Biophysical Reviews and Letters

A three-dimensional AB off-lattice protein model, which involves two species of residues interacting through simplified backbone and modified Lennard-Jones potentials, is studied. Incorporating an extra energy contribution into the original potential energy function, we develop and study a simple gradient algorithm for finding the lowest energy states of this protein model. The performance of our algorithm is tested on the Fibonacci sequences of lengths ranging from 13 to 55 residues previously studied by Hsu et al. Computational performance and behavior of our algorithm are also discussed.

DNA triplexes with 'tight turns', i.e., sharp turns without any intervening bases, are studied by fluorescence resonance energy transfer process (FRET). The particular turning motifs under consideration are CC and TT imbedded in triplexes (5′-F-(TC)₃(CT)₃-D + 5′-AGAGAG) and (5′-F-(CT)₃(TC)₃-D + 5′-GAGAGA), where F and D are 6-fluorescein and 4-(4-dimethylaminophenylazo) benzoic acid, respectively. The association equilibrium constants of the above two triplexes ranged from 1.7 × 10⁷ to 2.9 × 10⁴ and 0.75 × 10⁷ to 1.8 × 10⁴ from 10 to 35°C, respectively. The thermodynamic parameters of these two triplexes are comparable (△H: -46.0 vs. -45.0 Kcal/mol; △S: -129 vs -127 cal/mol K; △G: -7.5 vs. -7.2 Kcal/mol, respectively). Thus, the stability of the tight-turn triplex with a CC motif is comparable to that with a TT motif, but slightly favored over the latter. This is the first report of a py/pu/py type triplex containing such tight turns studied under pH at 7. The importance is manifested in their stabilities maintained under physiological neutral condition, as opposed to previous studies only obtainable in acidic conditions.

In this paper we present a novel 2-D graphical representation of DNA sequences in the first quadrant Cartesian coordinate system. This representation has been mathematically proven to be a zero length of circuit, i.e., without any degeneracy. A practicable formula based upon an iterative comparison method has been developed to calculate the frequencies of nucleic acid bases (A, T, G, and C) from the starting point to any considered point. Furthermore, this new graphical representation, in comparison with our previously published method, may have a unique application in representing the universal genetic code.

The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their end points to two opposing walls. The numbers of segments N, the distances d₁ and d₂ between the fixpoints, and the wall-to-wall distance z (as measured in segment lengths) determine an approximate value for the Kuhn segment length k_l. We have simulated the movement of the chromosomes using molecular dynamics to obtain the expected distance distribution between the genetic loci in the absence of further attractive or repulsive forces. A comparison to biological experiments on Drosophila Melanogaster yields information on the parameters for our model. With the correct parameters it is possible to draw conclusions on the strength and range of the attraction that leads to pairing.

The goal of the current study was to optimize important process parameters for electrospinning polycaprolactone (PCL) for growing 3T3 fibroblasts. We hypothesized that the smallest obtainable fiber diameter would provide the best cell growth kinetics and we tested this hypothesis for three different process parameters: solution concentration, voltage and collector screen distance. Beaded structures were formed when using low concentration electrospinning solutions (8 wt% to 13 wt%), in which the viscosity ranged from 16.0 cP to 340.0 cP. In this concentration range, cell growth kinetics was impeded when using a high concentration of cells (8–10 × 10⁵). Higher PCL concentration led to an increase in the average fiber diameter from 400 nm to 1600 nm when PCL solution concentration changed from 15 wt% to 20 wt%. Although, the mean values indicated that cell growth kinetics were higher at the lower end of the concentration (15% as opposed to 20%) and this correlated with lower average fiber diameter, the results in this range were not statistically significant (p > 0.05). The average fiber diameter of scaffolds first decreased and then increased when electrospinning voltage was increased. The cell growth kinetics demonstrated that smaller average diameter PCL fiber scaffolds had higher growth kinetics than larger average diameter scaffolds with the best conditions obtained at 15 KV. By increasing the screen distance, the average fiber diameter decreased but had no significant impact on cell growth kinetics. In summary, the optimal parametric space for 3T3 fibroblast growth for our studies was electrospinning a 15 wt% PCL solution using 15 kV voltage and a 25 cm collector distance.

Recent intense interest in nanoparticle materials and nanoparticle-based contrast enhancement agents for biophysical applications gives new relevance to Mie scattering theory in its original context of application. The Mie theory still provides the most exact treatment of scattering from single nanoparticles of the noble metals. When recast in terms of modern electrodynamic formalism, the theory provides a concise closed-form representation for the scattered fields and also serves as a vehicle to elaborate the formal electrodynamic technique. The behavior of the Debye truncation condition for the multipole expansion is illustrated with numerical examples, clearly showing the features of the transition between the Rayleigh, dipole and higher order multipole approximations for the scattered fields. The classical Mie theory is an approximation in that only the transverse field components are included in the calculation. Extensions to the classical theory which include the effects of longitudinal fields are discussed and illustrated numerically. The example of scattering from multilayer composite particles is used to examine the feasibility of engineering spectral features of the scattering cross-section to target the requirements of specific applications.

Organelles are subcellular compartments or structures that typically carry out a defined set of functions within the cell. The functions of many organelles are known or predicted, but without knowing all the components of any recognized organelle it is difficult to fully understand them. Mass spectrometry-based proteomics now allows for routine identification of several hundreds or thousands of proteins in very complex samples; for cell biologists, organelles represent perhaps the most interesting class of cellular components to apply this new technology to. However, in order to analyze the proteome of an organelle it first must be purified, and the limitations in purifying any biological sample to homogeneity quickly become apparent to the vigilant mass spectrometrist. At the end of an organelle proteomic investigation, investigators are left with a long list of proteins whose location needs to be verified by an orthogonal method, a daunting prospect; or, they must accept an unknown and possibly very high level of incorrect localizations. Some of these caveats can be partially overcome by incorporating quantitative aspects into organelle proteomic studies. This review discusses some alternative approaches to organelle proteomics where questions of specificity and/or functional relevance are addressed by incorporating a quantitative dimension into the experiment.