Living enantiosymmetric and enantioasymmetric polymerization of methylthiirane in homogeneous phase

The polymerization of racemic methylthiirane in homogeneous phase, initiated by bis(isopropyl-S-cysteinato) cadmium is a living process. The resulting polymers are isotactic and optically active at partial conversion. The optical purity of the residual monomer may reach 27% at half conversion. The propagation occurs mainly on one valency of Cd, however oligomers grow slowly on the second valency. The stereoregularity of the polymer chain appears only when the length of the oligomer becomes high enough, making possible a bicoordination of the Cd counterions. The stereoregularity of the polymer is characterized by the molar fraction σ of isotactic diads which varies from 0.5 for atactic chains—formed at the beginning—to about one for isotactic segments formed for longer chains. The stereospecifictity also depends on temperature of propagation and on initiator concentration. The kinetics observed (zero order in monomer and one-half in Cd) are explained by monomer coordination before insertion and dimeric association of the thiolate end groups. The enantioasymmetric process observed results from an unbalance in the number of the two different types of active sites and possibly from a difference in their reactivities. Enantioasymmetry has been found to decrease significantly when the dielectric constant ε of the medium increases.     

Characterization of Caulobacter crescentus FtsZ protein using dynamic light scattering

The self-assembly of the tubulin homologue FtsZ at the mid-cell is a critical step in bacterial cell division. We introduce dynamic light scattering (DLS) spectroscopy as a new method to study the polymerization kinetics of FtsZ in solution. Analysis of the DLS data indicates that the FtsZ polymers are remarkably monodisperse in length, independent of the concentrations of GTP, GDP, and FtsZ monomers. Measurements of the diffusion coefficient of the polymers demonstrate that their length is remarkably stable until the free GTP is consumed. We estimated the mean size of the FtsZ polymers within this interval of stable length to be between 9 and 18 monomers. The rates of FtsZ polymerization and depolymerization are likely influenced by the concentration of GDP, as the repeated addition of GTP to FtsZ increased the rate of polymerization and slowed down depolymerization. Increasing the FtsZ concentration did not change the size of FtsZ polymers; however, it increased the rate of the depolymerization reaction by depleting free GTP. Using transmission electron microscopy we observed that FtsZ forms linear polymers in solutions which rapidly convert to large bundles upon contact with surfaces at time scales as short as several seconds. Finally, the best studied small molecule that binds to FtsZ, PC190723, had no stabilizing effect on Caulobacter crescentus FtsZ filaments in vitro, which complements previous studies with Escherichia coli FtsZ and confirms that this class of small molecules binds Gram-negative FtsZ weakly.     

Mechanism of action of phalloidin on the polymerization of muscle actin

Under conditions where muscle actin only partially polymerizes, or where it does not polymerize at all, a significant enhancement of polymerization was observed if equimolar phalloidin was also present. The increased extent of polymerization in the the presence of phalloidin can be explained by the reduced critical actin concentration of partially polymerized populations at equilibrium. Under such conditions, the rate of polymerization, as judged by the length of time to reach half the viscosity plateau, was found to be essentially independent of the phalloidin concentration. Moreover, the initial rate of polymerization of actin was also found to be independent of phalloidin concentration. However, phalloidin apparently causes a reduction in the magnitude of the reverse rates in the polymerization reaction, as was demonstrated by the lack of depolymerization of phalloidin-treated actin polymers. This effect of phalloidin is also supported by the identification of actin nuclei and short polymers in populations of G-actin incubated with phalloidin in the absence of added KCl. Our conclusion, then, is that phalloidin influences the polymerization of actin by stabilizing nuclei and polymers as they are formed.     

Homochiral oligopeptides via surface recognition and enantiomeric cross impediment in the polymerization of racemic phenylalanine N-carboxyanhydride crystals suspended in water

As part of our program on the search of possible prebiotic routes for the formation of oligopeptides of homochiral sequence (isotactic) from racemic precursors in aqueous environment, we report the polymerization of racemic crystals of phenylalanine N-carboxyanhydrides, enantioselectively tagged with five deuterium atoms, suspended in water containing various amine initiators. Racemic mixtures of isotactic oligopeptides, comprising up to 25 repeat units of the same handedness, as the dominant component for each length, were observed in a MALDI-TOF mass spectrometry analysis. The racemic mixtures of the peptides could be desymmetrized by initiating the polymerization reaction with water-soluble methyl esters of either enantiopure alpha-amino acids or dipeptides. A three-step mechanism is proposed to account for these results: (i) Surface recognition of the chiral initiator by the chiral sites present at specific faces of the crystal; (ii) Oligopeptide elongation at the polymer/crystal interface; and (iii) Self-assembly of the short isotactic peptides into racemic antiparallel beta-sheets as templates followed by cross-enantiomeric impediment in the growth of enantiomeric chains at the peptide beta-sheet/crystal interface.     

