Thermodynamic Aspects of cAMP Dependent Protein Kinase Catalytic Subunit Allostery

Kinetics of thermal inactivation of acrylodan-labeled cAMP dependent protein kinase catalytic subunit, its binary complexes with ATP and peptide inhibitor PKI[5–24], respectively, and the ternary complex involving both of these ligands were studied at different temperatures (5–50 °C). The thermodynamic parameters ΔH and ΔS for ligand binding equilibria as well as for the allosteric interaction between the binding sites of these ligands were obtained by using the Van’t Hoff analysis. The results indicated that more inter- and intra-molecular non-covalent bonds were involved in ATP binding with the protein when compared to the peptide binding. Similarly, nucleotide and peptide binding steps were accompanied with different entropy effects, while almost no entropy change accompanied PKI[5–24] binding, suggesting that the protein flexibility was not affected in this case. Differently from the binary complex formation the ternary complex formation was accompanied by a significant entropy change and with intensive formation of new non-covalent interactions (ΔH). At the same time both ligand binding steps as well as the allosteric interaction between ligand binding sites could be described by a common entropy–enthalpy compensation plot, pointing to a similar mechanism of these phenomena. It was concluded that numerous weak interactions govern the allostery of cAMP dependent protein kinase catalytic subunit.     

Relationship Between Protein Denaturation and Water Holding Capacity of Pork During Postmortem Ageing

This study investigated water holding capacity (WHC), water distribution, and protein denaturation of pork loin chops (longissimus lumborum) packaged in polyethylene bags throughout display at 4?±?1 °C for up to 1, 3, 5, 7 and 9 days. The drip loss of pork eventually increased following a decrease during the first 5 days of storage. Nuclear magnetic resonance (NMR) analysis revealed an increase in population of immobilized water P₂₂ from day 1 to day 5, meanwhile a sharp decrease after 9 days was noticed. However, an opposite trend was observed for the population of free water P₂₃. Correlation analysis indicated that myofibrillar protein solubility was negatively correlated with drip loss (p?<?0.05), whereas sarcoplasmic protein measurement were not related to drip loss (p?>?0.05). Furthermore, the content of α-helices increased during the first 5 days of storage (p?<?0.05), which suggested increased WHC during the earlier period of postmortem storage. During the subsequent postmortem storage, the content of α-helices decreased significantly (p?<?0.05), while the β-sheets and β-turns increased. The maximum temperatures (T_max) of three endothermic peaks were found to be 53.6 °C, 65.2 °C, and 77.6 °C at 1 day postmortem. A significant decrease were observed for T_{max peakI},T_{max peakII},T_{max peakIII} at 9 d when compared to 1 d postmortem (p?<?0.05), suggesting loss of thermal stability and protein denaturation.     

Heat Denaturation and Emulsifying Properties of Plasma Protein

The effects of pH and NaCl on the denaturation of plasma protein during heat treatment were investigated, as well as the relationship between protein structure and emulsifying properties. When the plasma protein solution (1% w/v) was heated at 80°C, precipitation was accelerated by the presence of NaCl. The measurement of SH groups, surface hydrophobicity and CD spectrum revealed that denaturation occurs easily by heat treatment in the neutral pH region and in the presence of NaCl. The emulsifying activity index (EAI) did not change much after heat treatment at pH 3 irrespective of the presence of NaCl, but it decreased about 60% after heat treatment at pH 7 in the absence of NaCl. Gel filtration patterns indicated that a high molecular weight peak arose upon heat treatment at neutral pH. We concluded that the decrease in EAI was owing to the polymerization of serum albumin and γ-globulin, which are the main components of plasma protein, and disulfide bonds participated in this process.     

Kinetics of Thermal Denaturation and Aggregation of Bovine Serum Albumin

Thermal aggregation of bovine serum albumin (BSA) has been studied using dynamic light scattering, asymmetric flow field-flow fractionation and analytical ultracentrifugation. The studies were carried out at fixed temperatures (60°C, 65°C, 70°C and 80°C) in 0.1 M phosphate buffer, pH 7.0, at BSA concentration of 1 mg/ml. Thermal denaturation of the protein was studied by differential scanning calorimetry. Analysis of the experimental data shows that at 65°C the stage of protein unfolding and individual stages of protein aggregation are markedly separated in time. This circumstance allowed us to propose the following mechanism of thermal aggregation of BSA. Protein unfolding results in the formation of two forms of the non-native protein with different propensity to aggregation. One of the forms (highly reactive unfolded form, U_hr) is characterized by a high rate of aggregation. Aggregation of U_hr leads to the formation of primary aggregates with the hydrodynamic radius (R_h,1) of 10.3 nm. The second form (low reactive unfolded form, U_lr) participates in the aggregation process by its attachment to the primary aggregates produced by the U_hr form and possesses ability for self-aggregation with formation of stable small-sized aggregates (A_st). At complete exhaustion of U_lr, secondary aggregates with the hydrodynamic radius (R_h,2) of 12.8 nm are formed. At 60°C the rates of unfolding and aggregation are commensurate, at 70°C the rates of formation of the primary and secondary aggregates are commensurate, at 80°C the registration of the initial stages of aggregation is complicated by formation of large-sized aggregates.     

