Physicochemical Studies on Sulfated Polysaccharides Extracted from Seaweeds at Various Temperatures

Sulfated polysaccharides (SPS) were extracted from three species of seaweeds of Ulvacea (Ulva pertusa, Ulva conglobata and Entromorpha prolifera) for 4 hr at various temperatures and their physicochemical properties were studied using viscometric and equilibrium sedimentation measurements in order to determine the optimum extracting condition.

Sulfated polysaccharides extracted at various temperatures from the seaweed of U. pertusa had the same physicochemical properties, while the larger molecular components of SPS was not extracted from U. conglobata and E. prolifera, at the low temperature of 30~40°C. This was confirmed by analyses of their viscosity and molecular weight and by gel filtration chromatography, in which each SPS showed two or three peaks.

The larger molecular component of SPS could be extracted at the high temperature of 80~90°C in the thermostable form.     

The isolated MUC5AC gene product from human ocular mucin displays intramolecular conformational heterogeneity

Atomic force microscopy (AFM) has been used to show that human ocular mucins contain at least three distinct polymer conformations, separable by isopycnic density gradient centrifugation. In this work we have used affinity purification against the anti(mucin peptide core) monoclonal antibody 45M1 to isolate MUC5AC gene products, a major component of human ocular mucins. AFM images confirm that the affinity-purified polymers adopt distinct conformations that coidentify with two of those observed in the parent population, and further reveal that these two different conformations can be present within the same polymer. AFM images of the complexes formed after incubation of 45M1 with the parent sample reveal different rates of binding to the two MUC5AC polymer types. The variability of gene products within a mucin population was revealed by analyzing the height distributions along the polymer contour and periodicities in distances between occupied antibody binding sites. AFM analysis of mucin polymers at the single molecule level provides new information about the genetic origins of individual polymers and the contributions of glycosylation to the physicochemical properties of mucins, which can be correlated with information obtained from biochemistry, antibody binding assays, and molecular biology techniques.     

Stereochemistry of collagen

This review article, based on a lecture delivered in Madras in 1985, is an account of the author's experience in the working out of the molecular structure and conformation of the collagen triple-helix over the years 1952-78. It starts with the first proposal of the correct triple-helix in 1954, but with three residues per turn, which was later refined in 1955 into a coiled-coil structure with approximately 3.3 residues per turn. The structure readily fitted proline and hydroxyproline residues and required glycine as every third residue in each of the three chains. The controversy regarding the number of hydrogen bonds per tripeptide could not be resolved by X-ray diffraction or energy minimization, but physicochemical data, obtained in other laboratories during 1961-65, strongly pointed to two hydrogen bonds, as suggested by the author. However, it was felt that the structure with one straight NH...O bond was better. A reconciliation of the two was obtained in Chicago in 1968, by showing that the second hydrogen bond is via a water molecule, which makes it weaker, as found in the physicochemical studies mentioned above. This water molecule was also shown, in 1973, to take part in further cross-linking hydrogen bonds with the OH group of hydroxyproline, which occurred always in the location previous to glycine, and is at the right distance from the water. Thus, almost all features of the primary structure, X-ray pattern, optical and hydrodynamic data, and the role of hydroxyproline in stabilising the triple helical structure, have been satisfactorily accounted for. These also lead to a confirmation of Pauling's theory that vitamin C improves immunity to diseases, as explained in the last section.     

Metastability and transformation of polymorphic crystals in biodegradable poly(butylene adipate)

