The Institute of Protein Research of the Russian Academy of Sciences Is 50 Years Old

Here I introduce collection of review articles written by members of the Institute of Protein Research of the Russian Academy of Sciences. This collection commemorates the 50th anniversary of the Institute. The review articles cover a broad range of problems concerning the spatial structure of protein molecules, including the state of the molten globule, protein–RNA interactions, polysome and ribosome structure, the molecular colony method, and the original methods for studying the structure of proteins. Several of the reviews consider the practical use of knowledge about the structure of proteins and protein polymers. They reflect both the long experience of the authors and contemporary scientific data.     

Apple tree water relations studied by means of the relative rate of water flow in the trunk xylem

The results of long-term investigations of variations of rates of water transport through the trunk xylem, its diameter, the leaf water potential and the transpiration rate of the apple tree showed that the daily rhythm of the relative rate of moisture flow in the trunk xylem is an obvious index of the state of the apple tree water exchange. This enables us to determine the period of its unbalance at intensive transpiration as well as the level of the forming water deficit with high accuracy and operativeness. Moreover, by the daily curve of the relative rate of xylem flow one can judge the role of contribution of the trunk reservoir to transpiration.     

An undiscovered facet of hydraulic redistribution driven by evaporation—a study from a Populus tomentosa plantation

Maintaining the activity and function of the shallow root system of plants is essential for withstanding drought stress, but the associated mechanism is poorly understood. By investigating sap flow in 14 lateral roots (LRs) randomly selected from trees of a Chinese white poplar (Populus tomentosa) plantation receiving three levels of irrigation, an unknown root water transport mode of simultaneous daytime bi-directional water flow was discovered. This mode existed in five LRs confined to the surface soil without attached sinker roots. In the longer term, the bi-directional water flow was correlated with the soil water content. However, within the day, it was associated with transpiration. Our data demonstrated that bi-directional root sap flow occurred during the day, and was driven by evaporative demand, further suggesting the existence of circumferential water movement in the LR xylem. We named this phenomenon evaporation-driven hydraulic redistribution (EDHR). A soil-root water transport model was proposed to encapsulate this water movement mode. EDHR may be a crucial drought-tolerance mechanism that allows plants to maintain shallow root survival and activity by promoting root water recharge under extremely dry conditions.     

Sap flow measurements with some thermodynamic methods,flow integration within trees and scaling up from sample trees to entire forest stands

Sap flow measurement techniques and evaluation of data are reviewed. Particular attention is paid to the trunk segment heat balance (THB) and heat field deformation (HFD) methods based on 30 years experience. Further elaboration of sap flow data is discussed in terms of integrating flow for whole stems from individual measuring points, considering variation of radial patterns in sapwood and variation around stems. Scaling up of data from sets of sample trees to entire forest stands based on widely available biometric data (partially on remote sensing images) is described and evaluated with a discussion of the magnitude of errors, the routine procedure applicable in any forest stand and practical examples.     

Microtubules' interaction with cell cortex is required for their radial organization, but not for centrosome positioning

Microtubules in interphase mammalian cells usually form a radial array with minus-ends concentrated in the central region and plus-ends placed at the periphery. This is accepted as correct, that two factors determinate the radial organization of microtubules - the centrosome, which nucleate and anchor the microtubules minus-ends, and the interaction of microtubules with cortical dynein, which positions centrosome in the cell center. However, it looks as if there are additional factors, affecting the radial structure of microtubule system. We show here that in aged Vero cytoplasts (17 h after enucleation) microtubule system lost radial organization and became chaotic. To clear up the reasons of that, we studied centrosome activity, its position in the cytoplasts and microtubule dynamics. We found that centrosome in aged cytoplasts was still active and placed in the central region of the cytoplasm, while after total disruption of the microtubules it was displaced from the center. Microtubules in aged cytoplasts were not stabilized, but they lost their ability to stop to grow near cell cortex and continued to grow reaching it. Aged cytoplast lamellae was partially depleted with dynactin though Golgi remained compact indicating dynein activity. We conclude that microtubule stoppage at cell cortex is mediated by some (protein) factors, and these factors influence radial structure of microtubule system. It seems that the key role in centrosome positioning is played by dynein complexes anchored everywhere in the cytoplasm rather than anchored in cell cortex.     

