Mutational analysis of hydrophobic domain interactions in gamma B-crystallin from bovine eye lens.

gamma B-crystallin is a monomeric member of the beta gamma-superfamily of vertebrate eye lens proteins. It consists of two similar domains with all-beta Greek key topology associating about an approximate two-fold axis. At pH 2, with urea as the denaturant, the domains show independent equilibrium unfolding transitions, suggesting different intrinsic stabilities. Denaturation experiments using recombinant one- or two-domain proteins showed that the N-terminal domain on its own exhibits unaltered intrinsic stability but contributes significantly to the stability of its C-terminal partner. It has been suggested that docking of the domains is determined by a hydrophobic interface that includes phenylalanine at position 56 of the N-terminal domain. In order to test this hypothesis, F56 was substituted by site-directed mutagenesis in both complete gamma B-crystallin and its isolated N-terminal domain. All mutations destabilize the N-terminal domain to about the same extent but affect the C-terminal domain in a different way. Replacement by the small alanine side chain or the charged aspartic acid residue results in a significant destabilization of the C-terminal domain, whereas the more bulky tryptophan residue causes only a moderate decrease in stability. In the mutants F56A and F56D, equilibrium unfolding transitions obtained by circular dichroism and intrinsic fluorescence differ, suggesting a more complex denaturation behavior than the one observed for gamma B wild type. These results confirm how mutations in one crystallin domain can affect the stability of another when they occur at the interface. The results strongly suggest that size, hydrophobicity, and optimal packing of amino acids involved in these interactions are critical for the stability of gamma B-crystallin.     

Co-axial association of recombinant eye lens aquaporin-0 observed in loosely packed 3D crystals

Aquaporin-0 (AQP0) is the major membrane protein in vertebrate eye lenses. It has been proposed that AQP0 tetramers mediate contact between membranes of adjacent lens fiber cells, which would be consistent with the extraordinarily narrow inter-cellular spacing. We have obtained 3D crystals of recombinant bovine AQP0 that diffract to 7.0 A resolution. The crystal packing was determined by molecular replacement and shows that, within the cubic lattice, AQP0 tetramers are associated head-to-head along their 4-fold axes. Oligomeric states larger than the tetramer were also observed in solution by native gel electrophoresis and analytical ultracentrifugation methods. In the crystals, there are no direct contacts between octamers, and it can thus be inferred that crystalline order is mediated solely by the detergent belts surrounding the membrane protein. Across the tetramer-tetramer interface, extracellular loops A and C interdigitate at the center and the perimeter of the octamer, respectively. The octamer structure is compared with that of the recently determined structure of truncated ovine AQP0 derived from electron diffraction of 2D crystals. Intriguingly, also in these crystals, octamers are observed, but with significantly different relative tetramer-tetramer orientations. The interactions observed in the loosely packed 3D crystals reported here may in fact represent an in vivo association mode between AQP0 tetramers from juxtaposed membranes in the eye lens.     

Comparative electrophoretic studies of muscle and eye lens proteins in freshwater fish of Iraq

Muscle myogens and eye lens proteins have been studied in ten species of freshwater fish from Iraq. The electrophoretic analysis revealed that the muscle myogens can be considered as a good taxonomic criterion to differentiate the family Mugilidae from the Cyprinodontidae and Cyprinidae, but not between the families Poeciliidae and Cyprinodontidae. Within the Cyprinidae the muscle myogens can be used to diferentiate Barbus grypus from the remaining species of this family. Eye lens proteins are not considered a good taxonomic criterion to differentiate the members of the four families studied, but can distinguish B. belawayei and B. grypus from the other Cyprinid species.     

Comparative electrophoretic studies of muscle, eye lens and heart protein in fishes from the Arabian Gulf

Muscle myogen, eye lens and heart protein have been studied in 31 species of fishes from Kuwait, Arabian Gulf. The electrophoretic analysis revealed that muscle myogen can be considered a good taxonomic criterion to differentiate the families Ariidae, Belonidae and Lutjanidae from the other fish families studied. Within the Lutjanidae and Pomadasyidae the muscle myogens can be used to differentiate Lutjanus kasmira and Pomadasys argenteus, respectively. The muscle myogens can also be used to differentiate Sardinella perforata, Platycephalus inducus, Drepane longemana and Psethodes erumei. Eye lens protein can be considered a good taxonomic criterion to differentiate between the fish species studied and especially among the families Belonidae, Lutjanidae, Pomadsyidae, Sparidae and Scaenidae. Within the Lutjanidae and Sparidae, the eye lens protein can be used to differentiate Lutjanus kasmira and Acanthopagrus berda, respectively. Heart protein is not considered a good taxonomic criterion to differentiate the species of fishes studied, but can distinguish Lutjanus coccineus from the remaining species studied.     

