The packing density in proteins: standard radii and volumes.

The sizes of atomic groups are a fundamental aspect of protein structure. They are usually expressed in terms of standard sets of radii for atomic groups and of volumes for both these groups and whole residues. Atomic groups, which subsume a heavy-atom and its covalently attached hydrogen atoms into one moiety, are used because the positions of hydrogen atoms in protein structures are generally not known. We have calculated new values for the radii of atomic groups and for the volumes of atomic groups. These values should prove useful in the analysis of protein packing, protein recognition and ligand design. Our radii for atomic groups were derived from intermolecular distance calculations on a large number (approximately 30,000) of crystal structures of small organic compounds that contain the same atomic groups to those found in proteins. Our radii show significant differences to previously reported values. We also use this new radii set to determine the packing efficiency in different regions of the protein interior. This analysis shows that, if the surface water molecules are included in the calculations, the overall packing efficiency throughout the protein interior is high and fairly uniform. However, if the water structure is removed, the packing efficiency in peripheral regions of the protein interior is underestimated, by approximately 3.5 %.     

The interpretation of protein structures: estimation of static accessibility

A program is described for drawing the van der Waal's surface of a protein molecule. An extension of the program permits the accessibility of atoms, or groups of atoms, to solvent or solute molecules of specified size to be quantitatively assessed. As defined in this study, the accessibility is proportional to surface area. The accessibility of all atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation. The accessibilities are also given for all atoms in ribonuclease-S, lysozyme and myogoblin. Internal cavities are defined and discussed. Various summaries of these data are provided. Forty to fifty per cent of the surface area of each protein is occupied by non-polar atoms. The actual numerical results are sensitive to the values chosen for the van der Waal's radii of the various groups. Since there is uncertainty over the correct values for these radii, the derived numbers should only be used as a qualitative guide at this stage.     

Characterisation of the surface of bovine milk fat globule membrane using microelectrophoresis

The nature of the ionogenic groups on the surface of the milk fat globule membrane was studied by microelectrophoresis of intact fat globules after chemical and enzymic modification. The changes in pH-mobility curves effected by formaldehyde and 2,4-dinitrofluorobenzene showed that the membrane surface contained amine groups. These were identified as arising from lysine and arginine by chromatography of their dinitrophenyl derivatives. The contribution of N-acetylneuraminic acid and phosphate to the surface charge was demonstrated by their specific removal by neuraminidase and phospholipase C, respectively. After removal of N-acetylneuraminic acid and phosphate, anionogenic effects remained which were attributed to protein carboxyl groups. These groups could be partially esterified using diazomethane. The effect of sodium dodecyl sulphate and of ionic strength on electrophoretic mobility indicated that the surface contains little neutral lipid and is predominantly ionogenic. The results obtained concerning the nature of the surface of the milk fat globule membrane support the hypothesis that the milk fat globule membrane originates from the plasmalemma of the mammary alveolar cell.     

Accuracy of specimen-specific nonlinear finite element analysis for evaluation of radial diaphysis strength in cadaver material

The feasibility of a user-specific finite element model for predicting the in situ strength of the radius after implantation of bone plates for open fracture reduction was established. The effect of metal artifact in CT imaging was characterized. The results were verified against biomechanical test data. Fourteen cadaveric radii were divided into two groups: (1) intact radii for evaluating the accuracy of radial diaphysis strength predictions with finite element analysis and (2) radii with a locking plate affixed for evaluating metal artifact. All bones were imaged with CT. In the plated group, radii were first imaged with the plates affixed (for simulating digital plate removal). They were then subsequently imaged with the locking plates and screws removed (actual plate removal). Fracture strength of the radius diaphysis under axial compression was predicted with a three-dimensional, specimen-specific, nonlinear finite element analysis for both the intact and plated bones (bones with and without the plate captured in the scan). Specimens were then loaded to failure using a universal testing machine to verify the actual fracture load. In the intact group, the physical and predicted fracture loads were strongly correlated. For radii with plates affixed, the physical and predicted (simulated plate removal and actual plate removal) fracture loads were strongly correlated. This study demonstrates that our specimen-specific finite element analysis can accurately predict the strength of the radial diaphysis. The metal artifact from CT imaging was shown to produce an overestimate of strength.     