Stress granules: RNP-containing cytoplasmic bodies springing up under stress. The structure and mechanism of organization

In this review recent data describing stress granules are summarized. Stress granules are specific RNA-containing structures in the cytoplasm of living cells which arise under stress conditions (e. g. heat shock, UV irradiation, energy depletion and oxidative stress). It became evident that stress granules accumulate non-canonical 48S initiation complexes and contain mRNA with associated proteins, small ribosomal subunits and some initiation factors. Stress granules are depleted with ternary complex and large ribosomal subunit. It's proposed that eIF2alpha phosphorylation and ternary complex decrease can be a trigger for stress granule formation. Shuttling nuclear and cytoplasmic RNA-binding protein TIA-1 plays a crucial role in this process. It's proposed that TIA-1 forms prion-like aggregates, and these aggregates are scaffolds for other components of stress granules. Cytoskeletal structures facilitate the accumulation of stress granule components in local cytoplasmic sites. Investigation of process of stress granule formation is important for understanding of cell reaction to stress and translation regulation mechanisms.     

Stochastic computer model of the cell microtubule dynamics

To study the effect of various factors on the microtubule system, one of the main cytoskeletal elements in the cell, which organizes the intracellular transport of different organelles and is necessary for mitosis and meiosis, a computer model of this system is created. Using a stochastic approach, the model describes the microtubule assembly/disassembly as a set of chemical reactions with certain rate constants. Microtubules are visualized in the computer program field, which makes the model vivid. The program imitates the dynamics and structure of the microtubule system with high reliability. The parameters calculated by the model correlate with the corresponding parameters of microtubules in living cells. This approach to modeling microtubules and similar systems continues to be developed so that the models would better describe living systems and the effect of a still broader range of factors could be studied.     

Stochastic computer model of cellular microtubule dynamics

A computer model of the system of microtubules has been developed to study the mechanisms of action of various factors on this system. The model describes the process of polymerization/depolymerization of microtubules as a set of chemical reactions with certain rate constants using a stochastic approach. Microtubules are visualized in the program field, which makes the model visual. The program imitates the dynamics and structure of the system of cellular microtubules with great, reliability. The parameters generated by the model correlate with the corresponding parameters of microtubules in living cells. We are going to develop this approach to modeling microtubules and similar structures to bring them into a better accord with living systems and to study the influence of various factors on these systems.     

Virions and the Coat Protein of the Potato Virus X Interact with Microtubules and Induce Tubulin Polymerization In Vitro

A study was made of the in vitro interactions of virions and the coat protein (CP) of the potato virus X (PVX) with microtubules (MT). Both virions and CP cosedimented with taxol-stabilized MT. In the presence of PVX CP, tubulin polymerized to produce structures resistant to chilling. Electron microscopy revealed the aberrant character of the resulting tubulin polymers (protofilaments and their sheets), which differed from MT assembled in the presence of cell MAP2. In contrast, PVX virions induced the assembly of morphologically normal MT sensitive to chilling. Virions were shown to compete with MAP2 for MT binding, suggesting an overlap for the MT sites interacting with MAP2 and with PVX virions. It was assumed that PVX virions interact with MT in vivo and that, consequently, cytoskeleton elements participate in intracellular compartmentalization of the PVX genome.     

Sap Flow Measurements in a Socotra Dragon’s Blood Tree (<Emphasis Type="Italic">Dracaena cinnabari</Emphasis>) in its Area of Origin

For the first time, in situ field measurements of sap flow were conducted in adult Dracaena cinnabari plant native to the arid tropical climate of Socotra Island. The heat field deformation (HFD) method was applied using both single and multi-point sensors to study azimuthal and radial sap flow variability in stem, roots and first-order branches over two weeks during a winter monsoon. The main aim of this work was to monitor sap flow in adult D. cinnabari in-situ to better understand its physiological adaptation to extreme arid environments. The second aim was to compare our results with earlier sap flow measurements in adult D. draco uing the same HFD method. The last question we wanted to answer was comparison of sap flow measurements in both, young and adult Dracaena species. We found that sap flow magnitude is low and of a similar range in all observed D. species. High sap flow variability was recorded in different parts of adult D. cinnabari plant which changed throughout the day responding to interplay between intrinsic and extrinsic water potential gradients induced by sunlight. Maximum sap flow levels had variable pattern around stem in response to sun exposure, similarly as it was observed in adult D. draco plant. Sensors installed tangentially in stem xylem showed that water transport in adult D. cinnabari may move in lateral direction. This work also presents several methodological aspects detected from earlier observations of dicots which proved to be more pronounced in adult D. species. These methodologies relate to interpreting negative sap flow rates in conjunction with established axial flow reversal during hydraulic redistribution usually occurring under low evaporative demands and dry soil. Conversely, flow reversal during the day under high evaporative demands and wet soil may designate lateral water movement induced by internal water redistribution.