The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database

The use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies

Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish these structures but in most cases they act in opposite directions. This fact, together with being overall interactions with different ranges, provides a nuanced equilibrium also modulated by the need to comply with steric hindrances and geometric frustration effects. This review focuses on the utility of using the hydrophobic and electrical dipole moment vectors to describe the interactions that give rise to the structures of biological macromolecules. Although different definitions of both electric dipole and hydrophobic moments have been described in the literature, results obtained in biological assemblies demonstrate the principle of the biological membrane model. According to this model, postulated by our group, biological macromolecules tend to associate by aligning their hydrophobic moments in a similar manner to phospholipids in a membrane. Examples of both closed and open structures are used to assess the predictability of our model. We seek agreement between our results with those described in the current literature. The review ends with possible future projections using this formalism.

Chromosome aberration in typical biological systems under exposure to low- and high-intensity magnetic fields

The aim of this study was to investigate the response of chromosomes in typical human and plant cells under applied low-frequency magnetic fields at low and high intensities. Neuronal-like cells and roots of Allium sativum and Vicia faba were used to investigate chromosome's response to a static and 50 Hz magnetic fields at intensities ranging from 1 mT to 0.8 T, generated by two Helmholtz coils driven by direct current or alternate current voltage. Vertex spectrometer and Olympus microscope with camera were used. A significant decrease in intensity of the phosphate bands in the DNA infrared region was observed by FTIR spectroscopy analysis after exposure of neuronal-like cells to static and 50 Hz magnetic field at low intensity of 1 mT, which can be explained assuming that uncoiling and unpackaging of chromatin constituents occurred after exposure. This effect was directly observed by microscope in roots of Allium sativum and Vicia faba under exposure to a static magnetic field at high intensity of 0.8 T. These findings can be explained assuming that exposure to both low- and high-intensity magnetic fields of chromosomes in typical human and plant cells induces uncoiling and unpackaging of chromatin constituents, followed by chromosome alignment towards the direction of applied magnetic field, providing further demonstration that magnetic fields can induce the orientation of organic macromolecules even at low-intensity values.

The YlmG protein has a conserved function related to the distribution of nucleoids in chloroplasts and cyanobacteria

BACKGROUND

Reminiscent of their free-living cyanobacterial ancestor, chloroplasts proliferate by division coupled with the partition of nucleoids (DNA-protein complexes). Division of the chloroplast envelope membrane is performed by constriction of the ring structures at the division site. During division, nucleoids also change their shape and are distributed essentially equally to the daughter chloroplasts. Although several components of the envelope division machinery have been identified and characterized, little is known about the molecular components/mechanisms underlying the change of the nucleoid structure.

RESULTS

In order to identify new factors that are involved in the chloroplast division, we isolated Arabidopsis thaliana chloroplast division mutants from a pool of random cDNA-overexpressed lines. We found that the overexpression of a previously uncharacterized gene (AtYLMG1-1) of cyanobacterial origin results in the formation of an irregular network of chloroplast nucleoids, along with a defect in chloroplast division. In contrast, knockdown of AtYLMG1-1 resulted in a concentration of the nucleoids into a few large structures, but did not affect chloroplast division. Immunofluorescence microscopy showed that AtYLMG1-1 localizes in small puncta on thylakoid membranes, to which a subset of nucleoids colocalize. In addition, in the cyanobacterium Synechococcus elongates, overexpression and deletion of ylmG also displayed defects in nucleoid structure and cell division.

CONCLUSIONS

These results suggest that the proper distribution of nucleoids requires the YlmG protein, and the mechanism is conserved between cyanobacteria and chloroplasts. Given that ylmG exists in a cell division gene cluster downstream of ftsZ in gram-positive bacteria and that ylmG overexpression impaired the chloroplast division, the nucleoid partitioning by YlmG might be related to chloroplast and cyanobacterial division processes.

PHEMTO: protein pH-dependent electric moment tools

PHEMTO (protein pH-dependent electric moment tools) is released in response to the high demand in protein science community for evaluation of electrostatic characteristics in relations to molecular recognition. PHEMTO will serve protein scientists with new advanced features for analysis of protein molecular interactions: Electric/dipole moments, their pH-dependence and in silico charge mutagenesis effects on these properties as well as alternative algorithms for electric/dipole moment computation--Singular value decomposition of electrostatic potential (EP) to account for reaction field. The implementation is based on long-term experience--PHEI mean field electrostatics and PHEPS server for evaluation of global and local pH-dependent properties. However, PHEMTO is not just an update of our PHEPS server. Besides standard electrostatics, we offer new, advanced and useful features for analysis of protein molecular interactions. In addition our algorithms are very fast. Special emphasis is given to the interface--intuitive and user-friendly. The input is comprised of the atomic coordinate file in Protein Data Bank format. The advanced user is provided with a special input section for addition of non-polypeptide charges. The output covers actually full electrostatic characteristics but special emphasis is given to electric/dipole moments and their interactive visualization. PHEMTO server can be accessed at http://phemto.orgchm.bas.bg/.