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation

Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 10(6)-fold slower finite difference Poisson-Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent-accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pK(a)s of >200 ionizable groups from 15 proteins.     

Imaging scale surface topography of an endemic cyprinid fish,Garra sharq from the Arabian Peninsula: An integrated optical light and scanning electron microscopy approach

The optical light microscopy and scanning electron microscopy techniques have proven to play a key and noteworthy role in the advancement of morphological studies in general, and in investigating fish scale morphology in particular. These techniques have illustrated several hidden architectural structures in scales that contribute effectively to fish identification and classification. The scale morphological and topological characters such as type, size, shape, lateral surface, focus position, circuli appearance, radii type, lepidonts, and posterior and anterior margin shapes were obtained using macro- and microscopic analysis in six body regions for three size classes of Garra sharq, a cyprinid endemic fish of the Arabian Peninsula. The general scale type in the studied G. sharq species was a basal elasmoid cycloid and a sectioned type. As a protective structure, the scales display several specific characteristics including firm attachment to the fish body, overlapping, and thin structure with a high surface area and high strength. These characteristics improve scale resistance to penetration, increase protection against mechanical injury and microbial infection, enhance scale flexibility, reduce fish weight (reduce friction drag), and increase scale transparency. The scales demonstrate plasticity in focus shape, size, and position in the six fish body parts and fish size groups. The examined scales displayed narrow or wide grooves (radii) in three types including primary, secondary, and tertiary present in all four scale fields (anterior, posterior, and laterals), thus a tetra-sectioned type that is almost specific to the genus Garra. This characteristic also increases scale flexibility. The rostral margin of scales was characterized by the presence of waved and striate types. The lepidont shape and size varied being blunt, flat, pointed, tiny, sharp, short, and long. Some of these scale characters and their morphologies could be used as an alternative tool for identification, classification, and phylogenetic interpretation among the different freshwater fish species and genera.     

Dispersion and bilayer interaction of single-walled carbon nanotubes modulated by covalent and noncovalent PEGylation

Single-walled carbon nanotubes (SWNTs) covalently functionalised with polyethylene glycol (PEG) or noncovalently coated with PEGylated lipids were simulated in water and in lipid bilayers at different PEG sizes and grafting densities using coarse-grained force fields. Starting with the random position of three SWNT–PEG complexes in water, larger PEGs at higher grafting densities more significantly inhibit the aggregation of SWNTs because of larger radii of gyration and hydrodynamic radii of the SWNT–PEG complex, which influence the thickness and the wrapping extent of PEG layer. In particular, PEG-functionalised SWNTs, where PEGs are evenly grafted along the SWNT, disperse, while PEG-coated SWNTs aggregate because SWNTs are less covered by randomly adsorbed PEGylated lipids. Simulations of SWNT–PEGs in lipid bilayers show that PEG (M_w = 550 and 2000)-functionalised SWNTs bind to the bilayer surface but do not insert into the bilayer, while PEG-coated SWNTs insert into the bilayer because PEGylated lipids detach from SWNTs and mix with bilayer lipids. These findings support recent experiments at the same PEG size and density, which suggested that PEG-coated SWNTs may form bundles and thus cannot be easily excreted through the renal route, while PEG-functionalised SWNTs may remain individual and thus show more renal excretion.     

Typologie de bactéries prélevées devant le delta du Rhǒne. Utilisation d'une méthode objective: L'analyse des correspondances

Bacteria isolated from surface sea waters, brackish waters and from algal cultures were classified in nutritional clusters. Results obtained with an hierarchical method were improved by using the correspondence analysis. The former main statements appear confirmed and new informations are pointed out, mainly concerning the organic compounds which are the best indexes of the nutritional characteristics; e. g. a few organic acids and amino-acids can be used to estimate the versatility of bacteria; it also appears that strains which preferentially assimilate substrates of one chemical group, do not easily attack substances of other groups.     

