Other developments regarding the concept of energy in biological systems

In order to recognize the realizability of inputs with different physical natures through a component, Yoneda's Lemma is applied. The major utility of this Lemma is when the components produce only energy. From this, it is assumed that a new material input must exist which was not recognized in the original developments in biological systems representation. Moreover, simple transfers of energy, between objects, components, and among both objects and components are developed under the generic name; energetical evolution. Thus, energetical evolution appears as anew element in the abstract representation of biological systems. These new concepts are incorporated into a new abstract diagram and a newM _β category. This paper was made possible by a Fellowship from the Consejo Nacional de Investigaciones Científicas y Técnicas of the República Argentina.     

α-Glucosidase inhibition activity and in silico study of 2-(benzo[d][1,3]dioxol-5-yl)-4H-chromen-4-one,a synthetic derivative of flavone

A synthetic flavone derivative 2-(benzo[d][1,3]dioxol-5-yl)-4H-chromen-4-one (BDC) was synthesized by the one pot reaction method and assessed for α-glucosidase inhibitory activity. The BDC demonstrated dose dependent inhibition of α-glucosidase activity. A maximum inhibition (99.3 ± 0.26%) of α-glucosidase was observed at 27.6 µM. The maximum α-glucosidase inhibitory activity depicted by BDC 27.6 µM concentration was 22.4 fold over the maximum inhibition observed with acarbose (97.72 ± 0.59% at 669.57 µM), a standard commercial anti-diabetic drug. In contrast to acarbose that depicted competitive type inhibition, kinetic studies of α-glucosidase inhibition by BDC demonstrated non-competitive inhibition with Km of 0.71 mM⁻¹ and a Vmax of 0.028 mmol/min. In silico studies suggest allosteric interaction of BDC with α-glucosidase at a minimum binding energy (ΔG) of −8.64 kcal/mol and Ki of 465.3 nM, whereas, acarbose interacted at the active site of α-glucosidase with ΔG of −9.23 kcal/mol and Ki of 172 nM. Thus BDC significantly inhibited α-glucosidase in comparison to acarbose. Moreover, BDC has been endorsed for drug likeness by evaluating it as per Lipinski rule of five. Thus, BDC can be a lead compound for the management of type-2 diabetes mellitus.     

Involvement of glycans in the immunological cross-reaction between α-macroglobulin and hemocyanin of the gastropod Helix pomatia

By tandem-crossed immunoelectrophoresis and ELISA experiments an immunological relationship was observed between α-macroglobulin (αM) and hemocyanin (Hc) of the terrestrial snail Helix pomatia. Both glycoproteins occur in the hemolymph: αM (minor component) as a specific proteinase inhibitor, Hc (consisting of three components: α_D-HpH, α_N-HpH and β-HpH) as oxygen transport protein. The cross-reaction was found to be correlated with glycosylation. (i) With β-HpH, which is richer in carbohydrates than α_D-HpH and α_N-HpH, mainly due to a higher 3-O-methyl-d-galactose content, the cross-reaction with HpαM was highest. (ii) From the 8 functional units, designated a–h, isolated from β-HpH, two that lack carbohydrates (c and f) were not recognized by antibodies against HpαM, while the six glycosylated ones were strongly cross-reacting. The nearly complete loss of the cross-reactivity upon deglycosylation of functional units d and g and the inhibition in competitive ELISA experiments by glycopeptides isolated from both β-HpH and HpαM are further evidence that glycans are involved in the immunological relationship between HpH and HpαM. Carbohydrate analyses indicated that the glycan structures present on HpαM are very similar (or identical) to those found on HpH, suggesting that glycans are common epitopes on both proteins. Especially d-xylose and 3-O-methyl-d-galactose seem to be responsible for the cross-reactivity since the α-macroglobulin and hemocyanin of the cephalopod Sepia officinalis, which lack these two monosaccharides in their glycan structures, do not immunologically cross-react.     

