Thermodynamic regulation of human short-chain acyl-CoA dehydrogenase by substrate and product binding

Human short-chain acyl-CoA dehydrogenase (hSCAD) catalyzes the first matrix step in the mitochondrial beta-oxidation cycle for substrates with four and six carbons. Previous studies have shown that the act of substrate/product binding induces a large enzyme potential shift in acyl-CoA dehydrogenases. The objective of this work was to examine the thermodynamic regulation of this process through direct characterization of the electrochemical properties of hSCAD using spectroelectrochemical methodology. A large amount of substrate activation was observed in the enzymatic reaction of hSCAD (+33 mV), the greatest magnitude measured in any acyl-CoA dehydrogenase to date. To examine the role of the substrate as well as the product in electron transfer by hSCAD, a catalytic base mutation (E368Q) was constructed. The E368Q mutation inactivates the reductive and oxidative pathways such that the individual effects of substrate and product binding on the redox potential can be investigated. Optimal substrate (butyryl-CoA) was seen to shift the flavin redox potential slightly more positive (+38 mV) than did optimal product (crotonyl-CoA) (+31 mV), a finding opposite of that observed in another short-chain enzyme, bacterial SCAD. These results indicate that substrate redox activation occurs in hSCAD leading to a large enzyme midpoint potential shift. Substrate binding in hSCAD appears to make a larger contribution than does product to thermodynamic modulation.     

Recent advances in polyaniline based biosensors

The present paper contains a detailed overview of recent advances relating to polyaniline (PANI) as a transducer material for biosensor applications. This conducting polymer provides enormous opportunities for binding biomolecules, tuning their bio-catalytic properties, rapid electron transfer and direct communication to produce a range of analytical signals and new analytical applications. Merging the specific nature of different biomolecules (enzymes, nucleic acids, antibodies, etc.) and the key properties of this modern conducting matrix, possible biosensor designs and their biosensing characteristics have been discussed. Efforts have been made to discuss and explore various characteristics of PANI responsible for direct electron transfer leading towards fabrication of mediator-less biosensors.     

Biochemical properties associated with the immortalizing domain of the large T protein of polyoma virus

A fragment of polyoma virus DNA lacking the carboxy-terminal part of the large T antigen coding region is sufficient to express the functions of the entire gene in cell transformation. Two cell lines expressing this truncated DNA were studied, one of them producing a large T-related protein of the expected size (37 kDa) and the other one, a shorter product (34 kDa). Both proteins were phosphorylated and localized in the nucleus, but devoid of ATPase and nucleotide binding activities. As the complete protein, the larger product, but not the shorter variant, exhibited sequence-specific DNA binding properties. These results indicate that ATPase and nucleotide-binding activities are not required for immortalization, and suggest that recognition of specific DNA sequences may be dispensable.     

Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein.

The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue located in its C- or N-terminal domain, respectively. Methyl transfer to the N-terminal domain causes it to acquire a sequence-specific DNA binding activity, which directs binding to the regulatory region of several methylation-resistance genes. In this paper we show that the N-terminal domain of Ada contains a high-affinity binding site for a single zinc atom, whereas the C-terminal domain is free of zinc. The metal-binding domain is apparently located within the first 92 amino acids of Ada, which contains four conserved cysteine residues. We propose that these four cysteines serve as the zinc ligand residues, coordinating the metal in a tetrahedral arrangement. One of the putative ligand residues, namely, Cys69, also serves as the acceptor site for a phosphotriester-derived methyl group. This raises the possibility that methylation-dependent ligand reorganization about the metal plays a role in the conformational switching mechanism that converts Ada from a non-sequence-specific to a sequence-specific DNA-binding protein.     

DNA-ethidium reaction kinetics: demonstration of direct ligand transfer between DNA binding sites.

Study of the relaxation kinetics of the interaction of ethidium and DNA reveals a novel and potentially important general binding mechanism, namely direct transfer of the ligand between DNA binding sites without requiring dissociation to free ligand. The measurable relaxation spectrum shows three relaxation times, indicating that three bound dye species are present at equilibrium; about 80% of the dye is in the major intercalated form. For each relaxation the reciprocal relaxation time varies linearly with concentration up to very high DNA concentrations. The failure of the longer relaxation times to plateau at high concentration can be accounted for by including a bimolecular pathway for conversion from one complex form to another. This we envisage as direct transfer of an ethidium molecule, bound to one DNA molecule, to an empty binding site on another DNA molecule. Additional evidence for this direct transfer mechanism was obtained from an experiment showing that DNA (which binds ethidium relatively rapidly) accelerates the binding of ethidium to poly(rA) · poly(rU), presumably by first forming a DNA-ethidium complex and then transferring the ethidium to RNA. The bimolecular rate constant for transfer is found to be about four times larger than the constant for intercalating the free dye. The transfer pathway thus provides a highly efficient means for the ligand to equilibrate over its DNA binding sites, especially at high polymer concentration. The potential importance of direct transfer for DNA-binding regulatory proteins is emphasized.     

