Partition coefficient and molecular flexibility: the concept of lipophilicity space.

The rationale of this study was to investigate molecular flexibility and its influence on physicochemical properties with a view to uncovering additional information on the fuzzy concept of dynamic molecular structure. Indeed, it is now known that computed molecular interaction fields (MIFs) such as molecular electrostatic potentials (MEPs) and lipophilicity potentials (MLPs) are conformation-dependent, as are dipole moments. A database of 125 compounds was used whose conformational space was explored, while conformation-dependent parameters were computed for each non-redundant conformer found in the conformational space of the compounds. These parameters were the virtual log P (log P(MLP), calculated by a MLP approach), the apolar surface area (ASA), polar surface area (PSA), and solvent-accessible surface (SAS). For each compound, the range taken by each parameter (its property space) was divided by the number of rotors taken as an index of flexibility, yielding a parameter termed 'molecular sensitivity'. This parameter was poorly correlated with others (i.e., it contains novel information) and showed the compounds to fall into two broad classes. 'Sensitive' molecules are those whose computed property ranges are markedly sensitive to conformational effects, whereas 'insensitive' (in fact, less sensitive) molecules have property ranges which are comparatively less affected by conformational fluctuations. A pharmacokinetic application is presented.

Rational design of 4-aryl-1,2,3-triazoles for indoleamine 2,3-dioxygenase 1 inhibition.

Indoleamine 2,3-dioxygenase 1 (IDO1) is an important therapeutic target for the treatment of diseases such as cancer that involve pathological immune escape. Starting from the scaffold of our previously discovered IDO1 inhibitor 4-phenyl-1,2,3-triazole, we used computational structure-based methods to design more potent ligands. This approach yielded highly efficient low molecular weight inhibitors, the most active being of nanomolar potency both in an enzymatic and in a cellular assay, while showing no cellular toxicity and a high selectivity for IDO1 over tryptophan 2,3-dioxygenase (TDO). A quantitative structure-activity relationship based on the electrostatic ligand-protein interactions in the docked binding modes and on the quantum chemically derived charges of the triazole ring demonstrated a good explanatory power for the observed activities.

