Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes

The von Smoluchowski-Debye formulae for diffusion controlled reaction rates are extended to the more general case of spheroidal geometry. Their application to the association of represser and operator is thoroughly discussed in the light of recent experiments on the lac system by Riggs et al. The conclusions suggest that the surprisingly high association rate is not essentially due to electrostatic attraction but rather to unspecific binding of represser to nonoperator DNA with subsequent diffusion along the chain.     

Association kinetics with coupled diffusion: III. Ionic-strength dependence of the lac repressor-operator association

The repressor- operator association is treated in a model where the represser molecule can find its specific binding site the operator, on a large DNA chain by performing a one-dimensional diffusion along the chain. The ionic-strength depen deuce is calculated by introducing a screened electrostatic potential around the DNA chain and coupling the free diffusion of the represser in this potential to the proposed one-dimensional diffusion along the chain. The main influence on the association rate comes from the competitive binding of ions to the unspecific DNA sites. It is also demonstrated that during the time that the represser is bound in a global sense, the diffusion along the chain will be made up of a strictly one-dimensional motion over fairly short distances, interspersed with many local dissociations during which the repressor in essence is free in solution.     

Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the lac repressor-operator system.

The association of a molecule onto a specified binding site on a large chain-like macromolecule is described in the "sliding" model, where the molecule is allowed to move along the chain in a one-dimensional diffusion which is coupled to the three-dimensional diffusion in solution. The present work extends a previous one by treating the chains more generally as coiled instead of straight. The model is applied to the lac repressor-operator association. A general expression for the rate of unspecific attachment to a chain-like macromolecule is also derived.     

Direct detection of glycogenin reaction products during glycogen initiation

Glycogenin initiates glycogen synthesis in an autocatalytic reaction in which individual glucose residues are covalently linked to Tyrosine 194 in order to form a short priming chain of glucose residues that is a substrate for glycogen synthase which, combined with the branching enzyme, catalyzes the bulk synthesis of glycogen. We sought to develop a new enzymatic assay to better characterize both the chemical and enzymatic characteristics of this unusual reaction. By directly detecting the reaction products using electrospray mass spectrometry this procedure permits both the visualization of the intact individual reaction species produced as a function of time and quantitation of the levels of each of species. The quantitation of the reaction agrees well with previous measurements of both catalytic rate and the change in rate as a function of average glucosylation. The results from this assay provide new insight into the mechanism by which glycogenin catalyzes the initiation reaction.     

Interaction between the constituent A and B lens alpha-crystallin subunits leading to formation of alpha-neoprotein molecules

A and B constituent subunits associated in lens alpha-crystallin were found to interact with added B chains forming alpha-neoprotein molecules with lower A to B chain ratios than 2 A to 1 B in alpha-crystallin. Addition of 1% excess of B chains to the one in alpha-crystallin, which resulted in a ratio of 1.98 A to 1 B in the mixture, caused a change of quaternary structure in 30% of alpha-crystallin molecules within 18 h. At a ratio of 1.86 A to 1 B, all alpha-crystallin molecules were affected at this time. A maximum number of 495 B chains was found to form an association with 1 A chain, initially bound in alpha-crystallin. Such a high number may indicate that the reaction involves monomeric A chains binding aggregated macromolecules of B chains. It is in such form that B chains occur as macromolecules with an average molecular weight of 0.7 X 10(6) in aqueous solution. The alpha-neoprotein molecules selected for studies in this report had A to B chain ratios of 1.75:1, 1:1, and 0.2:1. Each behaved in immunodiffusion tests like single molecular entities. Antigenic determinants located on A as well as on B chains associated with each other in alpha-crystallin were found to be identical with determinants on the chains associated in the above alpha-neoprotein molecules. Determinants dependent on the quaternary structure of alpha-neoprotein and of alpha-crystallin molecules were completely different. Some of the quaternary determinants of various alpha-neoproteins were type specific and did not occur in molecules with different A to B chain ratios. Other quaternary determinants occurred in all alpha-neoproteins. An excess of A chains did not revert alpha-neoproteins to alpha-crystallin. However, alpha-neoprotein molecules did interact with added B chains forming neomolecules with lower A to B chain ratios.     

