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Eugene I. Shakhnovich
Department of Chemistry and Chemical Biology
Harvard University
12 Oxford Street
Cambridge, MA 02138
Tel: (617) 495-4130
Fax: (617) 384-9228
E-mail: eugene@belok.harvard.edu
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PEOPLE: CURRENT LAB MEMBERS
Dr. Igor N. Berezovsky [cv]
Postdoctoral Fellow
Department
of Chemistry and Chemical Biology
Harvard University
12 Oxford St., M-105
Cambridge, MA 02138
Tel: (617) 496-4368
Fax: (617) 384-9228
inberez@fas.harvard.edu
Education
1993 M.Sc.
Physics, Moscow Engineering
Physics Institute
1997 Ph.D.
Biophysics, Moscow Institute of Physics
and Technology
Working experience
Research interests
My research interests are mainly in the field
of protein structure, stability and evolution.
I am also interested in the bioinformatics of complete
genomes, analysis of organismal level of evolution,
adaptation, and diversity.
Current work
My current project has two major directions: (i) Monte Carlo (MC) simulation
on globular proteins and (ii) bioinformatical analysis of complete genomes
and structural databases. We use MC simulation followed by the structural/energetic
analysis in order to detect relative stability of homologues from organisms
with different thermostability. The bioinformatics of the sequences of
complete genomes serves as an independent source of information about the
basic and major contributors to stability and adaptation to divergent environmental
conditions. The combination of the above techniques provides us with an
understanding of mechanisms of molecular evolution and point to the possible
ways of design and engineering of proteins with desirable features.
Publications
1995
1. Berezovskii, I.N. & Tumanyan, V.G.
Objective
method for isolating the domains of globular proteins.
Biophysics 40,
1181-1187 (1995)
1997
2. Berezovsky, I.N., Kilosanidze, G.T., Tumanyan,
V.G. & Kisselev, L.
COOH-decamers
in proteins are non-random.
FEBS
Letters 404, 140-142 (1997) PDF
3. Berezovskii, I.N., Esipova, N.G. & Tumanyan,
V.G.
Isolation
of the energy-significant parts of the globule and
the
hierarchy
of the domain structure of the protein
macromolecule.
Biophysics 42, 557-565
(1997)
4. Berezovsky, I.N., Tumanyan, V.G. & Esipova,
N.G.
Representation
of amino acid sequence in terms of interaction
energy
in protein globule.
FEBS
Letters 418, 43-46 (1997) PDF
1998
5. Berezovskii, I.N., Esipova, N.G. & Tumanyan,
V.G.
Spatial
distribution of directed interactions in globular
protein structures.
Biophysics 43,
367-377 (1998) PDF
6. Berezovskii, I.N., Esipova, N.G., Tumanyan,
V.G. & Namiot, V.A.
A
new approach to calculating of van der Waals interaction
energies
in protein macromolecules.
Dielectric constant as a physical parameter.
Biophysics 43,
909-916 (1998) PDF
1999
7. Berezovsky, I.N., Kilosanidze, G.T., Tumanyan,
V.G. & Kisselev, L.L.
Amino acid composition
of protein termini are biased in different manner.
Protein
Engineering 12, 23-30 (1999) PDF
8. Berezovsky, I.N., Namiot, V.A., Tumanyan, V.G. & Esipova,
N.G.
Hierarchy
of the interaction energy distribution in the spatial
structure
of globular proteins
and the problem of domain definition.
J.
Biomol. Struct. Dyn. 17, 133-155 (1999) PDF
2000
9. Berezovsky, I.N., Grosberg, A.Y. & Trifonov,
E.N.
Closed
loops of nearly standard size: common basic element
of protein structure.
FEBS
Letters 466, 283-286 (2000) PDF
10. Berezovsky, I.N., Esipova, N.G., Tumanyan,
V.G. & Namiot, V.A.
A
new approach for the calculation of the energy of
van der Waals
interactions
in macromolecules of globular proteins.
J.
Biomol. Struct. Dyn. 17, 799-809 (2000) PDF
11. Berezovsky, I.N., Esipova, N.G. & Tumanyan,
V.G.
Hierarchy
of regions of amino acid sequence in aspect of their
role
in the protein spatial structure.
J.
Comp. Biol. 7, 183-192 (2000) PDF
2001
12. Berezovsky, I.N. & Trifonov, E.N.
Evolutionary
aspects of protein structure and folding.
Mol.
Biol. 35, 233-239 (2001) PDF
13. Berezovsky, I.N. & Trifonov, E.N.
Van
der Waals locks: loop-n-lock structure of globular
proteins.
J.
Mol. Biol. 307, 1419-1426 (2001) PDF
14. Lamarine, M., Mornon, J.-P., Berezovsky I.N. & Chomilier,
J.
Distribution
of tightened end fragments of globular proteins statistically
match
that of topohydrophobic positions: towards an efficient
punctuation of protein folding?
Cell.
Mol. Life Sci. 58, 492-498 (2001) PDF
15. Berezovsky, I.N. & Trifonov, E.N.
Loop
fold nature of globular proteins.
Protein
Engineering 14, 403-407 (2001) PDF
16. Trifonov, E.N., Kirzhner, A., Kirzhner, V.M. & Berezovsky,
I.N.
Distinct
stages of protein evolution as suggested by protein
sequence analysis.
J.
Mol. Evol. 53, 394-401 (2001) PDF
17. Berezovsky, I.N., Kirzhner, A., Kirzhner,
V.M. & Trifonov, E.N.