Plate tectonics of the Altaids

Abstract: The Altaids consist in a huge accretionary-type belt extending from Siberia through Mon-golia, northern China, Kyrgyzstan and Kazakhstan. They were formed from the Vendian through the Jurassic by the accretion of numerous displaced and exotic terranes (e.g. island arc, ribbon microcontinent, seamount, basaltic plateau, back-arc basin). The number, nature and origin of the terranes differ according to the palaeotectonic models of the different authors. Thanks to a geo- dynamic study (i.e. definition of tectonic settings and elaboration of geodynamic scenarios) and plate tectonics modelling, this work aims to present an alternative model explaining the Palaeozoic palaeotectonic evolution of the Altaids. Based on a large set of compiled geological data related to palaeogeography and geodyna¬mic (e.g. sedimentology, stratigraphy, palaeobiogeography, palaeomagnetism, magmatism, me- tamorphism, tectonic...), a partly new classification of the terranes and sutures implicated in the formation of the Altaids is proposed. In the aim to elaborate plate tectonics reconstructions, it is necessary to fragment the present arrangement of continents into consistent geological units. To avoid confusion with existing terminology (e.g. tectonic units, tectono-stratigraphic units, micro- continents, terranes, blocks...), the new concept of "Geodynamic Units (GDU)" was introduced. A terrane may be formed by a set of GDUs. It consists of a continental and/or oceanic fragment which has its own kinematic and geodynamic evolution for a given period. With the same ap-proach, the life span and type of the disappeared oceans is inferred thanks to the study of the mate-rial contained in suture zones. The interpretation of the tectonic settings within the GDUs comple-ted by the restoration of oceans leads to the elaboration of geodynamic scenarios. Since the Wilson cycle was presented in 1967, numerous works demonstrated that the continental growth is more complex and results from diverse geodynamic scenarios. The identification of these scenarios and their exploitation enable to elaborate plate tectonics models. The models are self-constraining (i.e. space and time constraints) and contest or confirm in turn the geodynamic scenarios which were initially proposed. The Altaids can be divided into three domains: (1) the Peri-Siberian, (2) the Kazakhstan, and (3) the Tarim-North China domains. The Peri-Siberian Domain consists of displaced (i.e. Sayan Terrane Tuva-Mongolian, Lake-Khamsara Terrane) and exotic terranes (i.e. Altai-Mongolian and Khangai-Argunsky Terrane) accreted to Siberia from the Vendian through the Ordovician. Fol-lowing the accretion of these terranes, the newly formed Siberia active margin remained active un-til its part collision with the Kazakhstan Superterrane in the Carboniferous. The eastern part of the active margin (i.e. East Mongolia) continued to act until the Permian when the North-China Tarim Superterrane collided with it. The geodynamic evolution of the eastern part of the Peri-Siberian Domain (i.e. Eastern Mongolia and Siberia) is complicated by the opening of the Mongol-Okhotsk Ocean in the Silurian. The Kazakhstan Domain is composed of several continental terranes of East Gondwana origin amalgamated together during the Ordovician-Silurian time. After these different orogenic events, the Kazakhstan Superterrane evolved as a single superterrane until its collision with a Tarim-North China related-terrane (i.e. Tianshan-Hanshan Terrane) and Siberian Continent during the Devonian. This new organisation of the continents imply a continued active margin from Siberia, to North China through the Kazakhstan Superterrane and the closure of the Junggar- Balkash Ocean which implied the oroclinal bending of the Kazakhstan Superterrane during the entire Carboniferous. The formation history of the Tarim-North China Domain is less complex. The Cambrian northern passive margin became active in the Ordovician. In the Silurian, the South Tianshan back-arc Ocean was open and led to the formation of the Tianshan-Hanshan Terrane which collided with the Kazakhstan Superterrane during the Devonian. The collision between Siberia and the eastern part of the Tarim-North China continents (i.e. Inner Mongolia), implied by the closure of the Solonker Ocean, took place in the Permian. Since this time, the major part of the Altaids was formed, the Mongol-Okhotsk Ocean only was still open and closed during the Jurassic. Résumé: La chaîne des Altaïdes est une importante chaîne d'accrétion qui s'étend en Sibérie, Mon-golie, Chine du Nord, Kirghizstan et Kazakhstan. Elle s'est formée durant la période du Vendian au Jurassique par l'accrétion de nombreux terranes déplacés ou exotiques (par exemple arc océa-nique, microcontinent, guyot, plateau basaltique, basin d'arrière-arc...). Le nombre, la nature ou encore l'origine diffèrent selon les modèles paléo-tectoniques proposés par les différents auteurs. Grâce à une étude géodynamique (c'est-à-dire définition des environnements tectoniques et éla-boration de scénarios géodynamiques) et à la modélisation de la tectonique des plaques, ce travail propose un modèle alternatif expliquant l'évolution paléo-tectonique des Altaïdes. Basé sur une large compilation de données géologiques pertinentes en termes de paléo-géographie et de géodynamique (par exemple sédimentologie, stratigraphie, paléo-biogéographie, paléomagnétisme, magmatisme, métamorphisme, tectonique...), une nouvelle classification des terranes et des sutures impliqués dans la formation des Altaïdes est proposée. Dans le but d'élabo¬rer des reconstructions de plaques tectoniques, il est nécessaire de fragmenter l'arrangement actuel des continents en unités tectoniques cohérentes. Afin d'éviter les confusions avec la terminolo¬gie existante (par exemple unité tectonique, unité tectono-stratigraphique, microcontinent, block, terrane...), le nouveau concept d' "Unité Géodynamique (UGD)" a été introduit. Un terrane est formé d'une ou plusieurs UGD et représente un fragment océanique ou continental défini pas sa propre cinétique et évolution géodynamique pour une période donnée. Parallèlement, la durée de vie et le type des océans disparus (c'est-à-dire principal ou secondaire) est déduite grâce à l'étude du matériel contenu dans les zones de sutures. L'interprétation des environnements tectoniques des UGD associés à la restauration des océans mène à l'élaboration de scénarios géodynamiques. Depuis que le Cycle de Wilson a été présenté en 1967, de nombreux travaux ont démontré que la croissance continentale peut résulter de divers scénarios géodynamiques. L'identification et l'ex-ploitation de ces scénarios permet finalement l'élaboration de modèles de tectonique des plaques. Les modèles sont auto-contraignants (c'est-à-dire contraintes spatiales et temporelles) et peuvent soit contester ou confirmer les scénarios géodynamiques initialement proposés. Les Altaïdes peuvent être divisées en trois domaines : (1) le Domaine Péri-Sibérien, (2) le Domaine Kazakh, et (3) le Domaine Tarim-Nord Chinois. Le Domaine Péri-Sibérien est composé de terranes déplacés (c'est-à-dire Terrane du Sayan, Tuva-Mongol et Lake-Khamsara) et exotiques (c'est-à-dire Terrane Altai-Mongol et Khangai-Argunsky) qui ont été accrétés au craton Sibérien durant la période du Vendien à l'Ordovicien. Suite à l'accrétion de ces terranes, la marge sud-est de la Sibérie nouvellement formée reste active jusqu'à sa collision partielle avec le Superterrane Ka-zakh au Carbonifère. La partie est de la marge active (c'est-à-dire Mongolie de l'est) continue son activité jusqu'au Permien lors de sa collision avec le Superterrane Tarim-Nord Chinois. L'évolu¬tion géodynamique de la partie est du Domaine Sibérien est compliquée par l'ouverture Silurienne de l'Océan Mongol-Okhotsk qui disparaîtra seulement au Jurassique. Le Domaine Kazakh est composé de plusieurs terranes d'origine est-Gondwanienne accrétés les uns avec les autres avant ou pendant le Silurien inférieur et leurs evolution successive sous la forme d'un seul superterrane. Le Superterrane Kazakh collisione avec un terrane Tarim-Nord Chinois (c'est-à-dire Terrane du Tianshan-Hanshan) durant le Dévonien et le continent Sibérien au Dévonien supérieur. Ce nouvel agencement des plaques induit une marge active continue le long des continents Sibérien, Kazakh et Nord Chinois et la fermeture de l'Océan Junggar-Balkash qui provoque le plissement oroclinal du Superterrane Kazakh durant le Carbonifère. L'histoire de la formation du Domaine Tarim-Nord Chinois est moins complexe. La marge passive nord Cambrienne devient active à l'Ordovicien et l'ouverture Silurienne du bassin d'arrière-arc du Tianshan sud mène à la formation du terrane du Tianshan-Hanshan. La collision Dévonienne entre ce dernier et le Superterrane Kazakh provoque la fermerture de l'Océan Tianshan sud. Finalement, la collision entre la Sibérie et la partie est du continent Tarim-Nord Chinois (c'est-à-dire Mongolie Intérieure) prend place durant le Permien suite à la fermeture de l'Océan Solonker. La majeure partie des Altaïdes est alors formée, seul l'Océan Mongol-Okhotsk est encore ouvert. Ce dernier se fermera seulement au Jurassique.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors.