Effects of curvature and composition on α-synuclein binding to lipid vesicles

Parkinson's disease is characterized by the presence of intracellular aggregates composed primarily of the neuronal protein α-synuclein (αS). Interactions between αS and various cellular membranes are thought to be important to its native function as well as relevant to its role in disease. We use fluorescence correlation spectroscopy to investigate binding of αS to lipid vesicles as a function of the lipid composition and membrane curvature. We determine how these parameters affect the molar partition coefficient of αS, providing a quantitative measure of the binding energy, and calculate the number of lipids required to bind a single protein. Specific anionic lipids have a large effect on the free energy of binding. Lipid chain saturation influences the binding interaction to a lesser extent, with larger partition coefficients measured for gel-phase vesicles than for fluid-phase vesicles, even in the absence of anionic lipid components. Although we observe variability in the binding of the mutant proteins, differences in the free energies of partitioning are less dramatic than with varied lipid compositions. Vesicle curvature has a strong effect on the binding affinity, with a >15-fold increase in affinity for small unilamellar vesicles over large unilamellar vesicles, suggesting that αS may be a curvature-sensing protein. Our findings provide insight into how physical properties of the membrane may modulate interactions of αS with cellular membranes.     

Internalization of alpha 2 macroglobulin in receptosomes. Studies with monovalent electron microscopic markers

Previous studies using multivalent, peroxidase-labeled antibody for localization of α₂ M have demonstrated that the binding of α₂-macroglobulin (α₂ M) to randomly distributed receptors on the surfaces of fibroblasts initiates the accumulation of α₂ M-receptor complexes in clathrin-coated pits. The α₂ M-receptor complexes are then internalized into a specialized vesicle termed the receptosome. In the present study we have used three different monovalent ligands to localize α₂ M and show that the endocytosis of α₂ M-receptor complexes by the receptosomal pathway is not initiated as a result of antibody-induced cross-linking of the α₂ M-receptor complexes. To perform these studies the following monovalent markers of α₂ M were prepared for electron microscopic visualization: (1) a monovalent hybrid antibody directed against α₂ M and ferritin; (2) a monovalent hybrid antibody directed against α₂ M-peroxidase; and (3) a direct 1:1 conjugate of α₂ M-peroxidase. We find that all three of the markers are internalized by the ligand pathway previously described using multivalent labels. The steps involved are clustering of α₂ M receptor complexes in coated regions of the plasma membrane followed by endocytosis of α₂ M into receptosomes. Our results are contrasted with previous studies on lymphocytes in which antibody induced cross-linking of membrane antigens was necessary for triggering their pinocytosis. The methods described in this paper are applicable for visualizing at the electron microscopic level the internalization of other ligands and hormones.     

Antioxidant and angiotensin-converting enzyme (ACE) inhibitory activity of thymosin alpha-1 (Thα1) peptide

In this research, the antioxidant property of thymosin alpha-1 (Thα1) peptide was investigated through various antioxidant methods. Thα1 showed 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity (IC₅₀ = 20 µM) and its 2,2-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) scavenging reached 45.33% at 80 µM (IC₅₀ = 85 µM). In addition, hydroxyl and superoxide radical scavenging of Thα1 peptide exhibited a concentration-depended manner. The IC₅₀ values of hydroxyl and superoxide radical scavenging were estimated to be 82 µM and 20 µM, respectively. The effect of Thα1 on eliminating superoxide radicals was higher (62.23%) than other antioxidant assays. Moreover, the antioxidant activity of Thα1 peptide was evaluated by measuring cellular reactive oxygen species (ROS). Results indicated that Thα1 decreased the generation of ROS level in 1321 N1 human neural asterocytoma cells. The inhibitory effect of Thα1 on angiotensin-converting enzyme (ACE) was determined. The kinetic parameters (K_m and V_max) and the inhibition pattern were examined. Based on the Lineweaver-Burk plot, Thα1 displayed a mixed inhibition pattern. The IC₅₀ and K_i values of Thα1 were 0.8 µM and 3.33 µM, respectively. Molecular modeling suggested that Thα1 binds to ACE-domains with higher affinity binding to N-domain with the binding energy of −22.87 kcal/mol. Molecular docking indicated that Thα1 interacted with ACE enzyme (N- and C-domains) due to electrostatic, hydrophobic, and hydrogen forces. Our findings suggested that Thα1 possess a multifunctional peptide with dual antioxidant and ACE-inhibitory properties. Further researches are needed to investigate the antioxidant and anti-hypertensive effect of Thα1 both in vitro and in vivo.     