Solute binding curves for (two polymer + solute)-complex systems. I. "One-solute-stack" systems

The matrix method is used for calculating the grand partition function for the reaction: 2 polymer + solute = complex. The homogeneous polymers are assumed to have two types of sites within each nucleotide unit: sites for the polymer–polymer association, i.e., (p-p) sites; sites for polymer–solute association i.e., (p-s) sites. The respective binding parameters, P and F , and nearest-neighbor interaction parameters, W and S , are assumed independent. Complications due to ring entropy are avoided by rest riding the model to one-solute-stack systems, which are physically realizable when the reciprocal of the solute cooperativity parameter is much larger than the number of nucleotides in the polymer. The 4 × 4 generating matrix is shown to be a tensor product of two 2 × 2 matrices, each the generating matrix of a particular type of site. The scalar product of the 4 × 4 matrix is shown to be equivalent to the scalar product of a 2 × 2 matrix in the weak interaction limit, W ≈ 0. Calculations are presented for the general case which restricts the (p-s) association to occur only with (p-p) associated nucleotide units. The nature of the binding curve in relation to partitioning the total interaction energy (F + P + S + W ) among the parameters is discussed. Also presented is a criterion for neglecting possible states in the calculation of the grand partition function.     

Motors and Their Tethers: The Role of Secondary Binding Sites in Processive Motility

Cytoskeletal motors convert the energy from binding and hydrolyzing ATP into conformational changes that direct movement along a cytoskeletal polymer substrate. These enzymes utilize different mechanisms to generate long-range motion on the order of a micron or more that is required for functions ranging from muscle contraction to transport of growth factors along a nerve axon. Several of the individual cytoskeletal motors are processive, meaning that they have the ability to take sequential steps along their polymer substrate without dissociating from the polymer. This ability to maintain contact with the polymer allows individual motors to move cargos quickly from one cellular location to another. Many of the processive motors have now been found to utilize secondary binding sites that aid in motor processivity.     

Calorimetric investigation of the protein-flexible chain polymer interactions and its relationship with protein partition in aqueous two-phase systems

The binding of polyethyleneglycol of molecular mass 1000, 3300 and 6000 and polyethylene-propylene oxide (molecular mass 8400) to lysozyme and ovoalbumin was measured by isothermal calorimetric titration. A binding process was found to be associated with a saturation effect, which suggests a protein-polymer interaction. The proteins showed an affinity for the polymers in the order of 10(2)M(-1) and it decreased with the increase in the polymer molecular mass. The number of polymer molecules bound per protein molecule varied from 0.01 to 0.2 for polyethyleneglycol 1000, 3300 and polyethylene-polypolypropylene oxide 8400, while for polyethyleneglycol 6000 such number got closer to the unity. The enthalpic change associated with the binding was positive in the order of 1 kcal/mol for lysozyme, while ovoalbumin showed values around 2-3 kcal/mol. Entropic changes were also positive with values around 17-20 e.u. for ovoalbumin and 1-7 e.u. for lysozyme. The heat associated with the protein transfer from a buffer to a medium containing the polymer or the salt (a process similar to protein partitioning in aqueous two-phase systems) was obtained. These results allow the direct calculation of the enthalpic change associated with a protein partition process in aqueous two-phase systems without applying the van'tHoff equation. In this way, it is possible to calculate the associated true heat when the protein is transferred from the bottom to the top phase.     

Affinity chromatography of a sequence-specific DNA binding protein using Teflon-linked oligonucleotides

An affinity matrix was constructed by synthesis of a DNA oligonucleotide on a Teflon fiber support followed by deblocking and hybridization of the complementary strand. It was used to purify a sequence-specific binding protein at least 100-fold to near homogeneity. This matrix is easily fabricated on an automated DNA synthesizer, contains high levels of attached DNA, and has superior mechanical properties. It should be generally useful for affinity chromatography of DNA binding proteins.     

The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1

Bacteria expand their genetic diversity, spread antibiotic resistance genes, and obtain virulence factors through the highly coordinated process of conjugative plasmid transfer (CPT). A plasmid-encoded relaxase enzyme initiates and terminates CPT by nicking and religating the transferred plasmid in a sequence-specific manner. We solved the 2.3 Å crystal structure of the relaxase responsible for the spread of the resistance plasmid pCU1 and determined its DNA binding and nicking capabilities. The overall fold of the pCU1 relaxase is similar to that of the F plasmid and plasmid R388 relaxases. However, in the pCU1 structure, the conserved tyrosine residues (Y18,19,26,27) that are required for DNA nicking and religation were displaced up to 14 Å out of the relaxase active site, revealing a high degree of mobility in this region of the enzyme. In spite of this flexibility, the tyrosines still cleaved the nic site of the plasmid’s origin of transfer, and did so in a sequence-specific, metal-dependent manner. Unexpectedly, the pCU1 relaxase lacked the sequence-specific DNA binding previously reported for the homologous F and R388 relaxase enzymes, despite its high sequence and structural similarity with both proteins. In summary, our work outlines novel structural and functional aspects of the relaxase-mediated conjugative transfer of plasmid pCU1.     

Determining transfer batch sizes in trip-based material handling systems

Trip-based material handling systems such as AGV systems or lift trucks are often designed with a given flow matrix (or from-to chart), which typically shows the number of loaded trips that the devices must perform per unit time between the workstations. A from-to chart that would result from the parts flow in a facility actually is dictated by the transfer batch size; that is, the number of parts transferred from one workstation to the next in one trip. In this paper, we present analytical and simulation results aimed at determining optimal or nearoptimal transfer batch sizes in manufacturing systems and develop an analytical relationship between the material handling capacity and the expected work in process (WIP) in a manufacturing system. Although the results apply to any discrete-parts flow, trip-based material handling system, they are particularly relevant for the electronics manufacturing industry, where parts (such as printed circuit boards or substrates for flat panel displays) typically are handled as a group (in specially designed containers such as cassettes) and the costs associated with WIP tend to be large. In such applications, the cassette size is the transfer batch size.