Yin Yeh

Processive translocation and DNA unwinding by individual RecBCD enzyme molecules

RecBCD enzyme is a processive DNA helicase and nuclease that participates in the repair of chromosomal DNA through homologous recombination. We have visualized directly the movement of individual RecBCD enzymes on single molecules of double-stranded DNA (dsDNA). Detection involves the optical trapping of solitary, fluorescently tagged dsDNA molecules that are attached to polystyrene beads, and their visualization by fluorescence microscopy. Both helicase translocation and DNA unwinding are monitored by the displacement of fluorescent dye from the DNA by the enzyme. Here we show that unwinding is both continuous and processive, occurring at a maximum rate of 972 ± 172 base pairs per second (0.30 µm s-1), with as many as 42,300 base pairs of dsDNA unwound by a single RecBCD enzyme molecule. The mean behaviour of the individual RecBCD enzyme molecules corresponds to that observed in bulk solution.

Sarcomere length determination using laser diffraction. Effect of beam and fiber diameter.

An experimental and theoretical analysis is presented involving the effect of variation in fiber and beam diameter upon the determination of average sarcomere length in isolated single muscle fibers using laser light diffraction. The muscle diffraction phenomenon is simplified by first considering diffraction order position and intensity to be the result of grating and Bragg diffraction. It is the product of the intensity profiles, which results from these types of diffraction, that produces the diffracted order. These simplifying assumptions are then extended to the case of the real muscle. Based on these considerations and the theory that we recently presented, conditions are set forth under which grating information (i.e., sarcomere length) can be maximally expressed to yield accurate average sarcomere length values.

Antifreeze proteins from fish bloods.

Publisher Summary Glycoproteins of molecular weights isolated from the blood sera of the two Antarctic fishes, Trematomus borchgrevinki and Dissostichus mawsoni, exhibit antifreezing properties in pure H2O or salt solutions. As the melting point is not affected, a hysteresis exists between the freezing and melting temperatures, and the glycoproteins are considered to lower the freezing temperature rather than the freezing point. The information obtained on the basic structure of these glycoproteins is shared, and models of antifreeze mechanism are discussed. In these models, the polypeptide is assumed to form a nonideal, nonregular solution in H20. In one model, the ability of the hydrophilic sites of these molecules to enter into favorable competition for hydrogen bonds among the H20 molecules themselves provides for a mechanism of lowering the freezing point. The only over-riding similarity amongthese antifreezing molecules is the predominance of alanine. It is this feature that has primary and critical importance in antifreeze function observed in these fishes. Antifreeze glycoprotein (AFGP) discussed is a collective name for a family of at least eight closely related glycoproteins that account for a major fraction of the protein in the blood serum of certain Antarctic fishes the eight originally observed glycoproteins during electrophoresis in acrylamide gel with borate buffer. Along with lowering the freezing temperature of water to an abnormal extent as based on their particle sizes, active AFGP components also are abnormal in several other properties related to lowering the freezing temperature and the freezing process itself.

Antifreeze proteins: Current status and possible food uses

Antifreeze proteins from the blood serum of cold-water ocean fish inhibit ice crystal growth, including recrystallization, and affect crystal morphology. They exist in relatively high concentrations, ∼30 mg/ml, and are peptides or small proteins, mainly with less than 40 amino acids. Structures include both glycoprotein and non-glycoproteins, some of which have been chemically synthesized. They have also been found in plants and insects. The most successful experiments on foods have been the reduction of recrystallization in frozen dairy products. Cost, however, is apparently presently blocking usage.

Theory of light diffraction by single skeletal muscle fibers

A theoretical discussion is presented describing the diffraction of laser light by a single fiber of striated muscle. The complete three-dimensional geometry of the fiber has been taken into consideration. The basic repeated unit is taken as the sarcomere of a single myofibril, including its cylindrical geometry. The single fiber is considered as the sum of myofibrils up to the fiber dimensions. When proper phasing is taken into account, three cases of interest are analyzed. (a) When the adjacent myofibrils are totally aligned with respect to their index of refraction regions (e.g., A and I bands), then the diffraction pattern reflects that of a larger striated cylinder with the dimensions of the fiber. (b) When a particular skew plane develops for the myofibril elements, additional Bragg reflection occurs at certain specific sarcomere lengths, and intensity asymmetry amongst the diffracted orders occurs. (c) When the myofibril phasing changes in a random fashion, while all sarcomeres remain at the same length, then intensity decrease is directly related to the phase deviation from a reference phase point. This condition may well describe a fiber undergoing active isometric contraction.