Altered clearance of human α2-macroglobulin complexes following reaction with cis-dichlorodiamineplatinum(II)

Clearance studies were performed in mice using α₂-macroglobulin (α₂M), α₂M-trypsin comlex and α₂M-CH₃NH₂ complex. All three species were incubated with cis-dichlorodiamine platinum(II) (cis-DDPt) at concentrations between 9.0 μM and 1.67 mM for 4 h and then dialyzed. The clearance rate of native α₂M was unchanged following incubation with cis-DDPt. α₂M-trypsin and α₂M-CH₃NH₂ cleared rapidly from the ciruculation; however, reaction with cis-DDPt significantly decreased the plasma elimination rate of both complexes. Non-denaturing gel electrophoresis and α₂M activity assays demonstrated relative stability following incubations with cis-DDPt which markedly altered clearance. Evidence for cis-DDPt crosslinking of α₂M subunits was obtained: however, whether this crosslinking is involved in altered clearance remains undetermined. Iodoacetamide treatment of α₂M did not duplicate the effect of cis-DDPton α₂M clearance, nor did it inhibit the effect of cis-DDPt on α₂M clearance. Plasma elimination of α₂M complex was also unaltered by pretreatment of mice with intravenous free cis-DDPt.     

α2-Macroglobulin-protease reactions: Relationship of covalent bond formation,methylamine reactivity,and specific proteolysis

Experiments were performed to define the relation between covalent binding of enzymes to β₂-macroglobulin (α₂M), the specific proteolysis of α₂M subunits to 85K fragments, and the reactivity of the methylamine site on α₂M. We studied the reaction of α₂M with native trypsin, anhydrotrypsin, and two active lysyl-blocked derivatives, methyl-trypsin and dimethylmaleyl-trypsin, the last with reversibly modified amino groups that can be regenerated at low pH. The results were: (1) All enzymes tested reacted with α₂M but only native trypsin formed covalent complexes (not dissociable by sodium dodecyl sulfate). Trypsin and the lysyl-blocked enzymes caused complete proteolysis of the α₂M subunits, in agreement with previous studies. (2) The dimethyl-maleyl-trypsin became covalently bound to α₂M only after removing the blocking groups of the bound enzyme, indicating that sequential proteolysis and covalent bond formation is possible. Under the conditions used for deblocking, there was no change in the covalent/noncovalent binding ratio of native trypsin, anhydrotrypsin, or the other lysyl-blocked derivative, methyl-trypsin. (3) Native trypsin or anhydrotrypsin displaced methyl- or dimethylmaleyl-trypsin from their α₂M complexes but the newly bound enzymes with free amino groups did not form covalent bonds indicating that enzymes must remain in association with the inhibitor for the bond to form. (4) Methylamine reacts with noncovalent α₂M complexes but not with covalent complexes. (5) Methylamine-treated α₂M can still form complexes with trypsin but at a drastically reduced rate and only noncovalent complexes are formed. In summary, sequential proteolysis and covalent bond formation is possible under certain conditions, and there is a strong correlation between covalent binding and loss of methylamine reactivity. The latter observation is suggestive evidence for the identity of the covalent binding site of α₂M and the putative thiol ester of the methylamine site. The enzyme lysyl amino groups, are likewise possible candidates for attacking nucleophile at that site.     

Anterior pituitary influence on adipokine expression and secretion by porcine adipocytes