Localized effects of microwave radiation on the intact eye lens in culture conditions

A novel experimental system was used to investigate the localized effects of microwave radiation on bovine eye lenses in culture for over 2 weeks. Using this setup, we found clear evidence that this radiation has a significant impact on the eye lens. At the macroscopic level, it is demonstrated that exposure to a few mW at 1 GHz for over 36 h affects the optical function of the lens. Most importantly, self-recovery occurs if the exposure is interrupted. At the microscopic level, close examination of the lens indicates that the interaction mechanism is completely different from the mechanism-causing cataract via temperature increase. Contrary to the latter's effect, that is particularly pronounced in the vicinity of the sutures and it is assumed to be a result of local friction between the edges of the fibers consisting the lens. Even if macroscopically the lens has recovered from the irradiation, microscopically the indicators of radiation impact remain.     

High-resolution X-ray crystal structures of human gammaD crystallin (1.25 A) and the R58H mutant (1.15 A) associated with aculeiform cataract

Several human cataracts have been linked to mutations in the gamma crystallin gene. One of these is the aculeiform cataract, which is caused by an R58H mutation in gammaD crystallin. We have shown previously that this cataract is caused by crystallization of the mutant protein, which is an order of magnitude less soluble than the wild-type. Here, we report the very high-resolution crystal structures of the mutant and wild-type proteins. Both proteins crystallize in the same space group and lattice. Thus, a strict comparison of the protein-protein and protein-water intermolecular interactions in the two crystal lattices is possible. Overall, the differences between the mutant and wild-type structures are small. At position 58, the mutant protein loses the direct ion-pair intermolecular interaction present in the wild-type, due to the differences between histidine and arginine at the atomic level; the interaction in the mutant is mediated by water molecules. Away from the mutation site, the mutant and wild-type lattice structures differ in the identity of side-chains that occupy alternate conformations. Since the interactions in the crystal phase are very similar for the two proteins, we conclude that the reduction in the solubility of the mutant is mainly due to the effect of the R58H mutation in the solution phase. The results presented here are also important as they are the first high-resolution X-ray structures of human gamma crystallins.     

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

The feasibility of determining the conformation of segments of a polypeptide chain up to six residues in length in globular proteins by means of a systematic search through the possible conformations has been investigated. Trial conformations are generated by using representative sets of phi, psi, and chi angles that have been derived from an examination of the distributions of these angles in refined protein structures. A set of filters based on simple rules that protein structures obey is used to reduce the number of conformations to a manageable total. The most important filters are the maintenance of chain integrity and the avoidance of too-short van der Waals contacts with the rest of the protein and with other portions of the segment under construction. The procedure is intended to be used with approximate models so that allowance is made throughout for errors in the rest of the structure. All possible main chains are first constructed and then all possible side-chain conformations are built onto each of these. The electrostatic energy, including a solvent screening term, and the exposed hydrophobic area are evaluated for each accepted conformation. The method has been tested on two segments of chain in the trypsin like enzyme from Streptomyces griseus. It is found that there is a wide spread of energies among the accepted conformations, and the lowest energy ones have satisfactorily small root mean square deviations from the X-ray structure.     

Three-dimensional model and quaternary structure of the human eye lens protein gamma S-crystallin based on beta- and gamma-crystallin X-ray coordinates and ultracentrifugation.

A 3-dimensional model of the human eye lens protein gamma S-crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3-dimensional structure of gamma-crystallin and beta-crystallin. The model is biased toward the monomeric gamma B-crystallin, which is more similar in sequence. Bovine gamma S-crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric gamma-crystallins. Because the linker has 1 extra residue compared with gamma B and beta B2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. gamma S-crystallin differs from gamma B-crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both beta- and gamma-crystallins, and may contribute to the different roles of these proteins in the lens.     