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.

Atomic force microscopy of nucleoprotein complexes.

Recent data on the AFM studies of nucleoprotein complexes of different types are reviewed in this paper. The first section describes the progress in the sample preparation methods for AFM studies of nucleic acids and nucleoprotein complexes. The second part of this paper reviews AFM data on studies of complexes of DNA with regulatory proteins. These studies include two different types of DNA distortion induced by proteins binding: local bending of DNA at sites of protein binding and formation of large loops due to protein-protein interactions between molecules bound to distant sites along the DNA molecules (DNA looping). The prospects for use of AFM for physical mapping of genomes are discussed in this section as well. The third part of the paper reviews data on studies of complexes of DNA with non-sequence specific binding proteins. Special emphasis is given to studies of chromatin which have resulted in progress in the understanding of structure of native chromatin fiber. In this section, novel data on AFM studies of RecA-DNA filaments and complexes of dsRNA with the dsRNA-specific protein p25 are also presented. Discussion of the substrate preparation procedures in relation to the AFM studies of nucleoprotein complexes is given in the final section.

PHYTOCHROME KINASE SUBSTRATE1 regulates root phototropism and gravitropism.

Light promotes the expression of PHYTOCHROME KINASE SUBSTRATE1 (PKS1) in the root of Arabidopsis thaliana, but the function of PKS1 in this organ is unknown. Unilateral blue light induced a negative root phototropic response mediated by phototropin 1 in wild-type seedlings. This response was absent in pks1 mutants. In the wild type, unilateral blue light enhanced PKS1 expression in the subapical region of the root several hours before bending was detectable. The negative phototropism and the enhanced PKS1 expression in response to blue light required phytochrome A (phyA). In addition, the pks1 mutation enhanced the root gravitropic response when vertically oriented seedlings were placed horizontally. The negative regulation of gravitropism by PKS1 occurred even in dark-grown seedlings and did not require phyA. Blue light also failed to induce negative phototropism in pks1 under reduced gravitational stimulation, indicating that the effect of pks1 on phototropism is not simply the consequence of the counteracting effect of enhanced gravitropism. We propose a model where the background level of PKS1 reduces gravitropism. After a phyA-dependent increase in its expression, PKS1 positively affects root phototropism and both effects contribute to negative curvature in response to unilateral blue light.