Polymorphism phenomenon of melt-crystallized poly(butylene adipate) (PBA) has been studied by wide-angle X-ray diffraction (WAXD), small-angle X-ray scattering (SAXS), and differential scanning calorimetry (DSC). It has been found that the isothermal crystallization leads to the formation of PBA polymorphic crystals, simply by changing the crystallization temperature. The PBA alpha crystal, beta crystal, and the mixture of two crystal forms grow at the crystallization temperatures above 32 degrees C, below 27 degrees C, and between these two temperatures, respectively. The relationship between PBA polymorphism and melting behaviors has been analyzed by the assignments of multiple melting peaks. Accordingly, the equilibrium melting temperatures Tm degrees of both alpha and beta crystals were determined by Hoffman-Weeks and Gibbs-Thomson equations for the purpose of understanding the structural metastability. The Tm degrees of the PBA alpha crystal was found to be higher than that of the beta crystal, indicating that the PBA alpha crystal form is a structurally stable phase and that the beta crystal form is a metastable phase. The analysis of growth kinetics of PBA polymorphic crystals indicates that the metastable PBA beta crystal is indeed the kinetically preferential result. Based on the thermal and kinetic results, the phenomenon of stability inversion with crystal size in melt-crystallized PBA was recognized, in terms of the growth mechanisms of PBA alpha and beta crystals and the transformation of beta to alpha crystals. The PBA beta --> alpha crystal transformation takes place at a sufficiently high annealing temperature, and the transformation has been evident to be a solid-solid-phase transition process accompanied by the thickening of lamellar crystals. The molecular motion of polymer chains in both crystalline and amorphous phases has been discussed to understand the thickening and phase transformation behaviors.     

Solvent effects on the conformational transition of a model polyalanine peptide

We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA(14)K-NH(2) molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain's hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: alpha-helix, beta-structures (including beta-hairpin and beta-sheet-like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an alpha-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a beta-hairpin, resulting in an alpha-helical conformation at low temperatures, a beta-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become beta-hairpins and beta-sheet-like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper.     

Physical properties of glycosyl diacylglycerols. 1. Calorimetric studies of a homologous series of 1,2-di-O-acyl-3-O-(alpha-D-glucopyranosyl)-sn-glycerols

The polymorphic phase behavior of aqueous dispersions of a homologous series of 1,2-di-O-acyl-3-O-(alpha-D-glucopyranosyl)-sn-glycerols was studied by differential scanning calorimetry. At fast heating rates unannealed samples of these lipids exhibit a strongly energetic transition, which has been identified as a lamellar gel/liquid crystalline (L beta/L alpha) phase transition (short- and medium-chain compounds) or a lamellar gel to inverted hexagonal (L beta/HII) phase transition (long-chain compounds) by X-ray diffraction studies (Sen et al., 1990). At still higher temperatures, some of the lipids that form lamellar liquid-crystalline phases exhibit an additional transition, which has been identified as a transition to an inverted nonbilayer phase by X-ray diffraction studies. The lamellar gel phase formed on initial cooling of these lipids is a metastable structure, which, when annealed under appropriate conditions, transforms to a more stable lamellar gel phase, which has been identified as a poorly hydrated crystal-like phase with tilted acyl chains by X-ray diffraction measurements (Sen et al., 1990). With the exception of the di-19:0 homologue, the crystalline phases of these lipids are stable to temperatures higher than those at which their L beta phases melt and, as a result, they convert directly to L alpha or HII phases on heating. Our results indicate that the length of the acyl chain affects both the kinetic and thermodynamic properties of the crystalline phases of these lipids as well as the type of nonbilayer phase that they form. Moreover, when compared with the beta-anomers, these alpha-D-glucosyl diacylglycerols are more prone to form ordered crystalline gel phases at low temperatures and are somewhat less prone to form nonbilayer phases at elevated temperatures. Thus the physical properties of glucolipids (and possibly all glycolipids) are very sensitive to the nature of the anomeric linkage between the sugar headgroup and the glycerol backbone of the lipid molecule. We suggest that this is, in part, due to a change in orientation of the glucopyranosyl ring relative to the bilayer surface, which in turn affects the way(s) in which the sugar headgroups interact with each other and with water.     

Single molecule thermodynamics in biological motors

Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.     