Kinetic mechanism of end-to-end annealing of actin filaments

We investigated the effect of actin filament length and capping protein on the rate of end-to-end annealing of actin filaments. Long filaments were fragmented by shearing and allowed to recover. Stabilizing filaments with phalloidin in most experiments eliminated any contribution of subunit dissociation and association to the redistribution of lengths but did not affect the results. Two different assays, fluorescence microscopy to measure filament lengths and polymerization to measure concentration of barbed filament ends, gave the same time-course of annealing. The rate of annealing declines with time as the average filament length increases. Longer filaments also anneal slower than short filaments. The second-order annealing rate constant is inversely proportional to mean polymer length with a value of 1.1 mM(-1) s(-1)/length in subunits. Capping protein slows but does not prevent annealing. Annealing is a highly favorable reaction with a strong influence on the length of polymers produced by spontaneous polymerization and should be considered in thinking about polymer dynamics in cells.     

The mechanism of ATP hydrolysis by polymer actin.

The rate of actin polymerization, the rate of nucleotide splitting and the rate of the nucleotide exchange have been measured simultaneously. Correlation of these three measurements demonstrated that nucleotide splitting and exchange were mainly connected with the association and dissociation reactions of actin protomers at the ends of actin filaments and were not caused by release and rebinding of nucleotide molecules at the binding sites along the filament. The observation made by others that the nucleotide exchange was accelerated in the presence of ATP was explained by the translocational head-to-tail polymerization of actin: Due to the simultaneous lengthening of the filament at one end and shortening at the other, nucleotide molecules are incorporated at one end and released at the other. In the absence of ATP, where the head-to-tail polymerization mechanism was not operative nucleotide exchange was brought about by the slow process of length fluctuation of polymers.     

Dynamic assembly of primers on nucleic acid templates

A strategy is presented that uses dynamic equlibria to assemble in situ composite DNA polymerase primers, having lengths of 14 or 16 nt, from DNA fragments that are 6 or 8 nt in length. In this implementation, the fragments are transiently joined under conditions of dynamic equilibrium by an imine linker, which has a dissociation constant of ~1 μM. If a polymerase is able to extend the composite, but not the fragments, it is possible to prime the synthesis of a target DNA molecule under conditions where two useful specificities are combined: (i) single nucleotide discrimination that is characteristic of short oligonucleotide duplexes (four to six nucleobase pairs in length), which effectively excludes single mismatches, and (ii) an overall specificity of priming that is characteristic of long (14 to 16mers) oligonucleotides, potentially unique within a genome. We report here the screening of a series of polymerases that combine an ability not to accept short primer fragments with an ability to accept the long composite primer held together by an unnatural imine linkage. Several polymerases were found that achieve this combination, permitting the implementation of the dynamic combinatorial chemical strategy.     

Ultrastructure of unit fragments of the skeleton of the human erythrocyte membrane

