Interactions between nanoparticles in nanosuspension

Nanoparticles are particles with a characteristic dimension below 100 nm. The properties of nanoparticles differ substantially from those of "big" colloidal particles (size bigger than 1 μm) because radius of surface forces, which is around 100 nm, is greater than or comparable with the nanoparticles size. The latter means that each nanoparticle could be completely covered by the surface forces of the neighbouring particles at small enough separation. It also means that the well-known Derjaguin approximation cannot be applied directly and some modifications are required. Pairwise interaction between nanoparticles can be used only at an extremely low volume fraction of nanoparticles (below some critical volume fraction, which is ~0.02%), and above this concentration a new theory based on many-particle interactions should be applied, which is yet to be developed. Some recent progress in the area of interaction between nanoparticles is reviewed and the properties of nanosuspensions based on interaction between nanoparticles are described. The authors have not attempted to cover all available literature in the area but instead have tried to underline the fundamental problems in the area which need to be addressed.

Recent Advances in Solid Hydrogen Storage Systems

Hydrogen energy offers great promise as an energy alternative. Hydrogen technologies can reduce and eliminate the release of carbon dioxide from fossil-fuel combustion, the main cause of global warming. One of the main challenges is hydrogen storage. Storing hydrogen in the solid-state hydride form holds a volumetric advantage over compressed and liquid hydrogen states. Solid hydrogen storage systems also have features of low-pressure operation, compactness, safety, tailorable delivery pressure, excellent absorption /desorption kinetics, modular design for easy scalability, and long cycle life.

In this paper, solid hydrogen storage systems (such as portable power canisters, lightweight fiber wrapped vessels, and aluminum tubular vessels, developed by Texaco Ovonic Hydrogen Systems LLC) will be discussed. A system of four canisters each storing approximately 80 grams of reversible hydrogen is shown to run a 1 kW PEM fuel cell for more than 247 minutes at full power. Canisters show no plastic deformation after more than 500 charge/discharge cycles. The measured strain on canister surfaces indicates that DOT stress limits are not exceeded. The canisters are in the early commercialization stage for uninterrupted power supply (UPS) and auxiliary power unit (APU) applications.

A lightweight fiber-wrapped vessel engineered with metal hydride and internal heat exchanger is being developed for onboard applications. At the system level, the vessel has a volumetric energy density of 50 grams of hydrogen per liter and a gravimetric density of 1.6 wt.%. The vessel is capable of storing 3 kg of hydrogen with a fast refueling capability. Ninety percent of the storable hydrogen can be refueled in 10 minutes at 1500 psig. The vessel can easily release the hydrogen at a rate of 350 slpm at 70°C.

Aluminum tubular vessels are being designed and tested for bulk storage and infrastructure applications including stationary power, hydrogen shipment and hydrogen service stations. The tubular vessel dimensions may be designed for specific applications. For example, a tubular vessel 6 inches in diameter and 62 inches in length can store up to 1 kg of hydrogen.

MYRRHA, a Pb-Bi experimental ADS: specific approach to radiation protection aspects

Since 1998, SCK*CEN, in partnership with IBA s.a. and many European research laboratories, is designing a multipurpose accelerator driven system (ADS) for Research and Development (R&D) applications-MYRRHA-and is conducting an associated R&D support programme. MYRRHA is an ADS under development at Mol in Belgium and is aiming to serve as a basis for the European experimental ADS to provide protons and neutrons for various R&D applications. It consists of a proton accelerator delivering a 350 MeV x 5 mA proton beam to a liquid Pb-Bi spallation target that in turn couples to a Pb-Bi cooled, subcritical fast core. In the first stage, the project focuses mainly on demonstration of the ADS concept, safety research on sub-critical systems and nuclear waste transmutation studies. In a later stage, the device will also be dedicated to research on structural materials, nuclear fuel, liquid metal technology and associated aspects, and on sub-critical reactor physics. Subsequently, it will be used for research on applications such as radioisotope production. A first preliminary conceptual design file of MYRRHA was completed by the end of 2001 and has been reviewed by an International Technical Guidance Committee, which concluded that there are no show stoppers in the project and even though some topics such as the safety studies and the fuel qualification need to be addressed more deeply before concluding it. In this paper, we are reporting on the state-of-the art of the MYRRHA project at the beginning of 2004 and in particular on the radiation shielding assessment and the radiation protection particular aspects through a remote handling operation approach in order to minimise the personnel exposure to radiation.

Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure

MOTIVATION

Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms.

RESULTS

We present computational methods based on the Voronoi procedure that provide rapid and exact solutions to solvent accessible surfaces, volumes, and atom contacts within macromolecules. Furthermore, we define a measure of atom-atom contact that is consistent with the calculation of solvent accessible surfaces, allowing the integration of solvent accessibility and inter-atomic contacts into a continuous measure. The speed and accuracy of the algorithm is compared to existing methods for calculating solvent accessible surfaces and volumes. The presented algorithm has a reduced execution time and greater accuracy compared to numerical and approximate analytical surface calculation algorithms, and a reduced execution time and similar accuracy to existing Voronoi procedures for calculating atomic surfaces and volumes.

Mucormycosis of the renal allograft: case report and review of the literature

Fungal infection is an uncommon complication after renal transplantation. We describe a rare form of mucormycosis in the renal graft. Our method was to review chart data and to perform medline searches. The patient was a 42-year-old man who underwent living-unrelated kidney transplantation in Egypt and returned to Israel on POD 8. Within the ensuing 4 weeks he experienced acute rejection which responded to treatment with steroids. Few days after discharge he was readmitted because of fever and graft dysfunction. An infected large perigraft collection was drained, but the patient became anuric and septic. Kidney biopsy showed infarcted necrotic tissue infiltrated by fungi which grew Mucor species. Despite initial improvement following graft nephrectomy and antifungal treatment the patient died of sepsis. Literature review revealed only three additional cases of graft infection due to Mucorales. We conclude that Renal graft infection due to Mucorales is an extremely rare and potentially lethal complication. Living unrelated donation in third world countries might be a possible risk factor. Fungal colonization may occur during transplantation. A high index of suspicion, leading to early diagnosis and initiation of antifungal treatment, in addition to graft nephrectomy, are keys to a more favorable outcome.

MutaProt: a web interface for structural analysis of point mutations

A web-based tool, termed 'MutaProt', is described which analyses pairs of PDB files whose members differ in one, or two, amino acids. MutaProt examines the micro environment surrounding the exchanged residue(s) and can be searched by specifying a PDB ID, keywords, or any pair of amino acids. Detailed information about accessibility of the exchanged residue(s) and its atomic contacts are provided based on CSU software (Sobolev et al., Bioinformatics, 15, 327-332, 1999). An interactive 3D presentation of the superimposed regions around the mutation(s) is included. MutaProt is updated weekly.

Side-chain flexibility in proteins upon ligand binding

Ligand binding may involve a wide range of structural changes in the receptor protein, from hinge movement of entire domains to small side-chain rearrangements in the binding pocket residues. The analysis of side chain flexibility gives insights valuable to improve docking algorithms and can provide an index of amino-acid side-chain flexibility potentially useful in molecular biology and protein engineering studies. In this study we analyzed side-chain rearrangements upon ligand binding. We constructed two non-redundant databases (980 and 353 entries) of "paired" protein structures in complexed (holo-protein) and uncomplexed (apo-protein) forms from the PDB macromolecular structural database. The number and identity of binding pocket residues that undergo side-chain conformational changes were determined. We show that, in general, only a small number of residues in the pocket undergo such changes (e.g., approximately 85% of cases show changes in three residues or less). The flexibility scale has the following order: Lys > Arg, Gln, Met > Glu, Ile, Leu > Asn, Thr, Val, Tyr, Ser, His, Asp > Cys, Trp, Phe; thus, Lys side chains in binding pockets flex 25 times more often then do the Phe side chains. Normalizing for the number of flexible dihedral bonds in each amino acid attenuates the scale somewhat, however, the clear trend of large, polar amino acids being more flexible in the pocket than aromatic ones remains. We found no correlation between backbone movement of a residue upon ligand binding and the flexibility of its side chain. These results are relevant to 1. Reduction of search space in docking algorithms by inclusion of side-chain flexibility for a limited number of binding pocket residues; and 2. Utilization of the amino acid flexibility scale in protein engineering studies to alter the flexibility of binding pockets.

Automated analysis of interatomic contacts in proteins

MOTIVATION

New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein.

RESULTS

Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues. Our approach is based on a detailed analysis of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-accessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of the ligand.

AVAILABILITY

Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.