Time Dependent Effects of 6-OHDA Lesions on Iron Level and Neuronal Loss in Rat Nigrostriatal System

The early changes in iron level and neuronal loss in rat nigrostriatal system were investigated using 6-hydroxydopamine (6-OHDA) unilaterally lesioned rats. The results showed that: 1, 3, 5, 7, and 14 days of postlesion, there was a progressive reduction in the density of the tyrosine hydroxylase immunoreactive (TH-ir) cells in the lesioned substantia nigra (SN). Iron level increased in the lesioned SN from 1–14 days following 6-OHDA lesions, but there were no differences in iron level among them. Only on 14 days of postlesion, did the DA release decrease in striatum (Str) of the lesioned side, while there were no changes in other groups. These results implied that the increased iron level in SN occured when there was a moderate reduction of DA neurons. However, the DA release in Str was unchanged until TH-ir cells were highly reduced due to the immense compensatory mechanism of the DA system.     

Water Vapour Loss from a Physical Model of a Substomatal Cavity

With the aid of a scale model of a substomatal cavity it hasbeen shown that the rates of evaporation inside such a cavityare greater from loci near the pore than from further away.Implications for the process of evaporation inside a real substomatalcavity are discussed, especially the contribution towards vapourloss from inner epidermal walls.     

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining ³J_NC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of ¹HN and ¹⁵N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and ³J_NC’ H-bond couplings, are identified with an accuracy of 90% by ¹HN temperature coefficients. The accuracy is improved to 95% when ¹⁵N temperature coefficients are also included. In contrast, the urea dependence of ¹HN and ¹⁵N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility.     

The Behavior of the Hydrophobic Effect under Pressure and Protein Denaturation

It is well known that proteins denature under high pressure. The mechanism that underlies such a process is still not clearly understood, however, giving way to controversial interpretations. Using molecular dynamics simulation on systems that may be regarded experimentally as limiting examples of the effect of high pressure on globular proteins, such as lysozyme and apomyoglobin, we have effectively reproduced such similarities and differences in behavior as are interpreted from experiment. From the analysis of such data, we explain the experimental evidence at hand through the effect of pressure on the change of water structure, and hence the weakening of the hydrophobic effect that is known to be the main driving force in protein folding.     

Thermal,Chemical and pH Induced Unfolding of Turmeric Root Lectin: Modes of Denaturation

Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol⁻¹ and 14.90 Kcal mol⁻¹ for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔC_p) is 3.42 Kcal mol⁻¹ K⁻¹ for dimer. The small ΔC_p for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.     

Effects of Meat Cooking,and of Ingested Amount,on Protein Digestion Speed and Entry of Residual Proteins into the Colon: A Study in Minipigs

The speed of protein digestion impacts on postprandial protein anabolism. After exercise or in the elderly, fast proteins stimulate protein synthesis more efficiently than slow proteins. It has been shown that meat might be a source of fast proteins. However, cooking temperature, acting on the macrostructure and microstructure of the meat could affect both the speed, and efficiency, of protein digestion. This study aims to evaluate, in vivo, the effect of meat cooking on digestion parameters, in the context of a complete meal. Six minipigs fitted with an ileal cannula and an arterial catheter were used. In order to measure the true ileal digestibility, tested meat was obtained from a calf, the muscle proteins of which were intrinsically labelled with ¹⁵N-amino acids. Three cooking temperatures (60, 75 and 95°C; core temperature for 30 min), and three levels of intake (1, 1.45, and 1.90 g protein/kg body weight) were tested. Following meat ingestion, ileal digesta and arterial blood were collected over a 9-h period. The speed of digestion, evaluated from the kinetics of amino acid appearance in blood within the first 3 h, was greater for the cooking temperature of 75°C, than for 60 or 95°C. The true ileal digestibility, which averaged 95%, was not affected by cooking temperature or by the level of meat intake. The amino acid composition of the digesta flowing at the ileum was not affected by cooking temperature. These results show that cooking temperature can modulate the speed of meat protein digestion, without affecting the efficiency of the small intestinal digestion, and consequently the entry of meat protein residues into the colon.     