Dielectric properties of Bauhinia monandra and concanavalin A lectin monolayers, part I

The dielectric properties of the galactose-binding lectins Bauhinia monandra (BmoLL) and Concanavalin A (Con A) were assessed by surface potential measurements of their spread monolayers on an aqueous subphase containing a monovalent electrolyte. For both lectins the curves of surface potential versus mean molecular area (DeltaV-A) and the independently recorded isotherms of surface pressure versus mean molecular area (Pi-A) were shown to be pH-dependent. As the subphase pH changed from 2 to 9, a noticeable trend to higher surface pressures accompanied the compression of the monolayers. Conversely, the surface potentials values of both monolayers decreased with increasing pH. For Con A, with the single exception of the pH 9 case, lowering the pH yielded DeltaV values higher than those for BmoLL. The contribution of the electric double layer (Psi0) to the overall DeltaV values at a given Pi (15 mN/m) was calculated using a modified Davies equation and assuming that at this surface pressure the monolayers of both studied lectins were stable. While at all studied pHs the Psi0 values for Con A exceeded those calculated for BmoLL, for both lectins they were insensitive to pH changes. This provided evidence that the reorientation of lectin molecules, during compression predominantly contributed to the alteration of the overall DeltaV values. The calculated Psi0 values made possible the evaluation of the dipole moments for BmoLL and Con A, and it has been estimated that the decrease in the pH of the subphase from 9 to 2 produced a 1.6-fold (twofold) increase in the value of for BmoLL (Con A). The differences in dielectric properties between the two film-forming lectins have been attributed to the differences in their structures. Indeed, the circular dichroism (CD) spectrum of Con A showed the predominance of beta-plated sheet structures while that of BmoLL was typically rich in alpha-helix structures.

Investigating the permanent electric dipole moment of β-lactoglobulin fibrils, using transient electric birefringence

Amyloid fibrils, which are polymeric assemblies of protein molecules, have been intensively studied on a structural level, yet due to complications such as the disorder within the molecules, several aspects of their structure remain mysterious. Similarly, the kinetics of assembly are not well understood. Here we investigate the electric dipole moment of beta-lactoglobulin fibrils, a model amyloid fibril system, by applying the technique of transient electric birefringence. This moment appears to be large, and comparable to the total moment of the constituent protein monomers if they were joined in a chain, head-to-tail, without changing conformation, suggesting an ordered joining of monomers in the fibril. Such an ordered assembly may have implications for the assembly mechanism of beta-lactoglobulin fibrils in particular, and amyloid fibrils in general.

Binding of TmHU to Single dsDNA as Observed by Optical Tweezers

Optical tweezers are employed to study the action of the histone-like protein from Thermotoga maritima (TmHU) on DNA at a single molecule level. Binding and disruption of TmHU to and from DNA are found to take place in discrete steps of 4-5 nm length and a net binding enthalpy of about 16kBT. This is in reasonable agreement with a microscopic model that estimates the extension of the binding sites of the protein and evaluates the energetics mainly for bending of the DNA in the course of interaction.

Moment-based prediction of DNA-binding proteins

Net charge, electric dipole moment and quadrupole moment tensors were calculated for 78 amino acid sequences from 62 representative DNA-binding proteins with known structures. It was found that the magnitudes of the moments of electric charge distribution in these chains differ significantly from those of a non-binding control data set. Net charge, net dipole moment and quadrupole moment could each distinguish binding and non-binding proteins with 82.6%, 77.4% and 73.7% accuracy by single-variable predictors without cross-validation. Using hybrid predictors with information of charge and both moments, the best predictions were 85.6% without cross-validation and 83.9% for the cross-validated data sets. This level of prediction accuracy obtained with these simple descriptors competes with the results obtained using more complex models including many descriptors. The coarse graining of atomic charges onto C(alpha) atoms did not reduce the prediction accuracy significantly. This result suggests that we can use C(alpha) coordinates derived from homology modeling to predict DNA-binding proteins. The speed and accuracy of this method, in combination with homology-based methods of structure prediction, should enhance genome-wide recognition of DNA-binding proteins.

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.