Nucleic-acid structural deformability deduced from anisotropic displacement parameters

The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.     

Population parameters. Acquisition and analysis of electrophoretic brain protein patterns by minicomputer-coupled densitometry.

Interfacing a minicomputer with a high resolution densitometer permits the online acquisition and statistical analysis of population parameters for experimental and control sample patterns of various macromolecules obtained by polyacrylamide gel electrophoresis. This technique, illustrated in this paper using protein from the brains of Japanese quail, enables the experimenter to make comparisons which were previously not readily available for electrophoresis.     

Biofilm image reconstruction for assessing structural parameters

The structure of biofilms can be numerically quantified from microscopy images using structural parameters. These parameters are used in biofilm image analysis to compare biofilms, to monitor temporal variation in biofilm structure, to quantify the effects of antibiotics on biofilm structure and to determine the effects of environmental conditions on biofilm structure. It is often hypothesized that biofilms with similar structural parameter values will have similar structures; however, this hypothesis has never been tested. The main goal was to test the hypothesis that the commonly used structural parameters can characterize the differences or similarities between biofilm structures. To achieve this goal (1) biofilm image reconstruction was developed as a new tool for assessing structural parameters, (2) independent reconstructions using the same starting structural parameters were tested to see how they differed from each other, (3) the effect of the original image parameter values on reconstruction success was evaluated, and (4) the effect of the number and type of the parameters on reconstruction success was evaluated. It was found that two biofilms characterized by identical commonly used structural parameter values may look different, that the number and size of clusters in the original biofilm image affect image reconstruction success and that, in general, a small set of arbitrarily selected parameters may not reveal relevant differences between biofilm structures.     

Low-cost two-dimensional gel densitometry

A major obstacle to full utilization of the powerful technique of two-dimensional (2-D) gel electrophoresis is the expense and complexity of quantifying the results. Using an analog-to-digital converter already present in the widely available Commodore 64 or Commodore 128 microcomputer, we have developed a 2-D gel densitometer (GELSCAN) which adds only $20.00 to the cost of the Commodore system (currently around $700.00). The system is designed to work with autoradiograms of 2-D gels. Spots of interest are identified visually and then positioned manually over a light source. A pinhole photoelectric sensor mounted in a hand-held, Plexiglas holder, or "mouse," is briefly rubbed over each spot. Maximum density of the spot is determined and its value is converted to counts per minute via an internal calibration curve which corrects for the nonlinear response of film to radiation. Local spot backgrounds can be subtracted and values can be normalized between gels to adjust for variation in amount of radioactivity applied or in exposure time. Reproducibility is excellent and the technique has some practical as well as theoretical advantages over other more complicated approaches to 2-D gel densitometry. In addition, the GELSCAN system can also be used for scanning individual bands in 1-D gels, quantitation of "dot-blot" autoradiograms and other tasks involving transmission densitometry.     

Three-dimensional biofilm image reconstruction for assessing structural parameters

Parameters representing three-dimensional (3D) biofilm structure are quantified from confocal laser-scanning microscope (CLSM) images. These 3D parameters describe the distribution of biomass pixels within the space occupied by a biofilm; however, they lack a direct connection to biofilm activity. As a result, researchers choose a handful of parameters without there being a consensus on a standard set of parameters. We hypothesized that a select 3D parameter set could be used to reconstruct a biofilm image and that the reconstructed and original biofilm images would have similar activities. To test this hypothesis, an algorithm was developed to reconstruct a biofilm image with parameters identical to those of the original CLSM image. We introduced an objective method to assess the reconstruction algorithm by comparing the activities of the original and reconstructed biofilm images. We found that biofilm images with identical structural parameters showed nearly identical activities and substrate concentration profiles. This implies that the set containing all common structural parameters can successfully describe biofilm structure. This finding is significant, as it opens the door to the next step, of finding a smaller standard set of biofilm structural parameters that can be used to compare biofilm structure.     

