The mouse factor Zif268, known also as early growth response protein EGR-1, is a classical representative for the Cys2His2 transcription factor family. It is required for binding the RNA polymerase with operator dsDNA to initialize the transcription process. We have shown that only in this family of total six Zn-finger protein families the Zn complex plays a significant role in the protein-DNA binding. Electrostatic feature of this complex in the binding of factor Zif268 from Mus musculus with operator DNA has been considered. The factor consists of three similar Zn-finger units which bind with triplets of coding DNA. Essential contacts of the factor with the DNA phosphates are formed by three conservative His residues, one in each finger. We describe here the results of calculations of the electrostatic potentials for the Zn-Cys2His2 complex, Zn-finger unit 1, and the whole transcription factor. The potential of Zif268 has a positive area on the factor surface, and it corresponds exactly to the binding sites of each of Zn-finger units. The main part of these areas is determined by conservative His residues, which form contacts with the DNA phosphate groups. Our result shows that the electrostatic positive potential of this histidine residue is enhanced due to the Zn complex. The other contacts of the Zn-finger with DNA are related to nucleotide bases, and they are responsible for the sequence-specific binding with DNA. This result may be extended to all other members of the Cys2His2 transcription factor family.

Methods and algorithms to analyze surfaces of globular and fibrillar proteins, DNA, and RNA have been developed. These methods for the construction of maps of fragments of these objects in the original cylindrical projection developed herein essentially broaden the possibilities for studying the distribution of charges and surface topography of biological structures. This approach significantly supplements the qualitative characteristics of methods of visualizing biopolymer structures.

Methods and algorithms for analysis of surfaces of globular and fibrillar proteins, DNA, and RNA have been developed. These methods of constructing cards of fragments of these objects, in the cylindrical projection original developed herein, essentially expand possibilities for studying distribution of charges and a relief of a surface of biological structures. This approach essentially supplements qualitative characteristics of methods of visualization of biopolymer structures.

Abstract The spatial arrangement of interfaces between homeodomain transcription factors and operator DNA has been considered. We analyzed the binding contacts for a representative set of 22 complexes of homeodomain transcription factors with a double-stranded operator DNA in the region of the major groove. It was shown that the recognition of DNA by the recognizing α-helix of protein is governed by two contact groups. Invariant protein-DNA group of contacts includes six contacts, formed by atomic groups of coding and non-coding DNA chains with the groups of amino acids. The recognizing α-helix forms contacts by polar groups of residues Trp2 (NE1), Asn5, and Lys9 with the canonical sequence T1A2A3T4 of the coding DNA chain, and contacts by residues Lys0, Arg7 and Lys11 with the sequence A4X5X6X7 of a non-coding DNA chain, where X is any nucleotide. Variable protein-DNA group of contacts comprises two groups bound with the sequence T3A4X5X6 of the non-coding DNA-chain. These contacts are mainly with the bases and specify the binding pattern of individual homeodomains. The invariant contact group represents a recognition pattern for transcription factors of the homeodomain family: multiple adenine-asparagine contact and six position-specific phosphate contacts mainly with lysine or arginine. Within this group, we have found three most significant invariant contacts which allow deducing the recognition rules for homeodomains. These rules are inherent for different taxonomic groups of the homeodomain family and can distinguishing members of this family from any other family of transcription factors.

At present, after 120 years of theoretical and experimental studies, the problem of the genome macroarchitecture as the highest level of interphase chromosome organization in the nucleus of somatic cells is still open. The problem of spatial organization of interphase chromosomes in the haploid nucleus of germ cells has never been studied. The three-dimensional modeling of spatial organization of part of the haploid genome (the second chromosome) in Drosophila melanogaster mature sperms is performed using mathematical methods and the methods of visualization of macromolecular biostructures. The frequency and arrangement of inversion breaks for 72 structural vg mutants were used as genetic markers under the assumption that both ends of each inversion are brought together and form loops of an appropriate size. For taking into account the spatial proximity and visualization of loop structures of the chromosome, modern methods of three-dimensional modeling with application of splines, Open GL library, Delphi, and Gmax were used. According to the model developed, the whole second chromosome in the nucleus of mature sperms is probably arranged in the form of the megarosette- loop structure, which can be assumed to be the fundamental ordered form of the genome macroarchitecture in haploid germs of higher organisms.