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| Eugene Krissinel, European Bioinformatics Institute |
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Dr. Eugene Krissinel, Curriculum Vitae
Education
1989 PhD in Chemical Physics from the USSR Academy of Sciences
Topics of research
* protein-protein interactions
* protein structure analysis and recognition
* numerical methods for differential equations, graph theory, computer science
* theory of diffusion-controlled processes
* theory of magnetic and spin effects in radical reactions
* theory of energy and electron transfers in solid and liquid solutions
* molecular dynamics
* dynamics of pollutants in natural water systems and atmosphere
Occupation history
2000 Researcher: European Bioinformatics Institute, Cambridge, UK
1997 Humboldt Fellow: University of Konstanz, Germany
1995 Scientific Associate: Argonne National Laboratory, Argonne, USA
1993 Visiting Scientist: University of Helsinki, Finland; Hebrew University of Jerusalem, Israel; Weizmann Institute of Sciences, Israel.
1990 Scientific Associate: Institute for Water and Environmental Problems, Russian Academy of Sciences
Selected publications
E. Krissinel and K. Henrick (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. D60, 2256-2268.
E. Krissinel and K. Henrick (2004) Common subgraph isomorphism detection by backtracking search. Software: Practice and Experience, 34, Iss. 6, p.591-607.
P.A. Frantsuzov, O.A. Igoshin and E.B. Krissinel (2000) Differential approach to the memory-function reaction kinetics, Chem. Phys. Lett. 317, Iss 3-4, 481-489.
E.B. Krissinel, A.I. Burshtein, N.N. Lukzen and U.E. Steiner (1999) Magnetic Field Effect as a probe of distance-dependent electron transfer in systems undergoing free diffusion, Molecular Physics 96, N7, 1083-1097.
E.B. Krissinel, J. Jellinek (1997) 13-atom Ni-Al alloy clusters:correlation between structural and dynamical properties, Chem. Phys. Lett., 272, Iss 3/4, 301-312.
E.B. Krissinel, N. Agmon (1996) The Spherically Symmetric Diffusion Problem, J. Comp. Chem., 17, Iss 9, 1085-1098.
E.B. Krissinel (1993) The CIDNP kinetics in homogeneous recombination of radicals, Chem. Phys., 169, N2, 207-217.
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Identification of biological units in protein crystals
Eugene Krissinel & Kim Henrick, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
PDB entries of protein structures solved by means of X-ray diffraction on protein crystals represent asymmetric units (ASU) of the crystals. In most instances, ASU may be chosen in many different ways and they do not necessarily coincide with the biological units, or stable protein assemblies that perform certain physiological functions. It is reasonable to expect that protein assemblies merge, rather than transform, during the crystallisation, therefore protein crystals do carry rather valuable data on the composition and geometry of biological units. Given that nearly 80% of PDB entries are obtained by means of protein crystallography and that direct experimental identification of assembly structure is difficult, detection of biological units in protein crystals is of considerable practical interest.
We propose a new approach to the problem from general principles of chemical thermodynamics, which is different from previous attempts [1,2] based on scoring of individual protein interfaces in crystal. We perform an exhaustive graph-theoretical search of all assemblies that are possible in a given crystal, and leave only those that appear to be thermodynamically stable. The stability estimate is based on the consideration of protein affinity and entropy change upon dissociation. Applied to PDB entries with oligomeric states known from the literature, our method gives 89% of correct predictions, which is higher than previously reported [2].
The method is implemented as a publicly available web server (http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver), which provides the assembly-related data for all PDB entries of structures solved by X-ray diffraction. The server can take PDB and mmCIF-formatted coordinate files for upload and calculate protein assemblies in real time (a few minutes in most instances). Detail, on-residue level, data on protein interactions, solvation energies, surface areas, hydrogen bonds and salt bridges are provided on output. Probable dissociation patterns of stable assemblies are also calculated. The calculated assemblies and individual crystal contacts (interfaces) may be visualised using the Rasmol software. The server includes a search facility for the identification of structurally equivalent protein interfaces in the PDB archive.
[1] Henrick, K.; Thornton, J. Trends Biochem. Sci., 1998, 23, 358.
[2] Ponstingl, H.; Kabir, T.; Thornton, J. J. Appl. Cryst. 2003, 36, 1116.
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