On the role of the crystal environment in determining protein side-chain conformations

The role of crystal packing in determining the observed conformations of amino acid side-chains in protein crystals is investigated by (1) analysis of a database of proteins that have been crystallized in different unit cells (space group or unit cell dimensions) and (2) theoretical predictions of side-chain conformations with the crystal environment explicitly represented. Both of these approaches indicate that the crystal environment plays an important role in determining the conformations of polar side-chains on the surfaces of proteins. Inclusion of the crystal environment permits a more sensitive measurement of the achievable accuracy of side-chain prediction programs, when validating against structures obtained by X-ray crystallography. Our side-chain prediction program uses an all-atom force field and a Generalized Born model of solvation and is thus capable of modeling simple packing effects (i.e. van der Waals interactions), electrostatic effects, and desolvation, which are all important mechanisms by which the crystal environment impacts observed side-chain conformations. Our results are also relevant to the understanding of changes in side-chain conformation that may result from ligand docking and protein-protein association, insofar as the results reveal how side-chain conformations change in response to their local environment.     

Bacterial abundance in relation to surface area and organic content of marine sediments

Based on direct measurements on surface sediments collected from an intertidal salt marsh, a positive relationship was demonstrated between bacterial abundance and specific surface area of sediment. While this relationship has been postulated previously, this is the first direct confirmation that it holds over a wide range of sediment types. A laboratory experiment was conducted to determine the effects of specific surface area, distribution of surface area, and organic loading on bacterial colonization. Model sediments included angular silica particles, kaolin, and spherical glass beads, used singly or in mixtures. Organic loading resulted in substantial enhancement of bacterial colonization. Distribution of surface area controlled by textural, shape, and sorting, had a complex effect, with glass bead sediments generally supporting better colonization than silica particles or kaolin. The effect of specific surface area was noted only in restricted comparisons of similarly shaped glass beads.     

Unique stabilizing interactions identified in the two-stranded alpha-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide

We determined the 1.17 A resolution X-ray crystal structure of a hybrid peptide based on sequences from coiled-coil regions of the proteins GCN4 and cortexillin I. The peptide forms a parallel homodimeric coiled-coil, with C(alpha) backbone geometry similar to GCN4 (rmsd value 0.71 A). Three stabilizing interactions have been identified: a unique hydrogen bonding-electrostatic network not previously observed in coiled-coils, and two other hydrophobic interactions involving leucine residues at positions e and g from both g-a' and d-e' interchain interactions with the hydrophobic core. This is also the first report of the quantitative significance of these interactions. The GCN4/cortexillin hybrid surprisingly has two interchain Glu-Lys' ion pairs that form a hydrogen bonding network with the Asn residues in the core. This network, which was not observed for the reversed Lys-Glu' pair in GCN4, increases the combined stability contribution of each Glu-Lys' salt bridge across the central Asn15-Asn15' core to approximately 0.7 kcal/mole, compared to approximately 0.4 kcal mole(-1) from a Glu-Lys' salt bridge on its own. In addition to electrostatic and hydrogen bonding stabilization of the coiled-coil, individual leucine residues at positions e and g in the hybrid peptide also contribute to stability by 0.7 kcal/mole relative to alanine. These interactions are of critical importance to understanding the stability requirements for coiled-coil folding and in modulating the stability of de novo designed macromolecules containing this motif.     

A novel type of crystallin in the frog eye lens. 35-kDa polypeptide is not homologous to any of the major classes of lens crystallins

The nucleotide sequence of a cloned DNA coding for the 35-kDa polypeptide of the eye lens of the frog (Rana temporaria) has been determined. The sequence without connectors and poly(A) tract is 889 nucleotides in length and shows no homology with sequences coding for other classes of crystallins: alpha-, beta-, gamma- or delta-crystallins. The sequence contains one reading frame 675 nucleotides in length, an apparently intact 3'-non-translated region with the polyadenylation signal sequence and a poly(A) tract; the 5'-non-translated region is lost along with part of the coding region; this accounts for about 1/4 of the total mRNA length. The secondary structure prediction according to the Ptitsin - Finkelstein method shows the presence of predominantly beta-strands with only a few alpha-helical regions. We conclude that the 35-kDa polypeptide from the frog eye lens belongs to a new class of eye lens crystallins for which we propose the name epsilon-crystallin.     

