Robust quantization of a molecular motor motion in a stochastic environment.

We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the pumping-quantization theorem (PQT) that identifies the conditions for robust integer quantized behavior of a periodically driven molecular machine. Implication of PQT on experiments with catenane molecules are discussed.

Pumping restriction theorem for stochastic networks.

We formulate an exact result, which we refer to as the pumping restriction theorem (PRT). It imposes strong restrictions on the currents generated by periodic driving in a generic dissipative system with detailed balance, and provides a universal nonperturbative approach to explore the stochastic pump effect in nonadiabatically driven systems.

Statistics of entropy production in linearized stochastic systems.

We consider a wide class of linear stochastic problems driven off the equilibrium by a multiplicative asymmetric force. The force breaks detailed balance, maintained otherwise, thus producing entropy. The large deviation function of the entropy production in the system is calculated explicitly. The general result is illustrated using an example of a polymer immersed in a gradient flow and subject to thermal fluctuations.

Induction of nonselective permeability of the inner membrane in deenergized mitochondria.

Induction of the nonselective cyclosporin-sensitive pore in the inner mitochondrial membrane under conditions of complete dissipation of ion gradients and transmembrane potential was studied. This approach allows the kinetics of Ca2+-dependent pore opening and the preceding processes of induction to be studied separately. The effects of mitochondrial heterogeneity were also minimized. We found that the kinetics of pore opening can be described by a minimal two-step scheme where only the rate constant at the first step depends on Ca2+ concentration. Oxidation of pyridine nucleotides in the matrix caused a slow transition in the pore complex and decreased the apparent dissociation constant of the Ca2+-binding site from >1 mM to approximately 30 microM. N-Ethylmaleimide (but not disulfide-reducing agents) prevented and slowly reverted the pore induction process. Data suggesting allosteric modulation of the pore by pyridine nucleotides are presented.

Structural and functional consequences of substitutions at the tyrosine 55-lysine 104 hydrogen bond in Escherichia coli inorganic pyrophosphatase.

Tyrosine 55 and lysine 104 are evolutionarily conserved residues that form a hydrogen bond in the active site of Escherichia coli inorganic pyrophosphatase (E-PPase). Here we used site-directed mutagenesis to examine their roles in structure stabilization and catalysis. Though these residues are not part of the subunit interface, Y55F and K104R (but not K104I) substitutions markedly destabilize the hexameric structure, allowing dissociation into active trimers on dilution. A K104I variant is nearly inactive while Y55F and K104R variants exhibit appreciable activity and require greater concentrations of Mg2+ and higher pH for maximal activity. The effects on activity are explained by (a) increased pK(a)s for the catalytically essential base and acid at the active site, (b) decreases in the rate constant for substrate (dimagnesium pyrophosphate) binding to enzyme-Mg2 complex vs enzyme-Mg3 complex, and (c) parallel decreases in the catalytic constant for the resulting enzyme-Mg2-substrate and enzyme-Mg3-substrate complexes. The results are consistent with the major structural roles of Tyr55 and Lys104 in the active site. The microscopic rate constant for PPi hydrolysis on either the Y55F or K104R variants increases, by a factor of 3-4 in the pH range 7.2-8.0, supporting the hypothesis that this reaction step depends on an essential base within the enzyme active site.

Visualization of reversible macromolecular reactions in an analytical ultracentrifuge.

It has been shown that the saw-like disturbances of sedimentation observed in an analytical ultracentrifuge are not caused by convective disturbances of the solution but result from a special type of intermolecular reaction of reversible association/dissociation. A qualitative theory of saw-like anomalies has been suggested and the sedimentation and kinetic conditions of their origin have been indicated. Such reactions are a frequent occurrence in the serum of patients affected with rheumatic diseases and acute myocardial infarction. Experimental data indicate the involvement of immunoglobulins (viz., low-affinity antibodies) which form reversible immune complexes. Saw-like sedimentation patterns, especially those of the schlieren type, are a direct testimony to reversible association/dissociation reactions in macromolecular solutions, whereas other experimental methods provide only oblique evidence.

The quaternary structure of bovine brain kinesin.