Effect of Sorbed Water on the Thermal Stability of Soybean Protein

A soybean protein isolate (SPI), and its β-conglycinin and glycinin componets were obtained from defatted soybean flour by applying dissolution and precipitation based on the difference in their solubility depending on each isoelectric point. The purity evaluated by SDS–PAGE of the β-conglycinin and glycinin preparations was about 84% and 80%, respectively, resulting in a clear difference in the pH dependence on solubility. A BET plot derived from the water sorption isotherm at 25 °C showed that the amount of the monolayer adsorption of these preparations was about 6–9%, the value for the β-conglycinin preparation being about 1.5 times higher than that for the glycinin preparation. The β-conglycinin and glycinin preparations were respectively denatured at around 75 °C and 86 °C in the presence of excess water, whereas the denaturation temperature of both preparations was markedly increased by decreasing sorbed water content below 40%, corresponding well with the unfrozen water content.     

Thermal Energy Exchange Model and Water Loss of a Barrel Cactus, Ferocactus acanthodes

The influences of various diurnal stomatal opening patterns, spines, and ribs on the stem surface temperature and water economy of a CAM succulent, the barrel cactus Ferocactus acanthodes, were examined using an energy budget model. To incorporate energy exchanges by shortwave and longwave irradiation, latent heat, conduction, and convection as well as the heat storage in the massive stem, the plant was subdivided into over 100 internal and external regions in the model. This enabled the average surface temperature to be predicted within 1 C of the measured temperature for both winter and summer days.     

Evolutionary Aspects of Protein Structure and Folding

Four basic stages of evolution of protein structure are described, basing on recent work of the authors aimed specifically to reconstruct the earliest events in the protein evolution. According to this reconstruction, the initial stage of short peptides comprising, probably, only a few amino acid residues had been followed by formation of closed loops of 25–30 residues, which corresponds to the polymer-statistically optimal ring closure size for mixed polypeptide chains. The next stage involved fusion of relatively small linear genes and formation of protein structures consisting of several closed loops of a nearly standard size, with 4–6 loops (100–200 amino acid residues) in a typical protein fold. The last, modern stage began with combinatorial fusion of the presumably circular 300–600 bp DNA units and, accordingly, formation of multidomain proteins.     

A Search for Extraterrestrial Eukaryotes: Physical and Paleontological Aspects

Physical and biochemical aspects of a proposed search for extraterrestrial eukaryotes (SETE) are considered. Such a program should approach the distinction between a primitive eukaryote and an archaebacteria. The emphasis on gene silencing suggests a possible assay suitable for a robotic investigation of eukaryoticity, so as to be able to decide whether the first steps towards eukaryogenesis have been taken in an extraterrestrial planet, or satellite. The experiment would consist of searching for cellular division and the systematic related delay in replication of heterochromatic chromosome segments. It should be noticed that the direct search for a membrane-bounded set of chromosomes does not necessarily determine eukaryotic identity, as there are prokaryotes that have membrane-bounded nucleoids. A closer look at the protein fraction of chromatin (mainly histones) does not help either, as there are some eukaryotes that may lack histones; there are also some bacteria as well as archaebacteria with histone-like proteins in their nucleoids. Comments on the recent suggestion of possible environments for a SETE program are discussed: the deep crust of Mars, and the Jovian satellite Europa, provided the existence of an ocean under its ice-covered surface is confirmed by the current Galileo mission.     

Time Dependent MHD Nano-Second Grade Fluid Flow Induced by Permeable Vertical Sheet with Mixed Convection and Thermal Radiation

The aim of present paper is to study the series solution of time dependent MHD second grade incompressible nanofluid towards a stretching sheet. The effects of mixed convection and thermal radiation are also taken into account. Because of nanofluid model, effects Brownian motion and thermophoresis are encountered. The resulting nonlinear momentum, heat and concentration equations are simplified using appropriate transformations. Series solutions have been obtained for velocity, temperature and nanoparticle fraction profiles using Homotopy Analysis Method (HAM). Convergence of the acquired solution is discussed critically. Behavior of velocity, temperature and concentration profiles on the prominent parameters is depicted and argued graphically. It is observed that temperature and concentration profiles show similar behavior for thermophoresis parameter Νt but opposite tendency is noted in case of Brownian motion parameter Νb. It is further analyzed that suction parameter S and Hartman number Μ depict decreasing behavior on velocity profile.