We have examined fragments of the filamentous network underlying the human erythrocyte membrane by high-resolution electron microscopy. Networks were released from ghosts by extraction with Triton X-100, freed of extraneous proteins in 1.5 M NaCl, and collected by centrifugation onto a sucrose cushion. These preparations contained primarily protein bands 1 + 2 (spectrin), band 4.1 and band 5 (actin). The networks were partially disassembled by incubation at 37 degrees C in 2 mM NaPi (pH 7), which caused the preferential dissociation of spectrin tetramers to dimers. The fragments so generated were fractionated by gel filtration chromatography and visualized by negative staining with uranyl acetate on fenestrated carbon films. Unit complexes, which sedimented at approximately 40S, contained linear filaments approximately 7-8 nm diam from which several slender and convoluted filaments projected. The linear filaments had a mean length of 52 +/- 17 nm and a serrated profile reminiscent of F-actin. They could be decorated in an arrowhead pattern with S1 fragments of muscle heavy meromyosin which, incidentally, displaced the convoluted filaments. Furthermore, the linear filaments nucleated the polymerization of rabbit muscle G-actin, predominantly but not exclusively from the fast-growing ends. On this basis, we have identified the linear filaments as F-actin; we infer that the convoluted filaments are spectrin. Spectrin molecules were usually attached to actin filaments in clusters that showed a preference for the ends of the F-actin. We also observed free globules up to 15 nm diam, usually associated with three spectrin molecules, which also nucleated actin polymerization; these may be simple junctional complexes of spectrin, actin, and band 4.1. In larger ensembles, spectrin tetramers linked actin filaments and/or globules into irregular arrays. Intact networks were an elaboration of the basic pattern manifested by the fragments. Thus, we have provided ultrastructural evidence that the submembrane skeleton is organized, as widely inferred from less direct information, into short actin filaments linked by multiple tetramers of spectrin clustered at sites of association with band 4.1.     

Effect of highly fragmented DNA on PCR.

We characterized the behavior of polymerase chain reactions (PCR) using degraded DNA as a template. We first demonstrated that fragments larger than the initial template fragments can be amplified if overlapping fragments are allowed to anneal and extend prior to routine PCR. Amplification products increase when degraded genomic DNA is pretreated by polymerization in the absence of specific primers. Secondly, we measured nucleotide uptake as a function of template DNA degradation. dNTP incorporation initially increases with increasing DNA fragmentation and then declines when the DNA becomes highly degraded. We demonstrated that dNTP uptake continues for >10 polymerization cycles and is affected by the quality and quantity of template DNA and by the amount of substrate dNTP. These results suggest that although reconstruction of degraded DNA may allow amplification of large fragments, reconstructive polymerization and amplification polymerization may compete. This was confirmed in PCR where the addition of degraded DNA reduced the resultant product. Because terminal deoxynucleotidyl transferase activity of Taq polymerase may inhibit 3' annealing and restrict the length of template reconstruction, we suggest modified PCR techniques which separate reconstructive and amplification polymerization reactions.     

Structure and mobility of actin filaments as measured by quasielastic light scattering, viscometry, and electron microscopy

Actin filaments of different lengths were prepared by polymerizing actin in the presence of various concentrations of gelsolin, a protein which accelerates actin polymerization by stabilizing nuclei from which filaments grow and which binds to their fast growing ends. The lengths of the actin filaments following polymerization were measured by electron microscopy and showed that the number-average filament length agreed with the predicted length if each gelsolin molecule acted as a seed for the growth of an actin filament. The distribution of lengths was independent of the actin:gelsolin ratio and was similar to that of actin filaments polymerized in the absence of gelsolin (Lw/Ln = 1.8). The mobility of these filaments in solution was studied by quasielastic light scattering and by viscometry. The translational diffusion constant determined by quasielastic light scattering was in agreement with the infinite dilution values calculated from the dimensions and the distribution of lengths determined by electron microscopy for relatively short filament lengths. Under conditions where overlap of the rotational domains of the filaments would be expected to occur, the measured diffusion rates deviated from their predicted dilute solution values and the solution viscosity increased abruptly. The dependence of the diffusion constant and the solution viscosity on the length of the actin filaments can be explained in terms of a theory that describes the restraints on diffusion of independent rigid rods in semi-dilute solution. The results suggest that the rheology of actin filaments can be accounted for by steric restraints. The length of cytoplasmic actin filaments in some cell types is such that these steric constraints are significant and could produce large changes in physical properties with small changes in filament length.     