Surface electric potential on rod-like polyelectrolyte

The electric potential on the surface of the rod-like polyelectrolyte with uniform charge distribution or periodically changing charge distribution on the surface is solved numerically by use of a power series method and an electronic computer. The deviation from the Linderstrøm-Lang's linear relation in the modified pH titration diagram, and the dependence of the surface electric potential on the radius of rod are discussed. Also, the radius of counterion and ionic strength, and the effect of non-uniformity of charge distribution are considered. Molecular radii were determined by comparing the calculated results with the pH titration data. The molecular radii of stereoregular poly-(methacrylic acid) and α-helical poly(glutamic acid) were found to be 5.5 Å and 15.0 Å, respectively, assuming uniform charge distribution. If nonuniform charge distribution was assumed, the molecular radii were calculated to be 5.0 Å and 14.0 Å, respectively. These values are discussed in relation to their molecular structures.     

Polyhydroxyalkanoates: Properties and chemical modification approaches for their functionalization

Polyhydroxyalkanoates (PHAs) have become an attractive biomaterial in research in the past few years due to their extensive potential industrial applications. Being long chain hydroxyl fatty acid molecules, the PHAs are hydrophobic in nature, and have less functional groups. These features limit their applications in various areas. To enhance their usage, these polymers may need to be modified including surface and chemical modifications. Such modifications may alter their mechanical properties, surface structure, amphiphilic character and rate of degradation to fulfil the requirements for their future applications. Chemical modifications allow incorporation of functional groups to PHAs that could not be introduced through biotechnological methods. These chemically reformed PHAs, with enhanced properties, could be used for broad range of applications. This review aims to introduce different chemical modification approaches including some recent methods that had not been explored or discussed so far for PHAs as possible technologies for widening the range of product and application potentials. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:29–41, 2018     

The surface ocean productivity response of deeper water benthic foraminifera in the Atlantic Ocean

We test the relationship of deep sea benthic foraminiferal assemblage composition to the surface ocean productivity gradient in the low latitude Atlantic Ocean using 81 surface sediment samples from a water depth range between 2800 and 3500 m. The samples are selected so that the surface ocean productivity gradient, controlling the flux of organic carbon to the seabed, will be the most important environmental variable. The first two principal components of the assemblage data account for 73% of data variance and are clearly linked to the productivity gradient across the Atlantic. These components show that under higher productivity the assemblages contain a higher abundance of Uvigerina peregrina, Melonis barleeanum, Globobulimina spp. and other taxa with probable infaunal microhabitats. Alabaminella weddellensis, a species linked to episodic phytoplankton debris falls, is also important in these assemblages. As productivity decreases there is a regular shift in assemblage composition so that low productivity assemblages are dominated by Globocassidulina subglobosa and several Cassidulina species along with Epistominella exigua. We hypothesize that these taxa are epifaunal to very shallow infaunal since nearly all organic carbon oxidation occurs near the sediment-water interface in low productivity settings. Discriminant function analysis of the foraminiferal assemblages, with groups selected on the basis of surface ocean productivity, shows clear separation among five productivity levels we used. This analysis demonstrates that productivity variations have a strong influence on assemblage composition. Finally, we used two groups of samples from the Rio-Grande Rise representing water depths from 2007 to 2340 m and 2739 to 3454 m to test for effects produced by changing water depth. All these samples are from a low productivity region and represent nearly identical environmental conditions. Although the low productivity nature of all the Rio-Grande Rise samples is obvious, there are assemblage differences between our depth groups. We cannot account for the assemblage differences with changes in organic carbon flux, dissolution effects or other physical/chemical properties of the ocean. Thus there are as yet unidentified factors related to water depth which cause some assemblage variation in the low productivity setting we investigated.     

Immobilization of glutathione by complementary coordination binding

A simple method was proposed for the immobilization of biologically important molecules consisting of many functional fragments, by means of the selective binding of their thiol groups to the surface carboxyl groups with participation of cadmium ions. Biofunctional properties of these structures were studied by the surface plasmon resonance method, with the example of glutathione (GSH), which was immobilized onto mixing thiol monolayers containing terminal groups of the carboxyl (a) and methyl/hydroxyl (b) types (a: b, from 1: 100 to 1: 700). The maintenance of the biofunctional conformation of glutathione-S-transferase (GST) after its interaction with GSH was monitored using specific anti-GST antibodies. The CH3 matrix was shown to be capable of considerable nonspecific binding and not suitable to form the biofunctional GST layer. At the same time, the OH-based structures demonstrated the specific GST-anti-GST interaction, with stoichiometry corresponding to the bidentate binding. The above simple method of the immobilization can be used to create functional surface architectures in analytical biochemistry and chemical analysis.     