In the present work we have studied the subunit composition of kinesin, the microtubule-activated, mechanochemical ATPase, isolated from bovine brain. Polypeptides with mol. wts of 120 and 62 kd are the major components of the kinesin preparation. These polypeptides could not be separated by electrophoresis under nondenaturing conditions or by FPLC on a MonoQ column, and are therefore assumed to form a tight complex. As shown by immunoblotting with polyclonal and monoclonal antibodies to the 120-kd polypeptide and by one-dimensional peptide mapping, the 62-kd polypeptide does not appear to be a proteolytic product of the 120-kd component. Densitometric scanning of polyacrylamide-SDS gels shows that these polypeptides are present in a complex in a 1:1 molar ratio. The mol. wt of native kinesin was studied by sedimentation equilibrium and was found to be 386 +/- 14 kd. A comparison of the mol. wts of individual polypeptides with the mol. wt of the intact molecule indicates that the native molecule contains two 120-kd subunits and two 62-kd subunits.

Structural rearrangements in soluble mitochondrial ATPase.

Treatment of isolated factor F1 by 1% dimethylsuberimidate in the presence of 50 mM (NH4)2SO4 leads to the formation of four different types of cross-linked dimers of the subunits, on average one dimer per molecule of the enzyme. This treatment results in 60-70% inactivation of factor F1. Factor F1 treated with dimethylsuberimidate does not show a change in the sedimentation coefficient and is not inactivated in the cold; it is not inactivated in the presence of Mg2+ either, nor is it activated by anions. Incubation of the cross-linked factor F1 with ADP does not lead to inactivation, although the ability to tightly bind ADP is retained. The total quantity of tightly bound ADP reaches 5 mol per mol of the cross-linked factor F1. Cross-linking of factor F1 also prevents the slow inactivation of the enzyme coupled with the hydrolysis of Mg-ATP and Mg-GTP. The dependence of the inactivation rate constant on the concentration of Mg-ATP and Mg-GTP at substrate concentrations of 0.05-2 mM is characterized by the same values of Km,app as those of the ATPase and GTPase activities of factor F1. The probability of the inactivation of factor F1 per turnover remains constant for all the concentrations of the substrates studied and is 2 . 10(-6) per turnover for the ATPase reaction and 2 . 10(-5) per turnover for the GTPase reaction. Moderate hydrostatic pressure (up to 150 atmospheres) greatly accelerates ATP-induced inactivation of factor F1. The activation volume (delta V*) of the inactivation process is equal to 5.1 . 10(-4) cm3/g, which is evidence of considerable changes in the extent of protein hydration during inactivation. Inactivation of the enzyme under pressure is accompanied by dissociation into subunits. Dimethyladipimidate, which does not cause intersubunit cross-linking in the molecule of factor F1, does not alter the properties of the native enzyme. It is suggested that the formation of one intersubunit cross-link in the molecule of factor F1 by dimethylsuberimidate affects the ability of the enzyme to undergo co-operative rearrangements of the quaternary structure under the influence of Mg2+, ADP, ATP, anions, and low temperature. The rate constants of ATP binding to the active site of factor F2 (k+1) = 2 . 10(8) M-1 . min-1), of ATP release from the active site (k-1 = 2 . 10(-2) min-1), and of ADP and Pi release from the active site (k2 = 5 . 10(3) min-1) have been determined. The results obtained confirm the correctness of Boyer's idea, according to which ATP is formed in the active site of mitochondrial ATPase without any external source of energy. Energy is used at the stage of the release of synthesized ATP from the active site of ATPase in the solution.

Investigation of soluble mitochondrial ATPase by the reacting enzyme sedimentation method.

Soluble mitochondrial ATPase from bovine heart (factor F1) loses its activity during ATP hydrolyses. The inactivation is accelerated by moderate pressure, which is generated in an ultracentrifuge cell. The rate of inactivation slows down if the concentration of the substrate (MgATP) is diminished. ATP hydrolysis proceeds at an almost constant rate if the substrate concentration is as low as 0.05 mM. One intersubunit cross-link formed by dimethylsuberimidate per molecule of factor F1, prevents its inactivation during the ATPase reaction both without pressure and in an ultracentrifuge. Sedimentation coefficients measured by the reacting enzyme centrifugation method of both unmodified factor F1 at a low (about 0.05 mM MgATP) substrate concentration and of its dimethylsuberimidate cross-linked form in the presence of 10 mM MgATP, were determined to be s20, w = 12.4 +/- 0.4 S. The value is the same as that obtained by the conventional boundary sedimentation method in the absence of the substrate. This result testifies to the fact that the conformation of reacting factor F1 in solution is similar to that of the enzyme in the absence of the substrate.

Molecular weight of base plates of bacteriophage T4D.

Highly purified base plates of bacteriophage T4D were obtained from lysate of gene 19 am mutant of this phage by differential centrifugation and sucrose gradient. Base plates were studied by means of high speed sedimentation equilibrium. The molecular weight determined by this method is (6.7 plus or minus 0.2)-10-6.