A quantitative analysis of microtubule elongation

Methods have been developed for differentially inhibiting microtubule nucleation and elongation in vitro. By use of polyanions, assembly- competent tubulin solutions of several milligrams/milliliter can be prepared which do not exhibit appreciable spontaneous assembly during the time-course of an experiment. Microtubule elongation can be initiated by the addition of known numbers of microtubule fragments. A detailed analysis of the resulting process demonstrates that: (a) rings are not obligatory intermediates in the nucleation sequence, and neither rings nor protofilament sheets are obligatory intermediates in the elongation reaction. (b) The end of an elongating microtubule often has a short region of open protofilament sheet or "C-microtubule" similar to that observed in vivo. (c) The development of turbidity follows a simple exponential approach to an equilibrium value. (d) The final equilibrium values are independent of the number of added nucleating fragments, while the initial growth rates and half-times to reach equilibrium are dependent on the number of added nuclei. (e) The final lengths of the microtubules at equilibrium are inversely proportional to the number of added fragments. (f) The equilibrium constants are independent of microtubule length. (g) The number of assembly and disassembly sites per microtubule is not a function of microtubule length. (h) The forward rate constants, the final polymer concentrations, and growth rates of microtubules are dependent upon the concentration of polyanion present. These results are strongly supportive of the idea that microtubule assembly is a "condensation- polymerization" and provide basic information on the kinetics and length distributions of the elongation in vitro.     

Chromosome length controls mitotic chromosome segregation in yeast

We have examined the effect of physical length on the mitotic segregation of artificial chromosomes and fragments of natural yeast chromosomes. Increasing the length of artificial chromosomes decreases the rate at which they are lost during mitosis. We have made fragments of chromosome III by integrating new telomeres at different positions along the length of the chromosome. Chromosome fragments of 42 and 72 kb behave like artificial chromosomes: they are lost in mitosis much more frequently than natural chromosomes. In contrast, a chromosome fragment of 150 kb is as mitotically stable as the full-length chromosome from which it is derived. The structural instability of a short dicentric artificial chromosome demonstrates that, although short artificial chromosomes segregate poorly in mitosis, they do attach to the mitotic spindle. We discuss these results in the context of a model in which chromosome segregation is directed by the intercatenation of the segregating DNA molecules.     

Multi-Platform Compatible Software for Analysis of Polymer Bending Mechanics

Cytoskeletal polymers play a fundamental role in the responses of cells to both external and internal stresses. Quantitative knowledge of the mechanical properties of those polymers is essential for developing predictive models of cell mechanics and mechano-sensing. Linear cytoskeletal polymers, such as actin filaments and microtubules, can grow to cellular length scales at which they behave as semiflexible polymers that undergo thermally-driven shape deformations. Bending deformations are often modeled using the wormlike chain model. A quantitative metric of a polymer''s resistance to bending is the persistence length, the fundamental parameter of that model. A polymer''s bending persistence length is extracted from its shape as visualized using various imaging techniques. However, the analysis methodologies required for determining the persistence length are often not readily within reach of most biological researchers or educators. Motivated by that limitation, we developed user-friendly, multi-platform compatible software to determine the bending persistence length from images of surface-adsorbed or freely fluctuating polymers. Three different types of analysis are available (cosine correlation, end-to-end and bending-mode analyses), allowing for rigorous cross-checking of analysis results. The software is freely available and we provide sample data of adsorbed and fluctuating filaments and expected analysis results for educational and tutorial purposes.     

Homologous RNA polymerase binding to Escherichia coli DNA: a study of the distribution of stable binding sites.

The number and the distribution of the sites of Escherichia coli DNA that form stable complexes with the homologous RNA polymerase (class A sites according to Hinkle and Chamberlin [3]) have been investigated. Almost all the DNA can bind RNA polymerase, even when fragmented at short (undergenic) size; this general non-promoter-specific binding is highly labile and is not temperature-dependent. The range of RNA polymerase/DNA ratios that give rise to the stable temperature-dependent complexes was examined. The amount and the distribution of class A complexes were studied analysing the dissociation of complexes formed by RNA polymerase on DNA fragments of various length. The E. coli genome appears to form 3.8 X 10(3) stable complexes; the majority of these complexes shows a short-range distribution (800-1200 base pairs). The rest is more widely spaced (1200-6000 base pairs).     

Lithium increases actin polymerization rates by enhancing the nucleation step

Lithium affects the polymerization mechanism of some cytoskeletal proteins in vitro, so its biological activity could also reflect lithium influence on assembly processes. Our data demonstrate that lithium nucleates actin polymerization and, in parallel, is less effective in the elongation step. Furthermore, falling-ball and fluorimetric tests suggested that lithium-induced actin polymers at steady-state are shorter than K(+)-polymerized actin filamentous structures. The lithium-induced actin assembly seems to follow the "reversible polymerization model" and the critical concentration of Li(+)-assembled actin at steady-state is markedly lower than that of sister actin samples polymerized by potassium chloride. Finally, the stabilization of actin nuclei induced by lithium ions could be related to their effect of lowering the dissociation rate constant.     

