Conformational Dynamics of Biomolecules
`Electronic Structure and Conformational Dynamics of Biologically Active Organic Compounds and Proteins Related to Developing New Diagnostic Express Methods for Biomedical Applications
Tech Area / Field
- CHE-THE/Physical and Theoretical Chemistry/Chemistry
- PHY-OPL/Optics and Lasers/Physics
- MED-DID/Diagnostics & Devices/Medicine
8 Project completed
Senior Project Manager
Malakhov Yu I
B.I. Stepanov Institute of Physics, Belarus, Minsk
- Institute of Biophysics & Cell Engineering, Belarus, Minsk\nInstitute of Bioorganic Chemistry, Belarus, Minsk
- Technische Universität München / Lehrstunl fuer Theoretische Chemie, Germany, Garching\nCEA / Laboratoire Francis Perrin, France, Gif-sur-Yvette Cedex
Project summaryThe present Project is aimed at getting a new knowledge of biological model molecules, proteins, bioregulators, and also at developing new methods of express diagnostics for biomedical applications.
The stated objectives will be realized by conducting basic and applied studies at the act of performing the Project in the following science and technology lines.
(i) Experimental and theoretical studies of the electronic structure, structural conformations, and the intramolecular dynamics of inpidual biologically active organic compounds, proteins, bioregulators of brassinosteroid type with a high spectral resolution and over the time range from femtoseconds to milliseconds.
(ii) Spectroscopic and kinetic analysis of room-temperature tryptophan phosphorescence in the model systems and within the membrane proteins in an attempt to elucidate the mechanisms for interrelation between the dynamic structure and the physiological functions of protein macromolecules and to develop express methods for both screening of the protein structure and diagnostics of pathological damages (cataract) on the molecular-membrane level.
(iii) Synthesis and modification of brassinosteroids; use of NMR and FTIR spectroscopy, mass-spectrometry, and X-ray analysis for establishing the structure of biomolecules and their interaction with the environment; development of the biochemical fundamentals of physiological functions modulation of proteins when affected by brassinosteroid-type molecules; determination of “structure - physiological function” correlations; study of the proteins and lipids of human organ tissues in an effort to work out spectroscopic methods for diagnostics of pathological damages in oncological diseases.
State-of-the-art of the problem
Proteins play a decisive role in realizing the vital processes. The functioning of the proteins is closely related to the structural-dynamic state of their macromolecules. Therefore, the problem of studying the protein structure is central in biophysics, life sciences, biotechnologies, and medicine. Fluorescence methods are widespread in the studies of proteins. But nowadays, great interest is seen in studies of proteins using the phosphorescence method. However, this method is as a rule used for investigating proteins in solution, films, and crystals. In implementing the present Project the room-temperature tryptophan phosphorescence method will give unique grounds to investigate the membrane proteins directly in living functioning cells, not preliminarily separating the biomembranes from the cells.
First, the optical and laser-physical methods will be adopted to make comprehensive studies of both the electronic structure and the conformational properties of the biological model molecules that are the elements of protein macromolecules, and then those of membrane proteins and cells.
Another important problem is the development of the ways, how to affect the structure of proteins by bioregulators, whose biological activity is also governed by their electronic structure. In the course of experiments new bioregulators of brassinosteroid type will be synthesized. Their electronic structure will be widely investigated by physical and chemical methods at the first stage of work. It is planned to determine the efficiency of action of brassinosteroids upon the membrane proteins of the cells in order to evaluate their physiological activity.
From the detailed analysis of the state-of-the-art of the problems in biomedicine it follows that nowadays the evident advances are achieved in the field of application of laser and optical facilities for biomedicine needed for treatment of various diseases. At the same time the laser physical methods for diagnostics of pathological damages have not yet found a sufficiently wide use. At present, on the agenda is the problem to discover new bioregulators and pharmacological preparations. In this respect, the stated in the Project main lines of research are undoubtedly urgent.
Highly skilled specialists in the field of optics, laser physics, physical chemistry, and biophysics will participate in realizing the present Project. Among them are physicist, Academician of the National Academy of Sciences of Belarus and the Russian Academy of Sciences, Professor N.A. Borisevich (Project Scientific Leader); biophysicist, Corresponding-Member of NAS B, Professor V.M. Mazhul; biochemist, Corresponding-Member of NAS B, Professor V.A. Khripach; physicist, Professor G.B. Tolstorozhev (Project Manager) and also 2 Doctors and 7 Candidates of Science (Phys.& Math.).
Expected results and application
Implementation of the methods of kinetic laser spectroscopy over the time range from femtoseconds to milliseconds and also of those for supersonic jet-cooling of molecules to units of Kelvin with a view to get a high spectral resolution will yield new information on the primary photophysical and photochemical processes in the molecules of indole and tryptophan derivatives and also in biologically active brassinosteroids. Analysis of the conformational dynamics of biomolecules and study of solvated electrons and ion-radicals to be formed, when indole and tryptophan derivatives are subjected to photoexcitation in aqueous solution, will enable one to elucidate the role of the environment in realizing the biological functions of molecules.
