V. A. Namiot

Magnetoliposomes: Another principle of cell sorting

Liposomes bearing anti-fibronectin antibodies and associated with ferromagnetic particles bound firmly to the surface of mouse embryo fibroblasts. Upon binding magnetoliposomes, the cells could be sorted in a magnetic field.

Hierarchy of the Interaction Energy Distribution in the Spatial Structure of Globular Proteins and the Problem of Domain Definition

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density. Various levels of hierarchy in the protein spatial structure are discerned by analysis of the energy interaction between structural units of different scales. Thus the level of energy hierarchy plays role of sole parameter, and the method obviates the use of complicated geometrical criteria with numerous fitting parameters. The algorithm readily and accurately locates domains formed by continuous segments of the protein chain as well as those comprising non-sequential segments, sets no limit to the number of segments in a domain. We have analyzed 309 protein structures. Among 277 structures for which our results could be compared with the domain definitions made in other works, 243 showed complete or partial coincidence, and only in 34 cases the domain structures proved substantially different. The domains delineated with our approach may coincide with reference definition at different levels of the globule hierarchy. Along with defining the domain structure, our approach allows one to consider the protein spatial structure in terms of the spatial distribution of the interaction energy in order to establish the correspondence between the hierarchy of energy distribution and the hierarchy of structural elements.

Physical model for monitoring the position of a quantum particle

Abstract A simple model for continuously measuring the position of a quantum particle is considered and compared with the phenomenological path-integral approach. The model contains a net of quantum oscillators having a finite range of interaction with the particle. Tracing out the variables of the measuring oscillators, one obtains a density matrix for the particle undergoing the influence of the continuous measurement. This density matrix coincides with that obtained earlier with the help of the path-integral method.

HOW TO VISUALIZE A QUANTUM TRANSITION OF A SINGLE ATOM

Abstract The previously proposed visualization of Rabi oscillations of a single atom by a continuous fuzzy measurement of energy is specified for the case of a single transition between levels caused by a π-pulse of a driving field. An analysis in the framework of the restricted-path-integral approach (which reduces effectively to a Schrodinger equation with a complex Hamiltonian) shows that the measurement gives reliable information about the system evolution, but the probability of the transition becomes less than unity. In addition an experimental setup is proposed for continuously monitoring the state of an atom by observation of electrons scattered by it. It is shown how this setup realizes a continuous fuzzy measurement of the atom energy.

On the optimal folding of protein molecules

The process of formation of a globular structure by a long molecular chain has been examined. In this process, various regions of the chain interact with one another. We classify the contacts thus formed as “correct” and “erroneous” ones. The correct contacts are those characteristic of the final native globular structure. All other contacts can be treated as erroneous. It is demonstrated that globule formation may proceed actually without formation and subsequent decay of erroneous contacts. Our model permits avoiding examination of numerous erroneous variants inasmuch as the regions of the chain that form correct contacts enter “long-range” interactions that at the same time can be highly selective. The existence of interactions of this kind facilitates the mutual approach and interaction of just those regions of the chain that yield correct contacts. Based on database analysis, it is shown that the model is valid not only for abstract structures but also for real polypeptide chains capable of forming protein globules and helical fibrils.

A new approach for the calculation of the energy of van der Waals interactions in macromolecules of globular proteins.

Abstract Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation. The approach takes into account local peculiarities of protein spatial structure and physical-chemical characteristics of amino acid residues and molecular groups.

Nanotechnologies in medicine

The paper discusses some already available nanotechnology-based methods for treating oncological diseases. Consideration is given to the potentialities of essentially new approaches whereby devices built into cells could govern their behavior. Conceptually, such “controlled” cells can be caused to fight against tumors.

On the possibility of using ‘dusty’ plasma for X-ray generation by ultra-relativistic electrons

Abstract The possibility of using ‘dusty’ plasma, in which the dusty particles form a crystalline lattice, as an undulator for X-ray generation by ultra-relativistic electrons is discussed. For increasing effect, it is suggested that ‘magnetic dusty crystals’ be used by introducing the ferro-magnetic particles in plasma.

The structural and physicochemical characteristics of conformationally stable α-helical oligopeptides

An analysis of conformationally stable (conformationally conservative) tetrapeptides selected from protein structures that are deposited in the PDBSelect database has been carried out. The set contained 943 different tetrapeptide sequences, with each sequence occurring at least five times in different fragments of protein structure. Analysis of conformations based on DSSP markup revealed that the conformation of most peptides (900 of 943 sequences) was α-helical, while 43 sequences had different conformations, of which the left-handed polyproline II helix is especially worth mentioning. The physicochemical properties of conformationally stable peptides from each subset were inferred from the average hydropathicity of the tetrapeptides. The results of the calculations revealed “neutral” hydropathicity of the conformationally stable oligopeptides. Notably, the distribution of hydropathicity values for the conformationally stable peptides was considerably narrower than those for the control sets of peptides. Thus, conformationally stable oligopeptides form a specific group of local protein structures with nearly uniform conformational and physicochemical properties. The theory of specific long-range interactions that was previously developed by the authors of the present study assumes such peptides to be well adapted for efficient mutual recognition of molecules.

On general physical aspects of a problem of in vivo effective detection and recognition of malignant cells

A fundamentally new recognition method of bio-objects (in particular malignant cells) that escape the immune system supervision control is suggested. Recognition of such bio-objects should be carried out by the unified complex consisting of several molecular groups (for example, antibodies) bound to each other, each group identifies on a surface of this bio-object its target binding site. The choice of such targets is determined by a specific surface-antigen expression profiling. Thus the efficiency of recognition appears to be many times higher, than that in a situation when these molecular groups do not form a uniform complex and operate separately. The possibilities of destruction of such recognized cells are discussed.