Collagen: the organic matrix of bone

Collagen is the principal organic matrix in bone. The triple helical region of the molecule is 1014 amino acids long. In fibrils these molecules are staggered axially by integers of 234 residues or 68 nm (D). This axial shift occurs by self-assembly and can be understood in terms of a periodicity in the occurrence of apolar and polar residues in the amino acid sequence. Because the molecular length L = 4.47 D, there are gaps 1.5 X 36.5 nm regularly arrayed throughout the fibrils. The three-dimensional molecular arrangement is a quasi-hexagonal lattice with three distinct values for the principal interplanar spacings. Analysis of the intensity distribution in the medium-angle X-ray diffraction patterns from tendons has produced the following picture of the molecular arrangement in fibrils (Fraser et al. 1983). The molecular helices have a coherent length of 32 nm and are tilted parallel to a specific place within the lattice. A regular azimuthal interaction exists between these helices. This crystalline region could be the overlap region with a non-crystalline gap region. However, the gap is still regular axially and the molecular helices retain their structure; their lateral packing is perturbed although they retain a 'gap'. Neutron and X-ray scattering experiments have shown that calcium hydroxyapatite crystals occur in the gap and are nucleated at a specific though unknown location within the gap. The c-axis of the apatite crystals is parallel to the fibril axis and its length c = 0.688 nm is close to the axial periodicity in a protein with an extended beta-conformation. If the telopeptides at the end of a collagen molecule do have this conformation they would either have a highly heterogeneous conformation or exist in a folded manner because the overall length of the telopeptides is shorter than a regular collagen repeat of 0.029 nm would allow.     

The molecular basis of class II MHC allelic control of T cell responses.

To identify the molecular basis for the effects of MHC molecule polymorphism on T cell responses, we have combined functional T cell response testing with measurements of peptide binding to the class II MHC molecules on transfected cells. Our studies identify a small subset of spatially localized polymorphic residues of the E alpha E beta dimer (strand residue beta 29, and helix residues beta 72 and beta 75) regulating cytochrome c peptide presentation by two distinct mechanisms. The first effect is on quantitative control of net peptide binding. The replacement of the valine found at position beta 29 in E beta k with the glutamic acid found in E beta b results in a selective loss of pigeon cytochrome peptide but not moth cytochrome peptide binding to the resultant mutant E alpha E beta k molecule. Reciprocally, the replacement of glutamic acid at beta 29 in E beta b with valine results in a gain of pigeon peptide binding. These changes in binding parallel changes in T cell responses in vitro to these peptide-E alpha E beta combinations and mirror the in vivo immune response gene phenotypes of mice expressing E alpha E beta k and E alpha E beta b. E alpha E beta s molecules, which have a beta 29 glutamic acid, are nevertheless able to bind and present pigeon cytochrome peptides, and this is due to changes in helix residues beta 72 and beta 75 that compensate for the negative effect of the beta 29 glutamic acid. The second activity is a critical change in the conformation of the peptide bound to the same extent by distinct MHC molecules, as revealed by changes in T cell responses to moth cytochrome peptides presented by two E alpha E beta molecules differing only at position beta 29. Both of these effects can be ascribed to a single polymorphic residue modeled to be inaccessible to TCR contact (beta 29), providing a striking demonstration of how MHC molecule polymorphism can modify T cell-dependent immune responses without direct physical participation in the receptor recognition event.     

Preliminary X-ray diffraction analysis of crystalline lectins from the seeds and leaves of Sophora japonica

The Japanese Pogada Tree (Sophora japonica) contains at least four distinct lectins distributed among seeds, bark, and leaf tissues of the plant. All of these lectins are N-acetylgalactosamine-specific, have molecular weights of about 130,000, are glycoproteins and possess substantial sequence homology. However, they are products of distinct genes. We have crystallized Sophora lectins from bark, seeds, and two different lectins from leaves. Multiple crystal forms of each variety have been obtained by vapor diffusion with polyethylene glycol 4,000 solutions, and five of the crystal forms have been characterized by X-ray diffraction. The data demonstrates that at least in the case of leaf lectin II, the tetrameric molecule contains at least one exact dyad axis. Several of the crystals appear suitable for high resolution structure analysis.     