Origin of the spectral shifts among the early intermediates of the rhodopsin photocycle.

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one correspondence between the structures of the different early intermediates (dark, batho, BSI, lumi) involved in the initial steps of the rhodopsin photoactivation mechanism and their optical spectra. A systematic analysis of the results based on a correlation-based feature selection algorithm shows that the origin of the color shifts among these intermediates can be mainly ascribed to alterations in intrinsic properties of the chromophore structure, which are tuned by several residues located in the protein binding pocket. In addition to the expected electrostatic and dipolar effects caused by the charged residues (Glu113, Glu181) and to strong hydrogen bonding with Glu113, other interactions such as π-stacking with Ala117 and Thr118 backbone atoms, van der Waals contacts with Gly114 and Ala292, and CH/π weak interactions with Tyr268, Ala117, Thr118, and Ser186 side chains are found to make non-negligible contributions to the modulation of the color tuning among the different rhodopsin photointermediates.

Non-Corrosive Tie Reinforcing and Dowel Bars for Highway Pavement Slabs, HR-343, 1993

The use of non-metallic load transfer and reinforcement devices for concrete highway pavements is a possible alternative to avoid corrosion problems related to the current practice of steel materials. Laboratory and field testing of highway pavement dowel bars, made of both steel and fiber composite materials, and fiber composite tie rods were carried out in this research investigation. Fatigue, static, and dynamic testing was performed on full-scale concrete pavement slabs which were supported by a simulated subgrade and which included a single transverse joint. The bahavior of the full-scale specimens with both steel and fiber composite dowels placed in the test joints was monitored during several million load cycles which simulated truck traffic at a transverse joint. Static bond tests were conducted on fiber composite tie rods to determine the required embedment length. These tests took the form of bending tests which included curvature and shear in the embedment zone and pullout tests which subjected the test specimen to axial tension only. Fiber composite dowel bars were placed at two transverse joints during construction of a new concrete highway pavement in order to evaluate their performance under actual field conditions. Fiber composite tie rods were also placed in the longitudinal joint between the two fiber composite doweled transverse joints.

Composite Precast Prestressed Concrete Bridge Slabs, HR-310, 1991

Precast prestressed concrete panels have been used as subdecks in bridge construction in Iowa and other states. To investigate the performance of these types of composite slabs at locations adjacent to abutment and pier diaphragms in skewed bridges, a research prcject which involved surveys of design agencies and precast producers, field inspections of existing bridges, analytical studies, and experimental testing was conducted. The survey results from the design agencies and panel producers showed that standardization of precast panel construction would be desirable, that additional inspections at the precast plant and at the bridge site would be beneficial, and that some form of economical study should be undertaken to determine actual cost savings associated with composite slab construction. Three bridges in Hardin County, Iowa were inspected to observe general geometric relationships, construction details, and to note the visual condition of the bridges. Hairline cracks beneath several of the prestressing strands in many of the precast panels were observed, and a slight discoloration of the concrete was seen beneath most of the strands. Also, some rust staining was visible at isolated locations on several panels. Based on the findings of these inspections, future inspections are recommended to monitor the condition of these and other bridges constructed with precast panel subdecks. Five full-scale composite slab specimens were constructed in the Structural Engineering Laboratory at Iowa State University. One specimen modeled bridge deck conditions which are not adjacent to abutment or pier diaphragms, and the other four specimens represented the geometric conditions which occur for skewed diaphragms of 0, 15, 30, and 40 degrees. The specimens were subjected to wheel loads of service and factored level magnitudes at many locations on the slab surface and to concentrated loads which produced failure of the composite slab. The measured slab deflections and bending strains at both service and factored load levels compared reasonably well with the results predicted by simplified Finite element analyses of the specimens. To analytically evaluate the nominal strength for a composite slab specimen, yield-line and punching shear theories were applied. Yield-line limit loads were computed using the crack patterns generated during an ultimate strength test. In most cases, these analyses indicated that the failure mode was not flexural. Since the punching shear limit loads in most instances were close to the failure loads, and since the failure surfaces immediately adjacent to the wheel load footprint appeared to be a truncated prism shape, the probable failure mode for all of the specimens was punching shear. The development lengths for the prestressing strands in the rectangular and trapezoidal shaped panels was qualitatively investigated by monitoring strand slippage at the ends of selected prestressing strands. The initial strand transfer length was established experimentally by monitoring concrete strains during strand detensioning, and this length was verified analytically by a finite element analysis. Even though the computed strand embedment lengths in the panels were not sufficient to fully develop the ultimate strand stress, sufficient stab strength existed. Composite behavior for the slab specimens was evaluated by monitoring slippage between a panel and the topping slab and by computation of the difference in the flexural strains between the top of the precast panel and the underside of the topping slab at various locations. Prior to the failure of a composite slab specimen, a localized loss of composite behavior was detected. The static load strength performance of the composite slab specimens significantly exceeded the design load requirements. Even with skew angles of up to 40 degrees, the nominal strength of the slabs did not appear to be affected when the ultimate strength test load was positioned on the portion of each slab containing the trapezoidal-shaped panel. At service and factored level loads, the joint between precast panels did not appear to influence the load distribution along the length of the specimens. Based on the static load strength of the composite slab specimens, the continued use of precast panels as subdecks in bridge deck construction is recommended.

