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Fluorescent Protein Spectral Properties

#3874


Simulation and Prediction of Spectral Properties of Fluorescent Proteins as Perspective Biomarkers for Studying Processes in Vivo

Tech Area / Field

  • BIO-CHM/Biochemistry/Biotechnology

Status
3 Approved without Funding

Registration date
20.05.2008

Leading Institute
VNIIEF, Russia, N. Novgorod reg., Sarov

Supporting institutes

  • Moscow State University / Department of Chemistry, Russia, Moscow

Collaborators

  • University of Guelph / College of Physical and Engineering Science, Canada, ON, Guelph

Project summary

The colour or fluorescent proteins are genetically coded biomarkers with accessible image properties important for biology, biotechnology and medicine. They are widely used for monitoring, localization and dynamics of proteins in living cells.

During recent few years, it has become evident that the chromophore spectral properties of certain fluorescent proteins could be changed by using post-translation modifications. The already accomplished research suggests the general strategy to develop new families of fluorescent proteins with enhanced fluorescence quantum yield and photo stability, namely, site-directed mutagenesis of definite points in proteins can be used for selective tuning theirs spectroscopic properties.

The practical goal of the project is to predict nontoxic proteins with stable fluorescence that could be used in bio-technology as more effective biomarker as compared with initial green fluorescent protein. Such experimental works are being performed in several laboratories of the world including Russian Federation.

The molecular dynamics (MD) method and quantum chemistry approaches will be used among the other methods to simulate the protein properties.

An experimental strategy of trials and errors in site-directed mutagenesis is expensive and time-consuming, therefore, molecular simulations may be efficiently applied to guiding searches for improving protein properties.

The use of reliable simulation methods including molecular dynamics (MD), quantum mechanics (QM) and hybrid approaches (QM/MM and QМ/МD) can provide a considerable effort economy.

The virtual computational tests for each fluorescent protein should include the following stages: (i) prediction of possible amino-acid sequences modifications near chromophore as compared with native structures or with already studied mutated structures, (ii) characterization of modified structures including atomic coordinate, (iii) calculation of chromophore spectral bands for mutated species.

The classical calculations using the MD method will be used to predict unknown three-dimensional structures of point-mutated proteins by considering as the reference points the crystal structures obtained in X-ray structure analysis for other protein compositions (native or mutated). The calculations using QМ and QМ/ММ methods are indispensable for theoretical evaluations of absorption and fluorescence bands.

The classical molecular dynamics method should be used in project activities. At present, this method is a well-developed methodology widely applied to the protein structures. AMBER, CHARMM, OPLS, GROMACS and other libraries will be employed to calculate interatomic and intermolecular interaction forces.

Initial coordinates of heavy atoms will be taken from the appropriate X-ray structures deposited in the Protein Data Bank. The hydrogen atoms will be added to these structures by using the corresponding software packages for molecular simulation. The calculations with classical MD method and hybrid QM/MD method are planned to be realized mainly in Sarov using the calculation resources and experience of the RFNC-VNIIEF group.

Besides, the modern quantum chemistry methods available in the last versions of PC GAMESS, namely, CASSCF, MCQDPT2, TDDFT, in combination with the original QМ/ММ methodology will be used to evaluate the absorption bands position and strength for the mutated fluorescent proteins, whose structures will be determined in preliminary MD calculations. We intend to use the modern QChem quantum-chemical package options as well. These calculations will be performed predominantly in the Laboratory of Chemical Cybernetics of M.V. Lomonosov Moscow state university in close cooperation with Sarov group. The close cooperation with experimental group from A.N. Bach Institute of Biochemistry is anticipated within the project. The most promising mutants predicted in computational experiments will be verified experimentally for theirs photo-physical and photochemical properties.

The collaboration with quantum chemistry group of Professor John D. Goddard, Department of Chemistry and Biochemistry, University of Guelph (Canada), should promote the successful development of the project, especially taking into account experience of this group in simulations of biomolecular processes.

The collaboration with highly qualified group for computational chemistry of Professor Anna Krylov from the University of Southern California (USA) should be an important element of the project. To calculate electronic behavior of chromophore in excited electronic states we plan to use the more modern Q-Chem software package parallel with PC GAMESS. Profesor Krylov is author of Q-Chem - modern quantum chemistry software package; she is also an advisor of Q-Chem, Inc.


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