The structural dependence of amino acid hydrophobicity parameters

Amino acid hydrophobicity parameters, G_hp log P (partition coefficient) values, free energies of solution, G_sol and hydration numbers, are well correlated by equations derived from the relationship O_X = Aα_X + Lσ_IX + Sν_X + I_iX + H₁n_HX + H₂n_nX + b₀ where O is the quantity correlated; X denotes the amino acid side chain; α is a polarizability parameter; σ_I, a localized electrical effect parameter; ν, a steric parameter; i, an indicator variable which accounts for an ionic X ; n_H and n_n the number of OH or NH bonds and of full nonbonding orbitals in X, respectively, and b₀ is the intercept. The equation is based on the assumption that Δ_hp log P and ΔG_sol are all functions of the difference in intermolecular forces between the amino acid and some medium, and the amino acid and water. The parameters were chosen to model the intermolecular forces of interest.Generally the most important factor is α_x. This is followed by ν, i, and n_H. Least important is σ_I. ΔG_sol depends on α, n_H and n_n. Hydration numbers depend on i, n_H and n_n. The hydrophobicity of amino acid side chains is the result of a preference for a nonpolar medium as a increases and for a polar medium as i, n_H and σ_I increase. It is quantitatively accounted for by the model, and no special “hydrophobic bond” need be involved. The results show that log P values for amino acids are composite quantities whose composition is variable.     

Transmission densitometry of stained nitrocellulose paper

We report a simple solution to the problem of quantitative densitometry of stained nitrocellulose paper. By immersing the paper in a household lubricating oil of matching refractive index, the light-scattering properties of the paper are largely eliminated, allowing precise transmission densitometry in any flat bed densitometer. The method was evaluated on immunochemically stained Western blots of the proteinases cathepsins B and L. An approximately linear relationship was found between the integrated absorbance of the stained zone and the logarithm of the amount of protease applied to the polyacrylamide gel over the range of 150 to 350 ng of cathepsin B and 50 to 250 ng of cathepsin L.     

Lead effects on structural and functional cellular parameters in human red cells from a prenatal hematopoiesis stage

An attenuation (or reversion) of the prolytic effect of lead on neonatal red cells is observed in iso- or hypotonic low ionic strength media. This effect correlates neither with concomitant activation of K+ (Ca2+ or Pb2+) channels nor with volume reduction. Neonatal erythrocytes were used in this study owing to their greater cellular density, as compared with adult red cells, for the above mentioned channels. The attenuation-reversion effect would be mediated through lead interactions with the cytoskeleton, a structure that is the limiting factor for red cell lysis in low ionic strength media.     

Lipid structural order parameters (reciprocal of fluidity) in biomembranes derived from steady-state fluorescence polarization measurements

This paper presents an interpretation of fluorescence polarization measurements in lipid membranes which are labelled with the apolar probe 1,6-diphenyl-1,3,5-hexatriene. The steady-state fluorescence anisotropy, $\text{r}{}_{\mathrm{<mtext>S</mtext>}}$, is resolved into a fast decaying or kinetic component, $\text{r}{}_{\mathrm{<mtext>f</mtext>}}$, and an infinitely slow decaying or static component, $\text{r}{}_{\mathrm{\infty }}$. The latter contribution, which predominates in biological membranes, is exclusively determined by the degree of molecular packing (order) in the apolar regions of the membrane; $\text{r}{}_{\mathrm{\infty }}$ is proportional to the square of the lipid order parameter. An empirical relation between $\text{r}{}_{\mathrm{<mtext>S</mtext>}}$ and $\text{r}{}_{\mathrm{\infty }}$ is presented, which is in agreement with a prediction based on a theory of rotational dynamics in liquid crystals. This relation enabled us to estimate a lipid structural order parameter directly from simple steady-state fluorescence polarization measurements in a variety of isolated biological membranes. It is shown that major factors determining the order parameter in biomembranes are the temperature, the cholesterol and sphingomyelin content and (in a few systems) the membrane intrinsic proteins.     

Electron densitometry of stained virus particles

Methods are described for determining the relative mass of particles in electron microscope specimens through the measurement of photographic densities in recorded images. These methods were applied to a quantitative study of the amounts of electron stains that could be associated with the particles of tomato bushy stunt virus (BSV) and tobacco mosaic virus (TMV). In the pH range above 2 where the viruses are stable, the amount of stain absorbed is too small to produce adequate contrast in the electron microscope. Maximum stain absorption was achieved at pH about 1 where with several reagents and combinations of reagents the mass of BSV could be increased to about four times that of the unstained particles. Optimum results were obtained with phosphotungstic acid alone or in combination with Pt, Th, or La ions. Since the pH conditions for high stain absorption are normally destructive, morphology is satisfactorily preserved only when the phosphotungstic acid is applied in concentrations of 10 per cent or greater or when the use of destructive reagents is preceded by a preliminary fixation under mild conditions. Maximum staining of TMV increased the mass of the particles to about two times that of the unstained. Estimates of the mass of heavily stained BSV particles indicate that their density is 3.3 gm./cm.(3) The high internal hydration of BSV probably accounts for the greater stain absorption and penetration compared to those of TMV which has very low or zero internal hydration. Anomalous images resulting from the use of electron stains are shown and discussed.     