Preventing Cracking at Diaphragm/Plate Girder Connections in Steel Bridges, HR-393, 1998

Some of the Iowa Department of Transportation (Iowa DOT) continuous, steel, welded plate girder bridges have developed web cracking in the negative moment regions at the diaphragm connection plates. The cracks are due to out-of-plane bending of the web near the top flange of the girder. The out-of-plane bending occurs in the "web-gap", which is the portion of the girder web between (1) the top of the fillet welds attaching the diaphragm connection plate to the web and (2) the fillet welds attaching the flange to the web. A literature search indicated that four retrofit techniques have been suggested by other researchers to prevent or control this type of cracking. To eliminate the problem in new bridges, AASHTO specifications require a positive attachment between the connection plate and the top (tension) flange. Applying this requirement to existing bridges is expensive and difficult. The Iowa DOT has relied primarily on the hole-drilling technique to prevent crack extension once cracking has occurred; however, the literature indicates that hole-drilling alone may not be entirely effective in preventing crack extension. The objective of this research was to investigate experimentally a method proposed by the Iowa DOT to prevent cracking at the diaphragm/plate girder connection in steel bridges with X-type or K-type diaphragms. The method consists of loosening the bolts at some connections between the diaphragm diagonals and the connection plates. The investigation included selecting and testing five bridges: three with X-type diaphragms and two with K-type diaphragms. During 1996 and 1997, these bridges were instrumented using strain gages and displacement transducers to obtain the response at various locations before and after implementing the method. Bridges were subjected to loaded test trucks traveling in different lanes with speeds varying from crawl speed to 65 mph (104 km/h) to determine the effectiveness of the proposed method. The results of the study show that the effect of out-of-plane loading was confined to widths of approximately 4 in. (100 mm) on either side of the connection plates. Further, they demonstrate that the stresses in gaps with drilled holes were higher than those in gaps without cracks, implying that the drilling hole technique is not sufficient to prevent crack extension. The behavior of the web gaps in X-type diaphragm bridges was greatly enhanced by the proposed method as the stress range and out-of-plane distortion were reduced by at least 42% at the exterior girders. For bridges with K-type diaphragms, a similar trend was obtained. However, the stress range increased in one of the web gaps after implementing the proposed method. Other design aspects (wind, stability of compression flange, and lateral distribution of loads) must be considered when deciding whether to adopt the proposed method. Considering the results of this investigation, the proposed method can be implemented for X-type diaphragm bridges. Further research is recommended for K-type diaphragm bridges.

Field Monitoring of Curved Girder Bridges with Integral Abutments, TPF-5(169), 2014