Nutritional stressors may cause negative effects on animal health and growth and lead to significant economic impact. Adipose tissue is an endocrine organ producing, mediators and hormones, called adipokines. They play a dynamic role in body homeostasis and in the regulation of energy expenditure, interacting with feeding behavior, hormones and growth factors. This in vitro study aimed to investigate how nutritional conditions and growth hormone (GH) can influence nitric oxide (NO) production and the expression and secretion of three important adipokines, that is leptin, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), by swine adipocytes. In our experimental model, mesenchymal stem cells from omental adipose tissue were induced to adipogenic differentiation. After differentiation, adipocytes were incubated for 24 h (T0) with DMEM/Ham’s F12 (group A) or DMEM/Ham’s F12 salts (group B), a DMEM/Ham’s F12 formulation deprived of nutritional components. Primary adipocyte cells were also co-cultured for 4 h (T+4) or 12 h (T+12) with or without anterior pituitary slices. To stimulate GH secretion by pituitary cells, growth hormone releasing hormone at 10⁻⁸ M was added at the start of the incubation times (4 or 12 h). At T0, T+4 and T+12, NO production, leptin, IL-6 and TNF-α expression and secretion were measured. NO increased (P<0.05) up to twofold in restricted culture conditions. Deprived medium and coincubation with anterior pituitary positively influenced leptin secretion and expression. TNF-α was expressed and secreted only in deprived culture condition groups (B, B1 and B2). Nutrients availability and pituitary co-culture did not affect IL-6 expression and secretion. Our study shows an endocrine function for porcine adipocytes. In our model, adipocytes readily responded to nutritional inputs by secretion of molecules affecting energy balance. This secretion capacity was modulated by GH. Improving our knowledge of the role of adipocyte in the endocrine system, may lead to a more complete understanding of regulating energy balance in swine.     

Conformational heterogeneity of α-synuclein in membrane

α-Synuclein (αS) is a natively disordered protein in solution, thought to be involved in the fusion of neurotransmitter vesicles to cellular membranes during neurotransmission. Monomeric αS has been previously characterized in two distinct membrane-associated conformations: a broken-helix structure, and an extended helix. By employing atomistic molecular dynamics and a novel membrane representation with significantly enhanced lipid mobility (HMMM), we investigate the process of spontaneous membrane binding of αS and the conformational dynamics of monomeric αS in its membrane-bound form.     

The mycocidal, membrane-active complex of Cryptococcus humicola is a new type of cellobiose lipid with detergent features

The chemical composition of the mycocidal complex (formerly known as microcin) secreted by Cryptococcus humicola was investigated by chemical, mass spectrometric and nuclear magnetic resonance methods. The results indicate that the mycocidal complex is composed of glycolipids with a highly acetylated (up to five acetyl groups) cellobiose backbone [β-D-Glcp-(1′→4)-β-D-Glcp] linked to the ω-hydroxyl group of α,ω-dihydroxy palmitate [16:0-α,ω-di-OH] with an unsubstituted carboxyl group. The acyl chain forming aglycon can be replaced by [18:0-(α,ω-di-OH)], [18:0-(α,ω-1,ω-tri-OH)], and [18:0-(α,ω-2,ω-tri-OH)]. The complex has a comparatively high surface activity; 0.5 mg/ml of it reduced the surface tension of 0.1 M NaHCO₃ from 71 mN/m to 37 mN/m and interfacial tension against n-hexadecane from 39 mN/m to 10 mN/m. The critical micelle concentration of the complex at pH 4.0, determined by the fluorometric method with N-phenyl-1-naphthylamine as fluorescent probe and by the De Nouy ring method, was 2×10⁻⁵ M (taking the average molecular mass of the complex to be 750); it did not depend on the presence of 100 mM KCl and was an order of magnitude higher at pH 7.0. By fluorescence resonance energy transfer spectroscopy with N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-phosphatidylethanolamine as energy donor and N-(rhodamine B sulfonyl)-phosphatidylethanolamine as energy acceptor the complex was shown to intercalate into the liposomal lipid matrix. Primary lesions caused by the complex in planar lipid bilayers were revealed as short-living current fluctuations of a broad spectrum of amplitudes. The mycocidal effect of the complex is suggested to be associated with its detergent-like properties.     

Co-clustering and internalization of low-density lipoproteins and alpha 2-macroglobulin in human skin fibroblasts

The endocytosis of low density lipoprotein (LDL) and α₂-macroglobulin (α₂M) has been examined simultaneously in human skin fibroblasts. Incubation of cells at 4 °C with rhodamine-α₂M and LDL plus [(dichlorotriazinyl)amino]fluorescein-anti-LDL gave a weak fluorescence for α₂M and a brighter, clustered fluorescence for LDL. Following warming to 37 °C, LDL and α₂M were observed to be coincident within endocytotic vesicles in the cell. By electron microscopy, LDL-ferritin and α₂M-colloidal gold were present in the same coated pit at 4 °C. After 7 min at 37 °C, both ligands were observed in the same receptosome. Pretreatment of fibroblasts at 37 °C with 200–300 μM dansylcadaverine or 50 mM methylamine blocked clustering and internalization of both LDL and α₂M. Bacitracin (5 mg ml^?) blocked clustering and endocytosis of α₂M, but not of LDL. These data indicate that both LDL and α₂M are processed via the same endocytotic pathway in skin fibroblasts.     