Protein
folding: looping from the hydrophobic nuclei.
PROTEINS:
Structure, Function, and Genetics 45, 346-350(2001)
PDF
18. Berezovsky, I.N. & Trifonov, E.N.
Protein
structure and folding: a new start.
J.
Biomol. Struct. & Dyn. 19, 397-403 (2001) PDF
19. Fain, A.V., Berezovskii, I.N., Tchehov, V.O.,
Ukrainskii, D.L. & Esipova N.G.
Double
and bifurkated bonds in alpha-helices of globular
proteins.
Biophysics 46,
921-928 (2001) PDF1, PDF2, PDF3
2002
20. Trifonov, E.N. & Berezovsky, I.N.
Proteomic
code.
Mol.
Biol. 36, 239-243 (2002) PDF
21. Berezovsky, I.N.
Protein
structure: chapters which have been missed.
In:
Recent Research Developments
in
Protein Folding, Stability and Design.
(Eds.
M.M. Gromiha and S. Selvaraj) vol.1, pp.1-23
Transworld
Research Network, Trivandrum, India (2002) PDF
22. Berezovsky, I.N. & Trifonov, E.N.
Loop
fold structure of proteins: resolution of Levinthal's
paradox.
J.
Biomol. Struct. & Dyn. 20, 5-6 (2002) PDF
23. Trifonov, E.N. & Berezovsky, I.N.
Molecular
evolution from abiotic scratch.
FEBS
Letters 527, 1-4 (2002) PDF
24. Berezovsky, I.N. & Trifonov, E.N.
Back
to units of protein folding.
J.
Biomol. Struct. & Dyn. 20, 315-316 (2002) PDF
Link contains all Opinion Pieces on Levinthal
paradox and protein folding
published in the issue
25. Berezovsky, I.N. & Trifonov, E.N.
Flowering
buds of globular proteins: transpiring simplicity
of protein organization.
Comparative
and functional genomics 3, 525-534 (2002) PDF
26. Berezovsky, I.N., Kirzhner, V.M., Kirzhner,
A., Rosenfeld V.R. & Trifonov, E.N.
Closed
loops: persistence of the protein chain returns.
Protein
Engineering 15, 955-957 (2002) PDF
2003
27. Berezovsky, I.N., Kirzhner, A., Kirzhner,
V.M. & Trifonov, E.N.
An
eye-opener to protein structure.
ComPlexUs 1, 29-37
(2003) PDF
28. Trifonov, E.N. & Berezovsky, I.N.
Evolutionary
aspects of protein strcuture and folding.
Curr.
Opin. Struct. Biol. 13, 110-114 (2003) PDF
29. Berezovsky, I.N.
Discrete
structure of van der Waals domains in globular proteins.
Protein
Engineering 16, 161-167 (2003) PDF
30. Berezovsky, I.N., Kirzhner, A., Kirzhner,
V.M., Rosenfeld V.R. & Trifonov, E.N.
Protein
sequnces yeild a proteomic code.
J.
Biomol. Struct. & Dyn. 21, 317-325 (2003) PDF
31. Berezovsky, I.N., Kirzhner, A., Kirzhner,
V.M. & Trifonov, E.N.
Spelling
protein structure.
J.
Biomol. Struct. & Dyn. 21, 327-339 (2003) PDF
32. Berezovsky, I.N. & Trifonov, E.N.
Protein
structure: marriage with polymer statistics.
In:
Protein Structures.
Kaleidoscope
of Structural Properties and Functions.
(Ed.
V.N. Uversky), vol.1, pp. 1-15.
Transworld
Research Network, Trivandrum, India (2003) PDF
2004
33. Papandreou, N., Berezovsky, I.N., Lopes, A.,
Eliopoulos, E. & Chomilier, J.
Universal
positions in globular proteins. From observation
to simulation.
Eur.
J. Biochem. 271, 4762-4768 (2004) PDF
2005
34. Berezovsky, I.N. & Shakhnovich, E.I.
Physics
and evolution of thermophilic adaptation.
Proc.
Nat. Acad. Sci. USA 102, 12742-12747 (2005) PDF
35. Berezovsky, I.N., Chen, W.W., Choi, P.J. & Shakhnovich,
E.I.
Entropic
stabilization of proteins and its proteomic consequences.
PLoS
Comp. Biol. 1, 322-332 (2005) PDF
2006
36. Zeldovich, K.B., Berezovsky, I.N. & Shakhnovich, E.I.
Physical origins
of protein superfamilies.
J.
Mol. Biol. 357, 1335-1343 (2006) PDF
37. Schneider, G., Neuberger, G., Wildpaner, M., Tian, S., Berezovsky, I., & Eisenhaber,
F.
Application of a
sensitive collection heuristic for very large protein families:
evolutionary relationship between adipose triglyceride lipase (ATGL)
and classic mammalian lipases.
BMC
Bioinformatics 7: 164 (2006) PDF
2007
38. Zeldovich, K.B., Berezovsky, I.N. & Shakhnovich, E.I.
Protein and DNA sequence determinants of
thermophilic adaptation.
PLoS
Comp. Biol. 3, 62-72 (2007) PDF
39. Berezovsky, I.N., Zeldovich, K.B. & Shakhnovich, E.I.
Positive and negative design in stability and
thermal adaptation of natural proteins.
PLoS
Comp. Biol. 3, 498-507 (2007) PDF
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