Nonenzymatic RNA ligation in water

We describe the nonenzymatic ligation of RNA oligomers in water. Dimers and tetramers are formed in a time-, pH-, and temperature-dependent reaction. Ligation efficiency depends on oligonucleotide length and sequence and is strongly enhanced by adenine-based nucleotide cofactors. Ligation of short RNA fragments could have liberated the prebiotic polymerization systems from the thermodynamically demanding task of reaching a (pre)genetically meaningful size by stepwise addition of one precursor monomer at the time.     

Reconstruction of protein and nucleic acid sequences. V. Computer-simulated tests of various tactics for reconstructing the sequences of transfer ribonucleic acids

One hundred hypothetical polynucleotides of varying chain length and composition and of random sequence were generated and their chemical degradation simulated by a computer. Included in the study were 20 hypothetical polymers with the composition and chain length of a transfer RNA. A second computer program attempted to reconstruct the sequences from the nucleotide composition and the simulated fragments produced. Approximately 700 reconstructions were attempted from various sets of fragments generated from the 100 polymers. The dependence of the probability of reconstructing the original sequences on the methods of producing and isolating the fragments was studied.     

In vitro assembly of tau protein: mapping the regions involved in filament formation

Unraveling the mechanism of self-assembly of the protein tau into paired helical filaments (PHFs) is a crucial step toward the understanding of Alzheimer's and other neuropathological diseases at the molecular level. In an effort to map the role of different regions of tau in the mechanism of self-assembly, we have studied the polymerization ability of different tau fragments using an in vitro assay. Our results indicate that the N-terminal domain interferes with tau's ability to polymerize in vitro. The effect seems to be size dependent. Particularly, an isoform of tau from the peripheral nervous system, which has a much larger N-terminal domain, was found unable to form filaments in our in vitro assay. This finding can explain why in Alzheimer's patients PHFs only accumulate in the neurons from the central nervous system. We also report that a short segment of tau located in the third microtubule binding repeat (residues 317 to 335, peptide 1/2R) is probably the minimal segment of that region able to grow into filaments in vitro and in the presence of heparin. In contrast with whole peptide 1/2R, peptides corresponding to either the N-terminal or C-terminal halves of this segment were unable to form filaments. Finally, our polymerization studies of peptides from the C-terminal domain reveal a short sequence spanning residues 391 to 407 that grows into filaments in vitro. This tau segment forms filaments regardless of whether is incubated with heparin. Moreover, such filaments differ in diameter and morphology, suggesting a different mechanism of self-assembly.     

Lac repressor-operator interaction: DNA length dependence

The interaction of the E. coli lac operon repressor with its operator DNA has been directly examined as a function of the length of operator-containing DNA. The apparent bimolecular association rate constants were calculated as ka = (kd/KD), where the dissociation equilibrium constant, KD and the dissociation rate constant, kd, were measured by nitrocellulose filter adsorption assays. The values obtained for the overall association rate constants are compared with theoretical association rate curves for specific mechanisms. Association of the repressor with short operator containing DNA fragments (less than 70 base pairs) occurs at rates expected of three-dimensional diffusion. Our data also imply that at longer DNA lengths a combination of three-dimensional diffusion with one-dimensional sliding along with hopping and/or intersegment transfer must be involved to facilitate the repressor operator association.     

Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

Discretization of protein conformational space and fragment assembly methods simplify the search of native structures. These methods, mostly of Monte Carlo and genetic-type, do not exploit, however, the fact that short fragments describing consecutive parts of proteins are conformation-dependent. Yet, this information should be useful in improving ab initio and comparative protein structure modeling. In a preliminary study, we have assessed the possibility of using greedy algorithms for protein structure reconstruction based on the assembly of fragments of four-residue length. Greedy algorithms differ from Monte Carlo and genetic approaches in that they grow a polypeptide chain one fragment after another. Here, we move one step further in complexity, and provide strong evidence that the dependence between consecutive local conformations during assembly makes possible the reconstruction of protein structures from their secondary structures using a Go potential. Overall our procedure can reproduce 20 protein structures of 50-164 amino acids within 2.7 to 6.5 A RMSd and is able to identify native topologies for all proteins, although some targets are stabilized by very long-range interactions.