Generation of a chromosome-22-specific c-DNA library as confirmed by FISH analysis

We have recently developed a strategy for the rapid enrichment of c-DNA fragments from selected human chromosomes. Heteronuclear RNA (hn-RNA) is isolated from a somatic cell hybrid that retains a single human chromosome in a rodent background. Following c-DNA synthesis, human sequences are selectively amplified by the Alu polymerase chain reaction (Alu-PCR). Here we have applied this protocol for the selective isolation of novel c-DNAs encoded by chromosome 22. Fluorescence in situ hybridization has been used to confirm the chromosome-22-specific origin of the c-DNA fragments. Controls show DNAse-free RNase-treated hn-RNA results in no c-DNAs or Alu-PCR products. As demonstrated by competitive in situ suppression hybridization (CISS), the majority of the Alu-PCR products from hybrid GM 10027 are located on chromosome 22. Without competition, hybridization signals have also been identified on other human chromosomes. These unspecific hybridization signals result from Alu sequences and can successfully be reduced by competition with cot 1 DNA. This is the first report of the use of CISS for the localization of chromosome-specific c-DNAs.     

NUCLEOSIDE PHOSPHATASE AND CHOLINESTERASE ACTIVITIES IN DORSAL ROOT GANGLIA AND PERIPHERAL NERVE

In dorsal root ganglia and peripheral nerve of the rat and other species, nucleoside phosphatase and unspecific cholinesterase reaction products are found in the plasma membranes and spaces between them at two sites: (1) Schwann cell-axon interfaces and mesaxons of unmyelinated fibers, and (2) sheath cell-perikaryon interfaces and interfaces between adjacent sheath cells. Acetylcholinesterase reaction product is found in the perikaryon (within the endoplasmic reticulum) and the axon (axoplasmic surface). Nucleoside phosphatase reaction product is also found in the numerous vacuoles at the surface of perineurium cells, ganglion sheath cells, and cells surrounding some ganglion blood vessels. Nucleoside phosphatase activities in the sections fail to respond, in the manner described for "transport ATPase," to diisopropylphosphofluoridate, sodium and potassium ions, and ouabain. Nucleoside diphosphates are hydrolyzed more slowly than triphosphates in unmyelinated fibers, and are not hydrolyzed at the perikaryon surface. Nucleoside monophosphates are either not hydrolyzed or hydrolyzed very slowly. In contrast to these localizations, which are believed to demonstrate sites of enzyme activity, it is considered likely that diffusion artifacts account for the nucleoside phosphatase reaction product frequently found along the outer surfaces of myelinated fibers and within vacuoles at the Schwann cell surfaces of these fibers. The diffuse reaction product seen in basement membranes of ganglion and nerve may also be artifact.     

The oxidation of cat,human, and the cat-human hybrid hemoglobins α2Humanβ2Cat and α2Catβ2Human by copper(II)

The heme iron of the β chains of mammalian hemoglobins are rapidly and selectively oxidized in the presence of excess Cu(II) ions in a reaction that requires the presence of a free -SH groups on the β globin chain. The presence of freely reactive -SH groups on the α chains of cat and sheep hemoglobins does not alter the course of this reaction: only the β hemes are oxidized rapidly by Cu(II) in these hemoglobins. Two equivalents of copper are required for the rapid oxidation of the two β chain hemes per mole of cat hemoglobin, in contrast with the four equivalents that are required for reaction with human hemoglobin. The human-cat hybrid hemoglobins, α₂^Humanβ₂^Cat and α₂^Catβ₂^Human, required two and four equivalents of copper/mol, respectively, for the reaction. Thus, the kinetics and stoichimetry of the reaction are determined by the nature of the β subunit. Analysis of the esr spectra of the products of the reaction of Cu(II) with these hemoglobins indicate that human hemoglobin and the hybrid α₂^Catβ₂^Human contain tight binding sites for two equivalents of Cu(II) that are not involved in the oxidation reaction and are not present in cat hemoglobin or α₂^Humanβ₂^Cat. Cat β globin like others (sheep, bovine) that lack the tight binding site, has no histidine residue at 2β. It has phenylalanine in this position. These results support the suggestion of Rifkind et al. (Biochemistry 15,5337[1976]) that the tight binding site is near the amino terminal region of the β chain and is associated with histidine 2β.     