Determination of the Volume and Surface Area of Tetrahymena pyriformis,and their Relationship to Endocytosis*

Methods are described for the determination of the mean cellular volume and surface area of Tetrahymena pyriformis GL by direct microscopic measurement or by Coulter counter. The results are compared and discussed. It is suggested that the latter is the more accurate method of estimation. Fed cells showed a bimodal size distribution by Coulter counter determination and had a mean volume of 10,000–11,000 μM³, whereas cells which had been starved for 1 or 2 days showed a unimodal distribution and had mean cellular volumes of ～ 1,600 and 1,200 μ³ respectively. The corresponding mean surface areas were ～ 1,900, 550 and 450 μM² respectively. The discrepancy between the results of the 2 methods of estimation was greater with starved than with fed cells because of the greater asymmetry of the former. Continued cell division during the early part of the starvation period had a considerable reducing effect upon the mean cellular volume, but other unidentified factors were also important in producing the observed diminution in volume. Comparison of the mean surface areas of starved cells with previously recorded rates of membranous utilization in endocytosis upon refeeding indicate that insufficient cell membrane was present to maintain the rates of vacuole formation observed.     

Mitochondria induce oxidative stress, generation of reactive oxygen species and redox state unbalance of the eye lens leading to human cataract formation: disruption of redox lens organization by phospholipid hydroperoxides as a common basis for cataract disease

The aging eye appears to be at considerable risk from oxidative stress. Lipid peroxidation (LPO) is one of the mechanisms of cataractogenesis, initiated by enhanced promotion of oxygen free radicals in the eye fluids and tissues and impaired enzymatic and non-enzymatic antioxidant defenses of the crystalline lens. The present study proposes that mitochondria are one of the major sources of reactive oxygen species (ROS) in mammalian and human lens epithelial cells and that therapies that protect mitochondria in lens epithelial cells from damage and reduce damaging ROS generation may potentially ameliorate the effects of free radical-induced oxidation that occur in aging ocular tissues and in human cataract diseases. It has been found that rather than complete removal of oxidants by the high levels of protective enzyme activities such as superoxide dismutase (SOD), catalase, lipid peroxidases in transparent lenses, the lens conversely, possess a balance between peroxidants and antioxidants in a way that normal lens tends to generate oxidants diffusing from lenticular tissues, shifting the redox status of the lens to become more oxidizing during both morphogenesis and aging. Release of the oxidants (O(2)(-)·, H(2)O(2) , OH·, and lipid hydroperoxides) by the intact lenses in the absence of respiratory inhibitors indicates that these metabolites are normal physiological products inversely related to the lens life-span potential (maturity of cataract) generated through the metal-ion catalyzed redox-coupled pro-oxidant activation of the lens reductants (ascorbic acid, glutathione). The membrane-bound phospholipid (PL) hydroperoxides escape detoxification by the lens enzymatic reduction. The lens cells containing these species would be vulnerable to peroxidative attack which trigger the PL hydroperoxide-dependent chain propagation of LPO and other damages in membrane (lipid and protein alterations). The increased concentrations of primary LPO products (diene conjugates, lipid hydroperoxides) and end fluorescent LPO products were detected in the lipid moiety of the aqueous humor samples obtained from patients with cataract as compared to normal donors. Since LPO is clinically important in many of the pathological effects and aging, new therapeutic modalities, such as patented N-acetylcarnosine prodrug lubricant eye drops, should treat the incessant infliction of damage to the lens cells and biomolecules by reactive lipid peroxides and oxygen species and "refashion" the affected lens membranes in the lack of important metabolic detoxification of PL peroxides. Combined in ophthalmic formulations with N-acetylcarnosine, mitochondria-targeted antioxidants are promising to become investigated as a potential tool for treating a number of ROS-related ocular diseases, including human cataracts.     

Diatoms in surface sediments of the Indonesian Archipelago and their relation to hydrography

Diatoms from 53 surface sediments (water depth 350–7200 m) of the Indonesian Archipelago were studied to determine the recent distribution of important assemblages. Three significant assemblages were distinguished, each related to hydrographic parameter(s) of the overlying water mass. The first assemblage is related to the warm saline surface waters of Pacific and Indian Ocean origin; the second assemblage reflects the low-salinity lobe in Makassar Strait; and the third corresponds to major seasonal upwelling areas in the Arafura Sea and south of Java.The normalized ratio of typically Pacific Ocean and Indian Ocean species reflects the fluctuations of the Pacific versus Indian Ocean inflow during the Late Quaternary.Absolute diatom abundances (ADA; in valves g^–1 carbonate-free dry wt) and diatom accumulation rates (DAR; in valves CM^–2 ka^–1) of autochthonous species did not correspond to daily rates of primary production in the photic zone and consequently cannot be used for paleoproductivity estimates.Besides vertical transport some lateral transport of diatoms occurs, as was demonstrated by the presence of three groups of allochthonous species. They are indicators of productivity in the littoral environment, bottom currents and river outflow.     