Sequence-dependent DNA structure: a database of octamer structural parameters

We have constructed the potential energy surfaces for all unique tetramers, hexamers and octamers in double helical DNA, as a function of the two principal degrees of freedom, slide and shift at the central step. From these potential energy maps, we have calculated a database of structural and flexibility properties for each of these sequences. These properties include: the values of each of the six step parameters (twist roll, tilt, rise, slide and shift), for each step of the sequence; flexibility measures for both decrease and increase in each property value from the minimum energy conformation for the central step; and the deviation from the path of a hypothetical straight octamer. In an analysis of structural change as a function of sequence length, we observe that almost all DNA tends to B-DNA and becomes less flexible. A more detailed analysis of octamer properties has allowed us to determine the structural preferences of particular sequence elements. GGC and GCC sequences tend to confer bistability, low stability and a predisposition to A-form DNA, whereas AA steps strongly prefer B-DNA and inhibit A-structures. There is no correlation between flexibility and intrinsic curvature, but bent DNA is less stable than straight. The most difficult deformation is undertwisting. The TA step stands out as the most flexible sequence element with respect to decreasing twist and increasing roll. However, as with the structural properties, this behavior is highly context-dependent and some TA steps are very straight.     

Effects of dimyristoylphosphatidylethanol on the structural parameters of neuronal membranes

Fluorescent probes located in different membrane regions were used to evaluate the effects of dimyristoylphosphatidylethanol (DMPEt) on the structural parameters (transbilayer rotational and lateral mobility, annular lipid fluidity and protein distribution) of synaptosomal plasma membrane vesicles (SPMV) from the bovine cerebral cortex. An experimental procedure was used based on selective quenching of 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1,3-di(1-pyrenyl)propane (Py-3-Py) by trinitrophenyl groups, and radiationless energy transfer from the tryptophans of membrane proteins to Py-3-Py. DMPEt increased the bulk lateral and rotational mobility, and annular lipid fluidity of SPMV lipid bilayers, and had a greater fluidizing effect on the outer monolayer than the inner monolayer. It also caused membrane proteins to cluster. These effects of DMPEt on neuronal membranes may be responsible for some, though not all, of the general anesthetic actions of ethanol.     

Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data

The implications of protein-water interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution. Starting from the atomic coordinates, by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably (Debye modeling, program HYDRO). By advanced modeling techniques the hydration can be taken into account appropriately: by some kind of rescaling procedures, by modeling a water shell, by iterative comparisons to experimental scattering curves (ab initio modeling) or by special hydration algorithms. In the latter case, the surface topography of proteins is visualized in terms of dot surface points, and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope. Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules. Among the tuning parameters, the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial. The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from X-ray crystallography, and the capability to predict hydration, structural and hydrodynamic parameters (hydrated volume, radius of gyration, translational diffusion and sedimentation coefficients) was compared with the findings generated by the water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.     

Definition of lipid membrane structural parameters from neutronographic experiments with the help of the strip function model.

Neutron diffraction is an effective method for investigating model and biological membranes. Yet, to obtain accurate structural information it is necessary to use deuterium labels and much time is needed to acquire experimental data as there are a large number of diffraction reflections to register. This paper offers a way to define the hydrophobic boundary position in lipid membranes with high accuracy and for this purpose it is sufficient to take into consideration three structural factors. The method is based on modeling the density of the neutron diffraction amplitude rho(x) in the direction of the bilayer plane normal by means of a strip function, but it also takes into consideration the fact that the multiplication of the strip function amplitude rho i by the step width zi-zi-1 makes the sum of neutron scattering amplitudes of the atoms included in the step region. On the basis of the analysis of a large number of experimental data for different membranes, the effectiveness of this method in the determination of the position of hydrophilic/hydrophobic boundary is demonstrated, including the case of various rho(x) modifications in the region of polar heads and also the different phase states of membranes. However, it is shown in the present paper that the strip function model is not an adequate instrument for the determination of other structural parameters of membranes.     

Expectations from structural genomics

Structural genomics projects aim to provide an experimental structure or a good model for every protein in all completed genomes. Most of the experimental work for these projects will be directed toward proteins whose fold cannot be readily recognized by simple sequence comparison with proteins of known structure. Based on the history of proteins classified in the SCOP structure database, we expect that only about a quarter of the early structural genomics targets will have a new fold. Among the remaining ones, about half are likely to be evolutionarily related to proteins of known structure, even though the homology could not be readily detected by sequence analysis.