Modeling the interaction of peroxynitrite with low-density lipoproteins. II: reaction/diffusion model of peroxynitrite in low-density lipoprotein particles

Peroxynitrite is a possible initiator for the free radical chain reaction that results in peroxidation of low-density lipoproteins (LDL) which is the first step in atherogenisis. This paper reports on the use of a diffusion/reaction model to examine the processes involved in peroxynitrite attack on LDL particles. Results indicate that because of the short distance involved, diffusion is much more rapid than chemical decomposition. Because of this decoupling the free radicals generated by peroxynitrite decomposition may be found at any point in the LDL particle. At the concentrations expected in physiological systems only a small proportion of LDL particles may contain peroxynitrite molecules. However, these particles may still be profoundly effected because of the long reaction chain length expected after initiation.     

Fatty acids diffusion in lecithin multilayers: hydration and PH effects.

The diffusion of the sodium salt of monocarboxylic fatty acids, from formate to stearate, has been studied as a function of water content and pH in lecithin--water lamellar phases. Evolution of the diffusion coefficients with increasing chain length reflects the different localizations of fatty acids in the system. From formate to butyrate, which are mainly restricted to the hydrophilic layer of the phase, diffusion rates decrease rapidly. From butyrate to stearate, fatty acids (anchored at the hydrophilic--lipophilic interface) undergo lateral diffusion and then the decrease of D with increasing chain length is much slower. The diffusion of stereate is already comparable to the diffusion of the lecithin molecule itself. The diffusion rates strongly depend upon phase hydration and pH: it is shown that both parameters control the fatty acid ionization. The variations in diffusion rates observed may be ascribed to the fact that, depending upon their state of ionization, fatty acids assume a different localization and therefore experience different interactions in the lamellar system.     

Kinetics of the reaction between hydrogen selenide ion and oxygen

Hydrogen selenide ion (HSe^?) reacts with oxygen in the following manner: HSe^? + 1/2O₂ → Se^o + OH^?. Interest in the kinetics of this reaction comes from the fact that selenide is an important product in the metabolism of the essential trace element selenium. Using polarography to monitor both selenide and oxygen, we have found the reaction exhibits complex kinetics, including autoaccelerating behavior and the generation of reactive intermediates capable of inducing reactions in other substances present. Probable intermediate species include superoxide, peroxide and polyselenides. The reaction is slow with respect to diffusion controlled reactions, but fast with respect to the time required to prepare solutions for biological study. Selenide concentrations greater than 10^?6 M decay to give solutions of predominantly colloidal elemental selenium less than 3 minutes after exposure to atmospheric levels of oxygen.     

In yeast, Ca2+ and octylguanidine interact with porin (VDAC) preventing the mitochondrial permeability transition

In yeast, Ca(2+) and long chain alkylguanidines interact with mitochondria modulating the opening of the yeast mitochondrial unspecific channel. Mammalians possess a similar structure, the mitochondrial permeability transition pore. The composition of these pores is under debate. Among other components, the voltage-dependent anion channel has been proposed as a component of either pore. In yeast from an industrial strain, octylguanidine and calcium closed the yeast mitochondrial unspecific channel. Here, the effects of the cations Ca(2+) or octylguanidine and the voltage-dependent anion channel effector decavanadate were evaluated in yeast mitochondria from either a wild type or a voltage-dependent anion channel deletion laboratory strain. It was observed that in the absence of voltage-dependent anion channel, the yeast mitochondrial unspecific channel was desensitized to Ca(2+), octylguanidine or decavanadate but remained sensitive to phosphate. It is thus suggested that in yeast mitochondria, the voltage-dependent anion channel has a cation binding site where Ca(2+) and octylguanidine interact, conferring cation sensitivity to the yeast mitochondrial unspecific channel.     

