentiation (bone regeneration), fibroblasts differentiation (biological sealing), antibiotic,... Specifically, we have obtained mechanically and thermochemically stable coatings made of recombinant elastin-like biopolymers. The biopolymers bear either a) the RODS peptide, which is a highly-specific cell-adhesion motif present in proteins of the extracellular matrix for different tissues including bone, or b) an acidic peptide sequence derived from statherin, a protein present in saliva with high affinity for calcium-phosphates and with a leading role in the remineralization processes of the hard tissues forming our teeth. Two different biomimetic strategies have been successfully developed combining topographical modification, inorganic treatments and/or biofunctionalization for improving bioactive integrative properties of cp Ti implants.

Keywords: Biomedical materials, Bone, Cellular biophysics, Dentistry, Molecular biophysics, Prosthetics, Proteins, Surface treatment, Titanium

Lundin, Daniel, Torrents, Eduard, Poole, Anthony, Sjoberg, Britt-Marie, (2009). RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank BMC Genomics , 10, (1), 589

BACKGROUND:Ribonucleotide reductases (RNRs) catalyse the only known de novo pathway for deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. While ribonucleotide reduction has a single evolutionary origin, significant differences between RNRs nevertheless exist, notably in cofactor requirements, subunit composition and allosteric regulation. These differences result in distinct operational constraints (anaerobicity, iron/oxygen dependence and cobalamin dependence), and form the basis for the classification of RNRs into three classes.DESCRIPTION:In RNRdb (Ribonucleotide Reductase database), we have collated and curated all known RNR protein sequences with the aim of providing a resource for exploration of RNR diversity and distribution. By comparing expert manual annotations with annotations stored in Genbank, we find that significant inaccuracies exist in larger databases. To our surprise, only 23% of protein sequences included in RNRdb are correctly annotated across the key attributes of class, role and function, with 17% being incorrectly annotated across all three categories. This illustrates the utility of specialist databases for applications where a high degree of annotation accuracy may be important. The database houses information on annotation, distribution and diversity of RNRs, and links to solved RNR structures, and can be searched through a BLAST interface. RNRdb is accessible through a public web interface at is a specialist database that provides a reliable annotation and classification resource for RNR proteins, as well as a tool to explore distribution patterns of RNR classes. The recent expansion in available genome sequence data have provided us with a picture of RNR distribution that is more complex than believed only a few years ago; our database indicates that RNRs of all three classes are found across all three cellular domains. Moreover, we find a number of organisms that encode all three classes.

Keywords: Enzymology (Biochemistry and Molecular Biophysics), Computer Applications (Computational Biology)

Sunyer, R., Ritort, F., Farre, R., Navajas, D., (2009). Thermal activation and ATP dependence of the cytoskeleton remodeling dynamics Physical Review E 79, (5), 51920

The cytoskeleton (CSK) is a nonequilibrium polymer network that uses hydrolyzable sources of free energy such as adenosine triphosphate (ATP) to remodel its internal structure. As in inert nonequilibrium soft materials, CSK remodeling has been associated with structural rearrangements driven by energy-activated processes. We carry out particle tracking and traction microscopy measurements of alveolar epithelial cells at various temperatures and ATP concentrations. We provide the first experimental evidence that the remodeling dynamics of the CSK is driven by structural rearrangements over free-energy barriers induced by thermally activated forces mediated by ATP. The measured activation energy of these forces is similar to 40k(B)T(r) (k(B) being the Boltzmann constant and T-r being the room temperature). Our experiments provide clues to understand the analogy between the dynamics of the living CSK and that of inert nonequilibrium soft materials.

Keywords: Biochemistry, Cellular biophysics, Free energy, Molecular biophysics, Physiological models