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding.

Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.     

Surface temperatures of growing pigs in relation to the duration of acclimation to air temperature or draught

The aim of this work was to study to what extent surface temperatures of growing pigs are altered during acclimation to a change of the air temperature and to exposure to draught.

4 groups of 10 pigs (Large White × Dutch Landrace) of approximately 10 weeks old were used. They were housed in 2 calorimeters with 2 pens each. In the reference chamber air temperature was kept constant at 25°C, in the other chamber air temperature could be lowered to 15°C, and a draught was also applied. Surface temperatures of the pigs were measured by means of Probey® Thermal Video System, with an accuracy of ±0.3°C.

Surface temperatures of growing pigs were obviously related to air temperature, draught and the duration of food withdrawal. Acclimation to air temperature or draught as measured by surface temperatures was not observed between days, but within and between night periods.

Also indications of huddling, vasocontriction and even cold-induced vasodilatation within the neck, chest and abdomen region of the pigs' body surface were observed.     

Distribution of specific proteins in the salivary gland lobes of Culicidae and their relation to age and blood sucking

Specific proteins are produced in different parts of the salivary glands of female Anopheles and Culex. In both species there are concentrated low molecular weight proteins in the median lobes and proteins in the mol. wt range 25,000–60,000 in the distal parts of the lateral lobes. These proteins are not identical in the two species. In the proximal parts of the lateral lobe there are only small amounts of protein in addition to an unknown high molecular weight substance. At the time of blood-sucking 15–35% of soluble gland proteins are injected with the saliva into the host animal, the proteins from the median lobes and the proximal part of the lateral lobes being released in greater quantities than the proteins from the distal parts of the lateral lobes. The typical gland proteins are only extractable in low concentrations from the salivary glands of the newly-hatched adult mosquito, they increase up to the 7th day of the adult development and are stored in the glands.     

Rapid migration in gel filtration of the Cf-4 and Cf-9 resistance proteins is an intrinsic property of Cf proteins and not because of their association with high-molecular-weight proteins

Gel filtration is frequently used to study the behaviour and composition of protein complexes. In previous studies, gel filtration analysis of solubilised membranes containing the tomato Cf-4 and Cf-9 resistance proteins indicated that these Cf proteins are present in an approximately 400- and 420-kDa protein complex, respectively, which contains only one Cf molecule per complex, does not contain Rho-related proteins, and does not alter in size upon elicitation. Here, we show that inactive Cf-4 and Cf-9 mutant proteins have a similar large apparent size upon gel filtration analysis. The size remains unaltered after pre-treating the samples under harsh conditions, such as boiling with SDS and incubation in 6 m urea. A similar large apparent size was found for Cf-4 and Cf-9 isolated from SDS gel and for Cf-9 expressed by insect cells. Therefore, the large apparent size observed in our studies appears to be an intrinsic property of the Cf proteins, rather than being caused by association with high-molecular-weight protein(s). Taken together, these results suggest that caution should be taken when interpreting data obtained from gel filtration of LRR-containing proteins.     

Association with HeLa cells of LPS mutants ofSalmonella typhimurium andSalmonella minnesota in relation to their physicochemical surface properties

Different LPS mutants ofSalmonella typhimurium andSalmonella minnesota have been investigated with respect to (1) their tendency to associate, with HeLa cell monolayers, and (2) their physicochemical surface properties. Aqueous biphasic partitioning, hydrophobic interaction chromatography, and ion exchange chromatography have been used to characterize the bacterial cell surface properties with respect to charge and hydrophobicity. Liability to hydrophobic interaction was defined either by the change of partition in a dextran-polyethylene-glycol (PEG) system by the addition of PEG-palmitate (P-PEG), or by the elution pattern from Octyl-Sepharose. Accordingly, charge was assessed by the effect of positively charged trimethylamino-PEG (TMA-PEG) on the partition, and by the elution from DEAE-Sephacel. Bacterial being negatively charged and liable to hydrophobic interaction had the highest tendency to associate with HeLa cells. In some cases the methods for surface analysis gave conflicting results on charge and/or liability to hydrophobic interaction of the same LPS mutant. Possible reasons for these differences and the role of bacterial cell surface structures contributing to physicochemical character are discussed.