Conformation-specific precipitation of human α2-macroglobulin by divalent zinc or calf thymus histone H3

Highly purified native α₂-macroglobulin (α₂M), α₂M-trypsin, and α₂M-methylamine were compared in experiments designed to study protein precipitation. Significant turbidity developed within 30 min in solutions containing histone H3 and either α₂M-methylamine or α₂M-trypsin, as determined by absorbance at λ = 550 nm. No turbidity was detected in solutions that contained histone H3 and native α₂M or histone H3 alone. Experiments with radioiodinated histone H3 or radioiodinated proteinase inhibitor confirmed that both the H3 and the α₂M “fast” forms (α₂M-methylamine, α₂M-trypsin) were present in the precipitates generated. As much as 70% of the ¹²⁵I-α₂M-methylamine was recovered in the precipitate after incubation with a 120-fold molar excess of H3 (concentration of α₂M-methylamine, 0.28 μm). The ratio of histone to proteinase inhibitor by weight in the precipitate was approximately two. Under comparable conditions, somewhat less α₂M-trypsin precipitated from solutions containing H3 than did α₂M-methylamine; however, inactivation of the α₂M-trypsin with phenylmethylsulfonyl fluoride prior to incubation increased the level of precipitation significantly. Solutions containing poly-l-lysine (M_r ~ 13,000) instead of histone did not form precipitates with any of the forms of α₂M studied. In a second set of experiments, radioiodinated native α₂M, α₂M-trypsin, and α₂M-methylamine were incubated in solutions containing ZnCl₂, BaCl₂, CdCl₂, CuSO₄, MgCl₂, or NiCl₂ (concentration of divalent cation between 5 μm and 1.0 mm). Native α₂M was soluble in all of these salts. By contrast, α₂M-methylamine and α₂M-trypsin precipitated extensively from solutions containing greater than 100 μm ZnCl₂. Precipitation was greater than 90% complete at 1 mm ZnCl₂. A similar effect was not observed with any of the other divalent cations.     

Urea Facilitates the Translocation of Single-Stranded DNA and RNA Through the α-Hemolysin Nanopore

The staphylococcal α-hemolysin (αHL) protein nanopore is under investigation as a fast, cheap detector for nucleic acid analysis and sequencing. Although discrimination of all four bases of DNA by the αHL pore has been demonstrated, analysis of single-stranded DNAs and RNAs containing secondary structure mediated by basepairing is prevented because these nucleic acids cannot be translocated through the pore. Here, we show that a structured 95-nucleotide single-stranded DNA and its RNA equivalent are translocated through the αHL pore in the presence of 4 M urea, a concentration that denatures the secondary structure of the polynucleotides. The αHL pore is functional even in 7 M urea, and therefore it is easily stable enough for analyses of challenging DNA and RNA species.     

A simple model for a regulatory enzyme

A simple model for a regulatory enzyme is described which leads to relationships between the initial velocity of the catalysed reaction and the varied concentration of a substrate that are of the non-inflected or sigmoidal varieties without a maximum. The model assumes that the most relevant measure of protein configuration (itself determining the kinetic behaviour of the enzyme) is the apparent association constant, α_i, measured for the given fractional saturation of the ligand under investigation. It is further assumed that the original state of the protein in solution, α₀, is destabilized by an increment of energy, ΔG_p⁰, that is proportional to the fractional saturation of the enzyme by ligand so that the formation of a new configurational state, a,, can be represented by ?ΔG_p⁰ = RT ln $\text{α}{}_1\text{α}{}_0$. The rate or fractional saturation equation that can be derived from this model predicts both positive and negative cooperativity. Either equation can be transformed for linear representation, provided the maximum velocity or its equivalent maximum saturation is known, and estimates of α₀ and α_i (the apparent association constants at zero and complete saturation) can be obtained thereby. A procedure is also described by which an initial estimate of the maximum velocity or saturation can be improved. The model is tested by application to a range of data in the literature and it is shown to give fits to the data comparable in quality to those provided by the model of Monod, Wyman &; Changeux (1965).     