Studies of the spectroscopic and kinetic properties of tryptophan room-temperature phosphorescence will enable one to make a detailed analysis of the structural-dynamic state of membrane proteins. Based on the results obtained, the express methods for screening of protein structures and for diagnostics of pathological damages (cataract) will be developed on the molecular-membrane level.
It is planned to synthesize, to modify new biologically active organic compounds of brassinosteroid type, and to investigate their spectral properties by the spectroscopic methods: NMR, FTIR, X-ray and mass-spectroscopy analysis. Detecting the differences in the IR spectra of the proteins and lipids in the healthy and cancer tissues of human organs will allow the methods for express diagnostics of oncological diseases to be realized. At the final stage, when the problems on the screening of the structural-dynamic state of the proteins are being solved, the efficiency of action of synthesized brassinosteroids on the cell membrane proteins will be determined in an effort to evaluate their physiological activity using the tryptophan phosphorescence method.
Potential demands for practical use of the Project results are suited to the modern needs of the social-economical requirements.
As additional applied developments on the Project, it is possible to consider the feasibility of designing a phosphorimeter for express diagnostics of changes in the intramolecular dynamics of proteins under pathological damage.
A plan of implementing the Project results in practice will be arranged as part of work. It is planned to get new patents.
The business network is considered as the essential points in the act of fulfilling the present Project.
The expected profits of the practical use of Project results are determined by the modern needs of biology, medicine, and biotechnology. Rights for the intellectual property of the tasks to be solved will be supported by the patents of Project participants.
Meeting ISTC Goals and Objectives
The Project profitably realizes the main ISTC tasks concerned with redirecting the attention of the “weapon” scientists to the peaceful activity and the decision of social-economical problems, with integrating the CIS scientists into the international research community. These goals can be attained by giving a group of the “weapon” scientists - who are the participants of this Project and have earlier designed lasers for the military industry (powerful lasers for material destruction, laser target detection systems, etc.) - a chance to concentrate their efforts on solving the modern problems in the fields of biophysics, biochemistry, and biomedicine.
Scope of activities
Studies in the above three research directions will be carried out at a time and logically complement each other. 19 co-workers will take part in implementing the Project. Among them are the specialists in physics, biophysics, and biochemistry from three Institutes of the National Academy of Sciences of Belarus: Institute of Molecular & Atomic Physics, Institute of Biophysics & Cell Engineering, and Institute of Bioorganic Chemistry. A total volume of work is 6537 man*days with an approximately equal portion according to years and quarters, including 4155 man*days for the “weapon” specialists. Work is pided into twelve periods - four quarters each year (12 quarters).
Foreign collaborators will take a direct part in discussing the results obtained and, if necessary, in correcting future plans of investigations. They will constantly receive the information on the obtained Project results and will be able to use it in their work. Meetings of Collaborators and Project participants at the International Conferences should be envisaged. A close cooperation between the Project participants and the Collaborators will be strengthened and broadened in the course of resolving the stated tasks in different areas of scientific exploration.
Technical approaches and methodology
A variety of optical and laser measuring techniques will be adopted to make experimental studies of the electronic structure and conformational dynamics of model biomolecules and proteins.
A femtosecond Sa: Ti laser spectrometer with 50 fs pulses and a picosecond YAG: Nd spectrometer with 3 ps pulses will be used for kinetic measurements of biomolecules characteristics. A fluorimeter will be employed for fluorescence spectra and kinetics measurements. A Sa: Ti laser phosphorimeter will be utilized for kinetic studies of biomolecules phosphorescence.
Biomolecules will be investigated using the highly time-resolved spectroscopic methods under the jet-cooling conditions up to units of Kelvin on a special laser-measuring facility.
NMR and FTIR spectroscopy methods, X-ray diffraction analysis, and mass-spectroscopy will be used, too. Of special importance are the methods of quantum chemistry and numerical simulation.
A particular stage of work will be concerned with the chemical synthesis of the objects of investigation, including brassinosteroids and their analogs of new type with the biological activity.
The basis for implementation of the Project tasks is the use of the interdisciplinary approaches in physics, chemistry, and biology. Studies of biologically important organic compounds and proteins are based on the long-standing experience of the Project participants in the field of designing and using ultrashort pulses lasers and lasers with a tuned narrow spectrum line.
The Project is related to the technology areas “Physics: Optics and Lasers (PHY-OPL)”, “Chemistry: Physical and Theoretical Chemistry (CHE-TEC)”, and “Biotechnology and Life Sciences: Biochemistry (BIO-BCH), Physiology (BIO-PHS)”.
The applied significance of the obtained Project results will realize the original methods for express diagnostics of proteins and cells under pathological damages in medicine (cataract, cancer). In practice, creating the technology of synthesizing biologically active brassinosteroids of new type will be important in an effort to evaluate their action upon the functioning of membrane proteins. It is planned to get patents.
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ISTC facilitates international science projects and assists the global scientific and business community to source and engage with CIS and Georgian institutes that develop or possess an excellence of scientific know-how.