Biomedical subjects

Igor Rojdestvenski

Publications and source records attributed to Igor Rojdestvenski.

6 recordsLinked to original sources

PubMed2003

Segregation of the photosystems in higher plant thylakoids and short- and long-term regulation by a mesoscopic approach.

In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory-Huggins theory for binary mixtures and the McMillan-Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids.

Models, Biological↗

PubMed2003

Metabolic pathways in three dimensions.

MOTIVATION: Currently a substantial research effort is devoted to automated representation of metabolic and gene networks. Automatic visualization plays a significant role in such efforts, and becomes an important problem on its own. Graphical visualization of metabolic pathways has to be information dense and not 'overloaded', recognizable and unified, close to traditional and algebraically consistent. The use of three-dimensional 'virtual reality' visualizations may help to understand better the intricate topology of metabolic and regulatory networks. RESULTS: A system of visualizing metabolic networks as graphs in three-dimensional space by means of Virtual Reality Modeling Language (VRML) is presented. The system is based on an XML-compliant MNV ('Metabolic Network Visualizer') language, and comprises MNV language standard and parser, MNV to VRML translator, and interactive pathway constructor, all unified by the HTML graphic user interface. AVAILABILITY: The MNV can be accessed in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html SUPPLEMENTARY INFORMATION: The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html

Computer Graphics↗

PubMed2003

Segregation of the photosystems in thylakoids depends on their size.

Lateral segregation of two types of photosystems in thylakoid membranes of green plants is one of the key factors that provide the stability and fine-tuning of the light quanta supply by pigment proteins and non-cyclic electron transport. Due to this specific feature of the membrane structural organization, the photosynthetic units function in the green plants with optimal performance. In this report a mesoscopic theory is outlined to address the physical aspects of segregation phenomenon. Results of theoretical studies and computer simulations suggest that charge mismatch and the size difference between two photosystems in grana are most responsible for their lateral segregation, which is driven by the screened electrostatic and lipid-induced interactions. Comparative simulations of photosystems of different sizes show the crucial dependence of their ordering on a geometrical parameter. It seems that the size effect alone may prevent photosystems from segregated arrangement in cyanobacterial thylakoids.

Computer Simulation↗

PubMed2003

Lateral heterogeneity of photosystems in thylakoid membranes studied by Brownian dynamics simulations.

The aggregation and segregation of photosystems in higher plant thylakoid membranes as stromal cation-induced phenomena are studied by the Brownian dynamics method. A theoretical model of photosystems lateral movement within the membrane plane is developed, assuming their pairwise effective potential interaction in aqueous and lipid media and their diffusion. Along with the screened electrostatic repulsive interaction the model accounts for the van der Waals-type, elastic, and lipid-induced attractive forces between photosystems of different sizes and charges. Simulations with a priori estimated parameters demonstrate that all three studied repulsion-attraction alternatives might favor the local segregation of photosystems under physiologically reasonable conditions. However, only the lipid-induced potential combined with the size-corrected screened Coulomb interaction provides the segregated configurations with photosystems II localized in the central part of the grana-size simulation cell and photosystems I occupying its margins, as observed experimentally. Mapping of thermodynamic states reveals that the coexistence curves between isotropic and aggregated phases are the sigmoidlike functions regardless of the effective potential type. It correlates with measurements of the chlorophyll content of thylakoid fragments. Also the universality of the phase curves characterizes the aggregation and segregation of photosystems as order-disorder phase transitions with the Debye radius as a governing parameter.

Computer Simulation↗

PubMed2003

VRML metabolic network visualizer.

A successful date collection visualization should satisfy a set of many requirements: unification of diverse data formats, support for serendipity research, support of hierarchical structures, algorithmizability, vast information density, Internet-readiness, and other. Recently, virtual reality has made significant progress in engineering, architectural design, entertainment and communication. We experiment with the possibility of using the immersive abstract three-dimensional visualizations of the metabolic networks. We present the trial Metabolic Network Visualizer software, which produces graphical representation of a metabolic network as a VRML world from a formal description written in a simple SGML-type scripting language.

Computational Biology↗

PubMed2002

Segregation of photosystems in thylakoid membranes as a critical phenomenon.

The distribution of the two photosystems, PSI and PSII, in grana and stroma lamellae of the chloroplast membranes is not uniform. PSII are mainly concentrated in grana and PSI in stroma thylakoids. The dynamics and factors controlling the spatial segregation of PSI and PSII are generally not well understood, and here we address the segregation of photosystems in thylakoid membranes by means of a molecular dynamics method. The lateral segregation of photosystems was studied assuming a model comprising a two-dimensional (in-plane), two-component, many-body system with periodic boundary conditions and competing interactions between the photosystems in the thylakoid membrane. PSI and PSII are represented by particles with different values of negative charge. The pair interactions between particles include a screened Coulomb repulsive part and an exponentially decaying attractive part. The modeling results suggest a complicated phase behavior of the system, including quasi-crystalline phase of randomly distributed complexes of PSII and PSI at low ionic screening, well defined clustered state of segregated complexes at high screening, and in addition, an intermediate agglomerate phase where the photosystems tend to aggregate together without segregation. The calculations demonstrated that the ordering of photosystems within the membrane was the result of interplay between electrostatic and lipid-mediated interactions. At some values of the model parameters the segregation can be represented visually as well as by analyzing the correlation functions of the configuration.

Biophysical Phenomena↗