Synthesis of 1H-1,2,3-triazole derivatives as new α-glucosidase inhibitors and their molecular docking studies

Inhibition of α-glucosidase is an effective strategy for controlling the post-prandial hyperglycemia in diabetic patients. For the identification of new inhibitors of this enzyme, a series of new (R)-1-(2-(4-bromo-2-methoxyphenoxy) propyl)-4-(4-(trifluoromethyl) phenyl)-1H-1,2,3-triazole derivatives were synthesized (8a–d and 10a–e). The structures were confirmed by NMR, mass spectrometry and, in case of compound 8a, by single crystal X-ray crystallography. The α-glucosidase inhibitory activities were investigated in vitro. Most derivatives exhibited significant inhibitory activity against α-glucosidase enzyme. Their structure-activity relationship and molecular docking studies were performed to elucidate the active pharmacophore against this enzyme. Compound 10b was the most active analogue with IC₅₀ value of 14.2 µM, while compound 6 was found to be the least active having 218.1 µM. A preliminary structure-activity relationship suggested that the presence of 1H-1,2,3-triazole ring in 1H-1,2,3-triazole derivatives is responsible for this activity and can be used as anti-diabetic drugs. The molecular docking studies of all active compounds were performed, in order to understand the mode of binding interaction and the energy of this class of compounds.     

Interaction of clonidine and clonidine analogs with human platelet α2-adrenergic receptors

Several new clonidine analogs were synthesized and their ability to inhibit [³H] phentolamine binding to human platelet α₂-adrenergic receptors was tested. The order of potency and calculated dissociation constants for clonidine and its analogs were as follows: clonidine (0.020 ± 0.005 μM) >p-aminoclonidine (0.100 ± 0.010 μM) > hydroxy-phenacetyl-aminoclonidine (0.20 ± 0.03 μM) >p-dansyl clonidine (1.00 ± 0.20 μM) >t-boc-tyrosine clonidine (1.80 ± 0.60 μM). Thus, p-amino substitution reduces α₂-adrenergic affinity in the platelet system. The effects of clonidine and its p-amino analogs on platelet adenylate cyclase were also evaluated. This enzyme is inhibited by epinephrine acting via α₂-adrenergic receptors. Both clonidine and p-aminoclonidine cause slight inhibition of basal adenylate cyclase and reverse the inhibition induced by epinephrine. These observations indicate that clonidine is a partial agonist for platelet α₂-adrenergic receptors.     

Linking the Acetylcholine Receptor-Channel Agonist-Binding Sites with the Gate

The gating isomerization of neuromuscular acetylcholine receptors links the rearrangements of atoms at two transmitter-binding sites with those at a distant gate region in the pore. To explore the mechanism of this reversible process, we estimated the gating rate and equilibrium constants for receptors with point mutations of α-subunit residues located between the binding sites and the membrane domain (N95, A96, Y127, and I49). The maximum energy change caused by a side-chain substitution at αA96 was huge (∼8.6 kcal/mol, the largest value measured so far for any α-subunit amino acid). A Φ-value analysis suggests that αA96 experiences its change in energy (structure) approximately synchronously with residues αY127 and αI49, but after the agonist molecule and other residues in loop A. Double mutant-cycle experiments show that the energy changes at αA96 are strongly coupled with those of αY127 and αI49. We identify a column of mutation-sensitive residues in the α-subunit that may be a pathway for energy transfer through the extracellular domain in the gating isomerization.     

A simple one-step purification of human α1-proteinase inhibitor by immunoadsorbent column chromatography

A one-step purification of human α₁-proteinase inhibitor was described using the rabbit anti-α₁-proteinase inhibitor antibody coupled to CNBr-activated Sepharose 4B. The elution of α₁-proteinase inhibitor from the immunoadsorbent column using 0.1 M Na₂CO₃/0.5 M NaCl solution gave an 85% yield. The properties of eluted α₁-proteinase inhibitor were identical with that of α₁-proteinase inhibitor that was purified by the conventional method. In addition, the specific activity of purified α₁-proteinase inhibitor was more than 93% of that of the theoretical value.