Biophysical, biochemical, and physiological characterization of Chlamydomonas reinhardtii mutants with amino acid substitutions at the Ala251 residue in the D1 protein that result in varying levels of photosynthetic competence

The QB binding site of the D1 reaction center protein, located within a stromal loop between transmembrane helices IV and V formed by residues Ile219 to Leu272, is essential for photosynthetic electron transport through photosystem II (PSII). We have examined the function of the highly conserved Ala251 D1 residue in this domain in chloroplast transformants of Chlamydomonas reinhardtii and found that Arg, Asp, Gln, Glu, and His substitutions are nonphotosynthetic, whereas Cys, Ser, Pro, Gly, Ile, Val, and Leu substitutions show various alterations in D1 turnover, photosynthesis, and photoautotrophic growth. The latter mutations reduce the rate of QA to QB electron transfer, but this is not necessarily rate-limiting for photoautotrophic growth. The Cys mutant divides and evolves O2 at wild type rates, although it has slightly higher rates of D1 synthesis and turnover and reduced electron transfer between QA and QB. O2 evolution, D1 synthesis, and accumulation in the Ser, Pro, and Gly mutants in high light is reduced, but photoautotrophic growth rate is not affected. In contrast, the Ile, Val, and Leu mutants are impaired in photoautotrophic growth and photosynthesis in both low and high light and have elevated rates of D1 synthesis and degradation, but D1 accumulation is normal. While rates of synthesis/degradation of the D1 protein are not necessarily correlated with alterations in specific parameters of PSII function in these mutants, bulkiness of the substituted amino acids is highly correlated with the dissociation constant for QB in the seven mutants examined. These observations imply that the Ala251 residue plays a key role in D1 protein.

CASP2 molecular docking predictions with the LIGIN software

Seven docking predictions were made with the LIGIN program. In six cases the location of the binding pocket was identified correctly by systematically docking everywhere within the protein structure. In two cases the ligand was docked to within 1.8 A RMSD of the experimentally determined structure. LIGIN has not been optimized to deal with highly flexible ligands that dock at the surface of proteins. Consequently, in three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made similar atomic contacts with the protein as in the experimentally determined structure.

Molecular cloning, structural analysis, and expression in Escherichia coli of a chitinase gene from Enterobacter agglomerans

The gene chiA, which codes for endochitinase, was cloned from a soilborne Enterobacter agglomerans. Its complete sequence was determined, and the deduced amino acid sequence of the enzyme designated Chia_Entag yielded an open reading frame coding for 562 amino acids of a 61-kDa precursor protein with a putative leader peptide at its N terminus. The nucleotide and polypeptide sequences of Chia_Entag showed 86.8 and 87.7% identity with the corresponding gene and enzyme, Chia_Serma, of Serratia marcescens, respectively. Homology modeling of Chia_Entag's three-dimensional structure demonstrated that most amino acid substitutions are at solvent-accessible sites. Escherichia coli JM109 carrying the E. agglomerans chiA gene produced and secreted Chia_Entag. The antifungal activity of the secreted endochitinase was demonstrated in vitro by inhibition of Fusarium oxysporum spore germination. The transformed strain inhibited Rhizoctonia solani growth on plates and the root rot disease caused by this fungus in cotton seedlings under greenhouse conditions.

Molecular docking using surface complementarity

A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the intermolecular atomic contacts. Docking is performed by maximization of a complementarity function that is dependent on atomic contact surface area and the chemical properties of the contacting atoms. The generality and simplicity of the complementarity function ensure that a wide range of chemical structures can be handled. The ligand and the protein are treated as rigid bodies, but displacement of a small number of residues lining the ligand binding site can be taken into account. The method can assist in the design of improved ligands by indicating what changes in complementarity may occur as a result of the substitution of an atom in the ligand. The capabilities of the method are demonstrated by application to 14 protein-ligand complexes of known crystal structure.

Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms

Functional identity and significant similarities in cofactors and sequence exist between the L and M reaction center proteins of the photosynthetic bacteria and the D1 and D2 photosystem-II reaction center proteins of cyanobacteria, algae, and plants. A model of the quinone (QB) binding site of the D1 protein is presented based upon the resolved structure of the QB binding pocket of the L subunit, and introducing novel quantitative notions of complementarity and contact surface between atoms. This model, built without using traditional methods of molecular mechanics and restricted to residues in direct contact with QB, accounts for the experimentally derived functional state of mutants of the D1 protein in the region of QB. It predicts the binding of both the classical and phenol-type PSII herbicides and rationalizes the relative levels of tolerance of mutant phenotypes.