A light-scattering characterization of membrane vesicles

A technique has been developed in this paper which enables quasi-elastic laser light scattering to be used to accurately and quantitatively measure the average vesicle diffusion coefficient and the relative dispersion in the diffusion coefficient about this average for dilute polydisperse vesicle suspensions. This technique relies on a theoretical analysis of a modified form of the Z-averaged diffusion coefficient. This modified Z-averaged diffusion coefficient explicitly incorporates vesicle size, structure, and polydispersity in a description of the scattered light autocorrelation spectrum. Light-scattering experiments were performed on a dilute, lobster sarcoplasmic reticulum vesicle suspension and the measured average diffusion coefficient and the diffusion coefficient relative dispersion about this average were determined with accuracies of 2 and 10%, respectively. A comparison of vesicle size inferred from light-scattering results was made with size results from electron microscopic analysis of the same sample.

Dynamics of Antifreeze Glycoproteins in the Presence of Ice

Antifreeze glycoproteins from the Greenland cod Boreogadus saida were dimethylated at the N-terminus (m*AFGP) and their dynamics and conformational properties were studied in the presence of ice using (13)C-NMR and FTIR spectroscopy. (13)C-NMR experiments of m*AFGP in D(2)O, in H(2)O, and of freeze-dried m*AFGP were performed as a function of temperature. Dynamic parameters ((1)H T(1 rho) and T(CH)) obtained by varying the contact time revealed notable differences in the motional properties of AFGP between the different states. AFGP/ice dynamics was dominated by fast-scale motions (nanosecond to picosecond time scale), suggesting that the relaxation is markedly affected by the protein hydration. The data suggest that AFGP adopts a similar type of three-dimensional fold both in the presence of ice and in the freeze-dried state. FTIR studies of the amide I band did not show a single prevailing secondary structure in the frozen state. The high number of conformers suggests a high flexibility, and possibly reflects the necessity to expose more ice-binding groups. The data suggest that the effect of hydration on the local mobility of AFGP and the lack of significant change in the backbone conformation in the frozen state may play a role in inhibiting the ice crystal growth.

Light diffraction study of single skeletal muscle fibres

Light diffraction patterns from isolated frog semitendinosus muscle fibers were examined. When transilluminated by laser light, the muscle striations produce a diffraction pattern consisting of a series of lines that are projected as points onto an optical detector by a lens system. Diffraction data may be sequentially stored every 18 ms for later processing by digital computer systems. First- and second-order diffraction line intensities were examined from intact, chemically skinned, and glycerinated single fibers. The diffraction line intensities demonstrated a strong length dependence upon passive stretch from reference length to 3.6 micrometer. The first-order intensity linearly increased an average of 15-fold over the range examined. The magnitude of the second order intensity was less than the first order and showed an exponential rise with increasing length. Both first- and second-order intensities decreased upon muscle activation. Data from chemically skinned and glycerinated single fibers were not significantly different from intact fibers, indicating that the membrane structure has little effect upon the diffraction phenomenon in muscle. Theoretical model systems are examined in an attempt to find the basis of these results. Neither an analysis based on a diffraction grating with variable spacing nor the unit cell model of Fujime provides an explanation for the observed length dependency of intensity. Though the origin of the intensity decrease upon stimulation is not known, we have suggested that it could result from lateral misalignment of myofibrils and can occur upon activation.

The Dynamics, Structure, and Conformational Free Energy of Proline-Containing Antifreeze Glycoprotein

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Raman spectroscopic investigations of sarcoplasmic reticulum membranes.

Raman spectra are presented for sarcoplasmic reticulum membranes. Interpretation of the 1000-1130 cm-1 region of the spectrum indicates that the sarcoplasmic reticulum membrane may be more fluid than erythrocyte membranes that have been examined by the I portion of the membrane spectrum with a strong 1658 cm-1 band characteristic of C=C stretching in hydrocarbon side chains exhibiting cis conformation. This band is unaltered in intensity and position in H2O and in 2H2O thus obscuring amide I protein conformation. Of particular interest is the appearance of strong, resonantly enhanced bands at 1160 and 1527 cm-1 attributable to membrane-associated carotenoids.