Nationally, there are questions regarding the design, fabrication, and erection of horizontally curved steel girder bridges due to unpredicted girder displacements, fit-up, and locked-in stresses. One reason for the concerns is that up to one-quarter of steel girder bridges are being designed with horizontal curvature. There is also an urgent need to reduce bridge maintenance costs by eliminating or reducing deck joints, which can be achieved by expanding the use of integral abutments to include curved girder bridges. However, the behavior of horizontally curved bridges with integral abutments during thermal loading is not well known nor understood. The purpose of this study was to investigate the behavior of horizontal curved bridges with integral abutment (IAB) and semi-integral abutment bridges (SIAB) with a specific interest in the response to changing temperatures. The long-term objective of this effort is to establish guidelines for the use of integral abutments with curved girder bridges. The primary objective of this work was to monitor and evaluate the behavior of six in-service, horizontally curved, steel-girder bridges with integral and semi-integral abutments. In addition, the influence of bridge curvature, skew and pier bearing (expansion and fixed) were also part of the study. Two monitoring systems were designed and applied to a set of four horizontally curved bridges and two straight bridges at the northeast corner of Des Moines, Iowa—one system for measuring strains and movement under long term thermal changes and one system for measuring the behavior under short term, controlled live loading. A finite element model was developed and validated against the measured strains. The model was then used to investigate the sensitivity of design calculations to curvature, skew and pier joint conditions. The general conclusions were as follows: (1) There were no measurable differences in the behavior of the horizontally curved bridges and straight bridges studied in this work under thermal effects. For preliminary member sizing of curved bridges, thermal stresses and movements in a straight bridge of the same length are a reasonable first approximation. (2) Thermal strains in integral abutment and semi-integral abutment bridges were not noticeably different. The choice between IAB and SIAB should be based on life – cycle costs (e.g., construction and maintenance). (3) An expansion bearing pier reduces the thermal stresses in the girders of the straight bridge but does not appear to reduce the stresses in the girders of the curved bridge. (4) An analysis of the bridges predicted a substantial total stress (sum of the vertical bending stress, the lateral bending stress, and the axial stress) up to 3 ksi due to temperature effects. (5) For the one curved integral abutment bridge studied at length, the stresses in the girders significantly vary with changes in skew and curvature. With a 10⁰ skew and 0.06 radians arc span length to radius ratio, the curved and skew integral abutment bridges can be designed as a straight bridge if an error in estimation of the stresses of 10% is acceptable.

Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the cross-recognition.

A semi-grand canonical Monte Carlo simulation model for ion binding to ionizable surfaces: proton binding of carboxylated latex particles as a case study

In this paper, we present a computer simulation study of the ion binding process at an ionizable surface using a semi-grand canonical Monte Carlo method that models the surface as a discrete distribution of charged and neutral functional groups in equilibrium with explicit ions modelled in the context of the primitive model. The parameters of the simulation model were tuned and checked by comparison with experimental titrations of carboxylated latex particles in the presence of different ionic strengths of monovalent ions. The titration of these particles was analysed by calculating the degree of dissociation of the latex functional groups vs. pH curves at different background salt concentrations. As the charge of the titrated surface changes during the simulation, a procedure to keep the electroneutrality of the system is required. Here, two approaches are used with the choice depending on the ion selected to maintain electroneutrality: counterion or coion procedures. We compare and discuss the difference between the procedures. The simulations also provided a microscopic description of the electrostatic double layer (EDL) structure as a function of p H and ionic strength. The results allow us to quantify the effect of the size of the background salt ions and of the surface functional groups on the degree of dissociation. The non-homogeneous structure of the EDL was revealed by plotting the counterion density profiles around charged and neutral surface functional groups.

Fate of Hydrophilic Nanoparticles in Biological Environments

The nanoparticles developed are based on chitosan, a biocompatible and biodegradable polysaccharide. The chitosan nanoparticles are formed in an entirely water-based process by electrostatic interactions with other biocompatible molecules. As a prerequisite to understand the fate of such nanoparticles in cells, comprehensive characterization and stability studies serve to identify quantitatively the impact of the raw material characteristics and preparation conditions on the nanoparticle characteristics. Methods included H-1 NMR spectroscopy, dilution viscometry, particle size analysis and electron microscopy. Cytotoxicity and cell uptake experiments on RAW 264.7 murine macrophages and p23 murine endothelial cells were performed to investigate the correlation with nanoparticle characteristics and effect of surface decoration with alginate. Cytotoxicity was assessed by the MTT survival test; cell uptake was monitored by fluorescent microscopy using labeled polymers.

Nanoparticles for fingermark detection: an insight into the reaction mechanism

This publication presents one of the first uses of silicon oxide nanoparticles to detect fingermarks. The study is not confined to showing successful detection of fingermarks, but is focused on understanding the mechanisms involved in the fingermark detection process. To gain such an understanding, various chemical groups are grafted onto the nanoparticle surface, and parameters such as the pH of the solutions or zeta potential are varied to study their influence on the detection. An electrostatic interaction has been the generally accepted hypothesis of interaction between nanoparticles and fingermarks, but the results of this research challenge that hypothesis, showing that the interaction is chemically driven. Carboxyl groups grafted onto the nanoparticle surfaces react with amine groups of the fingermark secretion. This formation of amide linkage between carboxyl and amine groups has further been favoured by catalyzing the reaction with a compound of diimide type. The research strategy adopted here ought to be applicable to all detection techniques using nanoparticles. For most of them the nature of the interaction remains poorly understood.