One gene, two diseases and three conformations: molecular dynamics simulations of mutants of human prion protein at room temperature and elevated temperatures

Fatal familial insomnia (FFI) and Creutzfeldt-Jakob disease (CJD) are associated to the same mutation at codon 178 but differentiate into clinicopathologically distinct diseases determined by this mutation and a naturally occurring methionine-valine polymorphism at codon 129 of the prion protein gene. It has been suggested that the clinical and pathological difference between FFI and CJD is caused by different conformations of the prion protein. Using molecular dynamics (MD), we investigated the effect of the mutation at codon 178 and the polymorphism at codon 129 on prion protein dynamics and conformation at normal and elevated temperatures. Four model structures were examined with a focus on their dynamics and conformational changes. The results showed differences in stability and dynamics between polymorphic variants. Methionine variants demonstrated a higher stability than valine variants. Elongation of existing beta-sheets and formation of new beta-sheets was found to occur more readily in valine polymorphic variants. We also discovered the inhibitory effect of proline residue on existing beta-sheet elongation.     

Subunit structure of high molecular weight mouse nerve growth factor

Studies from several laboratories have shown that mouse submandibular glands and mouse saliva contain nerve growth factor (NGF) as part of a high molecular weight oligomeric macromolecule composed of three different subunits, termed alpha, beta, and gamma. The beta-subunit is the nerve growth-promoting protein. The gamma-subunit is a serine protease class enzyme of highly restricted substrate specificity. The alpha-subunit has no known function. This high molecular weight form of nerve growth factor is also a Zn(II)-containing metalloprotein. In the present study, measurements of multiple physicochemical parameters have been used to deduce the subunit structure of high molecular weight NGF. Results demonstrate that it contains two alpha-, one beta- and one gamma-subunit together with one tightly bound Zn(II) ion per molecule.     

Solid-state characterization of chitosans derived from lobster chitin

Two samples of chitosan (CH1 and CH2) of different molecular weights and degrees of deacetylation were prepared from lobster chitin under two different processes. Solid-state properties of CH1 and CH2 were characterized and compared with four commercial chitosans prepared from crab and fresh shrimp shells. Infrared spectroscopy (IR), solid-state CP-MAS ¹³C NMR, powder X-ray diffraction and differential scanning calorimetric techniques were used to characterize the molecular structure and solid-state properties of the materials. Changes in the crystallinity and polymorphic forms of CH1 and CH2 were attributable to the different process conditions used. The differences in crystallinity were confirmed by powder X-ray diffraction data. The methods of preparation of CH1 and CH2 did not significantly influence the bulk, tap and true densities of the bulk material, but they affected the flow properties of CH1 and CH2. In conclusion, the physicochemical properties of the present chitosans prepared from lobster chitin (CH1 and CH2) are comparable with those of commercial chitosan materials of crab or shrimp shell origin.     

Muscle parvalbumin isoforms of Clarias gariepinus, Heterobranchus longifilis and Chrysichthys auratus: isolation, characterization and expression during development

The white-muscle parvalbumin isoforms of Clarias gariepinus, Heterobranchus longifilis and Chrysichthys auratus were purified and their physicochemical parameters determined. The three catfish isoforms are distinct but those of C. gariepinus and H. longifilis are more similar. In the course of development, the successive appearance of larval and adult parvalbumins was observed. Larval isoforms (PA I, PA IIa, PA IIb) displayed a lower isoelectric point (pI) and molecular mass than adult ones (PA IIc, PA IIIa, PA IIIb, PA III, PA IV). The PA IIa isoform appeared as an omnipresent typical larval isoform. PA IIb appeared mostly larval, being insignificant in adult specimens; its physicochemical features were the same in the three catfish species. In Chrysichthys auratus , there were three PA II isoforms, one appearing as an adult isoform (PA IIc). The fact that the two types of parvalbumin isoforms appear at different times should reflect specific physiological needs (mobility, feeding) of different developmental stages.     

Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K.

Structures using X-ray diffraction data collected to 1.5-A resolution have been determined for the protein ribonuclease-A at nine different temperatures ranging from 98 to 320 K. It is determined that the protein molecule expands slightly (0.4% per 100 K) with increasing temperature and that this expansion is linear. The expansion is due primarily to subtle repacking of the molecule, with exposed and mobile loop regions exhibiting the largest movements. Individual atomic Debye-Waller factors exhibit predominantly biphasic behavior, with a small positive slope at low temperatures and a larger positive slope at higher temperatures. The break in this curve occurs at a characteristic temperature of 180-200 K, perhaps indicative of fundamental changes in the dynamical structure of the surrounding protein solvent. The distribution of protein Debye-Waller factors is observed to broaden as well as shift to higher values as the temperature is increased.     

Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers.

Red clover is an important forage legume species for temperate regions and very little is known about the genetic organization of its breeding populations. We used random amplified polymorphic DNA (RAPD) genetic markers to address the genetic diversity and the distribution of variation in 20 breeding populations and cultivars from Chile, Argentina, Uruguay, and Switzerland. Genetic distances were calculated for all possible pairwise combinations. A high level of polymorphism was found and the proportion of polymorphic loci across populations was 74.2%. A population derived from a non-certified seedlot displayed a higher proportion of polymorphic loci than its respective certified seedlot. Gene diversity values and population genetics parameters suggest that the populations analyzed are diverse. An analysis of molecular variance (AMOVA) revealed that the largest proportion of variation (80.4%) resides at the within population level. RAPD markers are a useful tool for red clover breeding programs. A dendrogram based on genetic distances divided the breeding populations analyzed into three distinct groups. The amount and partition of diversity observed can be of value in identifying the populations that parents of synthetic cultivars are derived from and to exploit the variation available in the populations analyzed.     

Molecular imprinting of amino acid derivatives at low temperature (0 degrees C) using photolytic homolysis of azobisnitriles

Molecular imprints of L-phenylalanine anilide (print molecule) were prepared using a number of free radical initiation systems. Polymers were prepared using azobisnitriles as either thermal initiators or photoinitiators at temperatures ranging from 0 to 60 degrees C and evaluated in the high-performance liquid chromatographic mode for enantioselectivity. The results show that preparation of molecular imprints at 0 degrees C using photolytic homolysis of azobisnitriles significantly increases enantioselectivity and allows separations of the enantiomers of the print molecule to be performed at room temperature. This compares to previous reports of molecular imprints where separations needed to be performed at elevated temperatures (80-90 degrees C). The present method is also easier to perform and less time-consuming than those previously described.     

Cross-bridge conformation as revealed by x-ray diffraction studies on insect flight muscles with ATP analogues.

The effects of three ATP analogues, alpha,beta-methylene-ATP [ATP(alpha,beta-CH1)], adenosine 5'-0-(3-thiotrophosphate) [ATP(gamma-S)], and beta,gamma-amino-ATP [ATP(beta,gamma-NH)] at various concentrations and temperatures on the X-ray fiber diagrams of glycerinated flight muscles from a water bug (Lethocerus maximus) have been investigated. It is shown that the "relaxed" state can be obtained with all three analogues at high concentrations, the result being particularly clear with ATP(gamma-S). It is inferred that the binding of an ATP-like molecule suffices to produce the relaxed state. At low concentrations ATP(beta,gamma-NH) produces state intermediate between rigor and relaxed which is not simply a mixture of the two. The possible nature of the intermediate is discussed.     

Frequent recombination shapes the epidemic population structure of Planktothrix (Cyanoprokaryota) in Italian subalpine lakes

The planktonic genus Planktothrix, as other cyanobacteria, shows signals of both homologous and nonhomologous recombination. However, the frequency of recombination and its effect on Planktothrix population structuring is unknown. We isolated 290 Planktothrix strains from seven neighboring lakes in the subalpine Italian region and analyzed these using multilocus sequence typing. Four of six loci analyzed were polymorphic, resulting in 20 distinct multilocus genotypes. Association indices among alleles at different loci were suggestive of an “epidemic population structure,” resulting from an explosive (and temporary) dominance of one genotype against a panmictic background. ClonalFrame analyses supported this view by detecting: (i) three major clades affected by three distinct recombination events, (ii) a recombination rate about equal to the mutation rate, and (iii) the fact that recombination had an impact on introducing molecular diversity more than double the mutation rate. Furthermore, analysis of molecular variance over an annual cycle in three of seven lakes revealed that both local clonal expansion and recombination processes affected among‐lake diversity. Our observations suggest that recombination affects microevolution of Planktothrix and that an epidemic structure can emerge in populations of this genus.