Experimentally Approaching the Solvent-Accessible Surface Area of a Protein: Insights into the Acid Molten Globule of Bovine α-Lactalbumin

Each conformational state of a protein is inextricably related to a defined extent of solvent exposure that plays a key role in protein folding and protein interactions. However, accurate measurement of the solvent-accessible surface area (ASA) is difficult for any state other than the native (N) state. We address this fundamental physicochemical parameter through a new experimental approach based on the reaction of the photochemical reagent diazirine (DZN) with the polypeptide chain. By virtue of its size, DZN is a reasonable molecular mimic of aqueous solvent. Here, we structurally characterize nonnative states of the paradigmatic protein α-lactalbumin. Covalent tagging resulting from unspecific methylene (:CH₂) reaction allows one to obtain a global estimate of ASA and to map out solvent accessibility along the amino acid sequence. By its mild apolar nature, DZN also reveals a hydrophobic phase in the acid-stabilized state of α-lactalbumin, in which there is clustering of core residues accessible to the solvent. In a fashion reminiscent of the N state, this acid-stabilized state also exhibits local regions where increased :CH₂ labeling indicates its nonhomogenous nature, likely pointing to the existence of packing defects. By contrast, the virtual absence of a defined long-range organization brings about a featureless labeling pattern for the unfolded state. Overall, :CH₂ labeling emerges as a fruitful technique that is able to quantify the ASA of the polypeptide chain, thus probing conformational features such as the outer exposed surface and inner cavities, as well as revealing the existence of noncompact apolar phases in nonnative states.     

Study of thermodynamic properties of imidazolium-based ionic liquids and investigation of the alkyl chain length effect by molecular dynamics simulation

In this paper, structural and dynamical properties of five imidazolium-based ionic liquids (ILs) [amim]Br (a = methyl, ethyl, butyl, pentyl, hexyl) were studied by molecular dynamics simulations. United atom force field (UAFF) has been used for the representation of the interaction between ions. Good agreement with experimental data was obtained for the simulated density based on the UAFF. The calculated densities gradually decrease with an increase in the length of alkyl side chain, which is a result of weakening the electrostatic interaction between ions. The simulated heats of vaporisation are higher than that of non-ILs and decrease with an increase in temperature. Radial distribution function (RDF) was employed to analyse the local structure of ILs. Cation–anion RDFs show that the anions are well organised around the cation in two shells (0.41 and 0.6 nm). The velocity autocorrelation functions of the anion and cations show that the relaxation time increased with an increase in the length of the alkyl side chain. The diffusion coefficients of ions were calculated by mean square displacement of the centre of mass of the ions at 400 K. The calculated diffusion coefficients using UAFF agree well with other all atom force fields. Also diffusion coefficients decrease with an increase in the length of the alkyl side chain. The calculated transference numbers show that the cation contributes more than anion in the electrical current. The diffusion coefficients increase with temperature.     

Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: site-based and molecule-based association reactions

Domain effects on the pseudo-first-order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction-diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse-sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site-based and molecule-based elements to the rate constants.     

In yeast, Ca and octylguanidine interact with porin (VDAC) preventing the mitochondrial permeability transition

In yeast, Ca²⁺ and long chain alkylguanidines interact with mitochondria modulating the opening of the yeast mitochondrial unspecific channel. Mammalians possess a similar structure, the mitochondrial permeability transition pore. The composition of these pores is under debate. Among other components, the voltage-dependent anion channel has been proposed as a component of either pore. In yeast from an industrial strain, octylguanidine and calcium closed the yeast mitochondrial unspecific channel. Here, the effects of the cations Ca²⁺ or octylguanidine and the voltage-dependent anion channel effector decavanadate were evaluated in yeast mitochondria from either a wild type or a voltage-dependent anion channel deletion laboratory strain. It was observed that in the absence of voltage-dependent anion channel, the yeast mitochondrial unspecific channel was desensitized to Ca²⁺, octylguanidine or decavanadate but remained sensitive to phosphate. It is thus suggested that in yeast mitochondria, the voltage-dependent anion channel has a cation binding site where Ca²⁺ and octylguanidine interact, conferring cation sensitivity to the yeast mitochondrial unspecific channel.     