Size of Unfolded and Dissociated Subunits versus that of Native Multimeric Proteins

Two factors, unfolding and dissociation, act in opposition indetermining the size of the unfolded state of multimeric proteins. Ananalysis has been presented to correlate relative expansion of the unfoldedmonomers in absence of disulfide bridges over the native state of differenthomomultimeric proteins of varying molecular weights. The Stoke's radii ofabout 70 proteins of Mw between 6 kDa to 4000 kDa and ranging frommonomers to dodecamers were calculated both under native anddenatured condition induced by 8 M urea or 6 M guanidinium,HClaccording to relations derived by Uversky [Biochemistry 32 (1993), 13288–13298]. Stoke's radii of monomeric proteins were foundto increase by 1.6–2.2 times after denaturation as compared with the nativestate while that of the subunits of dimeric and tetrameric proteins wereincreased by factors 1.1–2.2 under the same conditions. For hexamericproteins this factor lies between 0.96–1.2. In each set the relativeincrement of the Stoke's radii followed a logarithmic relation with molecularweight and reached a minimum limiting value when Stoke's radii of nativeprotein became almost equal to that of the unfolded monomer.     

Taxonomic studies in the Miconieae (Melastomataceae). IX. Calycogonium formonense, a new species from the Massif de la Hotte, Haiti

Calycogonium formonense, a new species, is here described from the floristically diverse Massif de la Hotte of southern Haiti. It is compared to C. hispidulum, to which it is likely related. Although the genus Calycogonium is not monophyletic, C. formonense and C. hispidulum are probably related to other species, e.g., C. calycopteris, C. heterophyllum, and C. reticulatum, that exhibit reduced inflorescences and 4-merous flowers having hypanthia with four conspicuous lobes separated by longitudinal grooves and external calyx lobes that are flattened parallel to the floral radii. These distinctive species may form a clade. Calycogonium formonense is distinguished from C. hispidulum by its smaller leaves with the tertiary veins not raised on the abaxial surface, with entire margins (i.e., margin without elongate multicellular hairs), and usually solitary flowers.     

Potentiometric titration studies on globular proteins

A power series method was applied to solve the Poisson-Boltzmann equation for the spherical polyelectrolyte model and numerical calculation with an electronic computer was performed to obtain surface electric potential on rigid globular proteins. Deviation from the ideal linear relationship in Linderstrom-Lang's plot was found to become noticeable as the surface charge density and the radius of protein increases and ionic strength decreases. The calculated surface potential was compared with potentiometric titration data of several proteins whose radii have been analyzed. Assuming the radius of the counterions to be equal to about 1.0 Å, the data for phenolic groups in ribonuclease and for carboxyl groups in conalbumin were interpreted. Reversible intramolecular transformation was found for α-lactalbumin by comparing the present results with the potentiometric titration data for carboxyl groups. The molecular size of each protein was discussed.     

The scale characteristics of two Aphanius species from southern Iran (Teleostei: Aphaniidae)

Fish scales are morphologically diverse among species, within species, and even among individuals. The present study investigated macro- and micromorphology of the scales between two closely related Aphanius species in southern Iran including Aphanius hormuzensis, collected from Gotab/Mehran River and A. stoliczkanus, from Howba hot sulphuric spring. The results indicated clear interspecific differences in scale macromorphology and microstructures. The scales of A. hormuzensis are characterised by a rounded shape, 7–9 (mean 8.0±0.83) primary radii, and a relatively large focus with oblong shape that positioned centrally on the scale, while the scales of A. stoliczkanus are characterised by a polygonal shape with few spines in posterior region, 8–11 (mean 10.0±0.78) primary radii and a small rounded focus that positioned posterocentraly on the scale. These species are morphologically close but clearly distinguished by their scale morphology and habitat requirements (e.g. water depth and food availability). Therefore, it can be assumed that clear differences in their scale morphology have been resulted by the combination of both genetic and environmental factors.     