Multiple sites of inhibition of mitochondrial electron transport by chloramphenicol in Neurospora crassa

Abstract The effects in vitro of chloramphenicol on the mitochondrial electron transport of Neurospora crassa were investigated under phosphorylating, non-phosphorylating and uncoupled conditions. The antibiotic acted at more than one site of the respiratory chain: exogenous NADH dehydrogenase, Complex I, the rotenone-resistant by-pass and the alternative oxidase, although an unspecific effect could not be totally excluded.     

Adenovirus type 5 intrinsic adsorption rates measured by surface plasmon resonance

Intrinsic adsorption rates of whole adenovirus type 5 (Ad5) onto a diethylaminoethyl (DEAE) anion exchange surface are measured for the first time by surface plasmon resonance (SPR). Fitting SPR sensorgrams to a two-compartment mass transport reaction model distinguishes intrinsic adsorption rates from slow diffusive Ad5 mass transport. Ad5 is a widely used viral vector for gene therapy that binds electrostatically to surfaces of cells and synthetics such as membranes, chromatographic resins, and glass. Increasing NaCl concentration from 4.8 to 14.4mM shifts binding of whole Ad5 from diffusion control to a regime where both sorption and diffusion affect binding. Intrinsic adsorption rates for Ad5-DEAE interaction are 16 times faster than intrinsic adsorption rates for Ad5 fiber knob interacting with soluble extracellular domain of coxsackievirus adenovirus receptors (s-CAR).     

Characterization of advanced glycation end products: mass changes in correlation to side chain modifications

Advanced glycation end products (AGEs) that arise from the reaction of sugars with protein side chains are supposed to be involved in the pathogenesis of several diseases; therefore, the effects of AGEs on cells are the objective of numerous investigations. Because AGE modifications are an extremely heterogeneous group of side chain modifications, the exact characterization of an AGE-modified protein is impossible. To gain a deeper understanding about AGE formation kinetics and structures, AGEs can be characterized with respect to the degree of modification, specific side chain modifications, absorbance and fluorescence characteristics, and changes in the protein structure and molecular weight. For this study, human serum albumin (HSA)-AGEs derived from different concentrations of glucose, methyl glyoxal, and glyoxylic acid were used. The molecular mass of the obtained AGEs was determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The mass data were compared with earlier results concerning the degree of lysine and arginine side chain modifications and AGE-specific fluorescence and absorbance data. The molecular masses were found to gradually increase with increasing concentrations of the individual modifier without reaching a plateau. The mass increase correlates very well with the AGE-specific absorbance at 360 nm and with the degree of side chain modifications. The mass spectrometric data prove, for the first time, that an increasing absorbance at 360 nm is directly correlated to a mass increase during the AGE formation process.     

Detection of glycation sites in proteins by high-resolution mass spectrometry combined with isotopic labeling

The products of nonenzymatic glycation of proteins are formed in a chemical reaction between reducing sugars and the free amino group located either at the N terminus of the polypeptide chain or in the lysine side chain. Glycated proteins and their fragments could be used as markers of the aging process as well as diabetes mellitus and Alzheimer’s disease, making them an object of interest in clinical chemistry. In this article, we propose a new method for the identification of peptide-derived Amadori products in the mixtures obtained by enzymatic hydrolysis of glycated proteins. Two proteins, ubiquitin and human serum albumin (HSA), were modified with an equimolar mixture of glucose and [¹³C₆]glucose and were subjected to enzymatic hydrolysis. The obtained enzymatic digests were analyzed by high-resolution mass spectrometry (HRMS), and the peptide-derived Amadori products were identified on the basis of specific isotopic patterns resulting from ¹³C substitution. The number of glycated peptides in the digest of HSA detected by our procedure was in agreement with the data recently reported in the literature.