Polenecia producta and its web: structure and evolution (Araneae,Uloboridae)

Summary The web of Polenecia producta is interpreted as being a modified orb web. The position of the hub directly upon a twig amongst irregularly placed branches decides the web's structure. Since the radii have to be fixed in the vicinity corresponding to the local possibilities, and since these possibilities vary very much from case to case, a great variety of web scaffoldings results. All of them are characterized by a lack of symmetry. These asymmetries, for their part, prevent the production of capture threads by circling around and fixing them obliquely to the radii as do orb weavers. P. producta adapts itself to this situation by attaching the adhesive material along the radii. Under these circumstances temporary spirals, like those of orb weavers, would be without function. The short pieces of such spirals present in the webs of P. producta are interpreted as vestiges of once functional structures. The silk deposits P. producta lays down upon the hub can, in certain respects, be compared with stabilimenta of other Uloboridae. The relatively late onset of web building in P. producta (instar II spiderlings) is related to the ontogeny of the spinning apparatus.     

Exchange and aggregation in dispersions of dimyristoyl phosphatidylcholine vesicles containing myristic acid

Processes occurring in dispersions of dimyristoyl phosphatidylcholine containing myristic acid have been studied by light scattering of dilute dispersions (concn. ≤ 1 mg/ml) at temperatures above and below the phase transition temperatures of these dispersions. The transition temperatures increase with increasing mol fraction of myristic acid. Above these temperatures, vesicles with different mol fractions of myristic acid exchange lipid molecules. The exchange process leads to vesicles having phase transition temperatures and radii, which are both intermediate between the initial transitions and radii, respectively. In contrast with the observations above the phase transitions, it was found that when dimyristoyl phosphatidylcholine/myristic acid vesicles were cooled to a few degrees below the phase transition, larger particles were formed. These observations are consistent with a mechanism consisting of vesicle aggregation followed by fusion of the aggregated vesicles. The aggregation process is of second order in the vesicle concentration, and its rate increases with increasing mol fraction of myristic acid.     

Forces in the spider orb web

Summary Pretensile forces were measured in individual threads of intact spider webs. In the orb web of Araneus diadematus forces decrease from mooring threads to frame threads and radii, a typical ratio being 1071. The smaller number of radii in the upper than in the lower half of the orb is paralleled by force ratios of 21 to 31. A similar difference between radii built first during web construction and radii added after completion of the frame underlines the importance of the former as part of the scaffolding. High tensions in the auxiliary spiral stabilize the radii in addition to providing a pathway for the spider when inserting the sticky spiral. Radial pretension (F) changes with spider mass (m). F/m is similar for different animals indicating an adaptation of radial forces to those resulting from spider mass. Several observations suggest tension control by the spider. When forced to anchor its web to thin flexible rods tension in the threads remains in the normal range. Tension values are similar in the webs of A. diadematus, Zygiella x-notata, Nuctenea umbratica, and Nephila clavipes indicating independence from details of web geometry. Only the mooring threads of Nephila show unusually large forces suggesting a narrower working range of tensions for the catching area than for the scaffolding.     

Physicochemical characterization ofEscherichia coli

EightEscherichia coli strains were characterized by determining their adhesion to xylene, surface free energy, zeta potential, relative surface charge, and their chemical composition. The latter was done by applying X-ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR). No relationship between the adhesion to xylene and the water contact angles of these strains was found. Three strains had significantly lower surface free energies than the other strains. Surface free energies were either obtained from polar and dispersion parts or from Lifshitz-van der Waals and acid/base parts of the surface free energy. A correlation (r=0.97) between the polar parts and the electron-donor contributions to the acid/base part of the surface free energy was found. The zeta potentials of all strains, measured as a function of pH (2–11), were negative. Depending on the zeta potential as a function of pH, three groups were recognized among the strains tested. A relationship (r=0.84) was found between the acid/base component of the surface free energy and the zeta potential measured at pH=7.4. There was no correlation between results of XPS and IR studies. Data from the literature of XPS and IR studies of the gram-positive staphylococci and streptococci were compared with data from the gram-negativeE. coli used in this study. It appeared that in these three groups of bacteria, the polysaccharide content detected by IR corresponded well with the oxygen-to-carbon ratio detected by XPS.