Genome Diversity Center

at the Institute of Evolution, University of Haifa

(Since August 2000)
Head: Edward N. Trifonov




What are the ancestral modules of proteins?


Simple considerations in polymer statistics suggest a primordial unit of protein structure - a closed loop of 25-30 residues.
This expectation is amply confirmed by crystal and sequence data.
The modern proteins are largely built of these sequence/structure units.

A preliminary catalogue of standard prototype modules, prepared through different techniques
(which are detailed in Berezovsky et al. JBSD 2003 and in Aharonovsky & Trifonov, JBSD 2005), can be found in the following link:
prototype elements database

Relevant references:

Frenkel, Z. M., Trifonov, E. N.
From protein sequence space to elementary protein modules,
Gene 408, 64-71 (2008)

Sobolevsky, Y, Frenkel, ZM, Trifonov EN.
Combinations of ancestral modules in proteins,
J Molec Evol 65, 640-650 (2007)

Frenkel, Z. M., Trifonov, E. N.,
Evolutionary networks in the formatted protein sequence space,
J Comput Biol 14, 1044-1057 (2007)

Frenkel, Z. M., Trifonov, E. N.
Walking through the protein sequence space: Towards new generation of the homology modeling.
Proteins Str Function Bioinf 67, 271-284 (2007)

Frenkel, Z. M., Trifonov, E. N.,
Walking through protein sequence space.
J Theor Biol 244, 77-80 (2007)

Sobolevsky, Y., Trifonov, E. N.,
Protein modules conserved since LUCA.
J Mol Evol 63, 622-634 (2006)

Sobolevsky, Y., Trifonov, E. N.,
Conserved sequences of prokaryotic proteomes and their compositional age.
J Mol Evol 61, 591-596 (2005)

Aharonovsky, E., Trifonov, E. N.,
Protein sequence modules.
J Biomol Str Dyn 23, 237-242 (2005)

Frenkel Z., Trifonov, E. N.,
Closed loops of TIM barrel protein fold,
J Biomol Str Dyn 22, 643-656 (2005)

Aharonovsky, E., Trifonov, E.N.,
Sequence structure of van der Waals locks in proteins,
J. Biomol. Struct. Dyn., Vol 22, No. 5, 545-554 (2005)
full table of 14638 signatures and consensus sequences.

Berezovsky, I. N., Kirzhner, A., Kirzhner, V. M., Trifonov, E. N.,
Spelling protein structure, J. Biomol. Struct. Dyn. 21, 327-339 (2003)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A., Rosenfeld, V. R., Trifonov, E. N.,
Protein sequences yield a proteomic code,
J. Biomol. Struct. Dyn. 21, 317-325 (2003)

Trifonov, E. N., Berezovsky, I. N., Evolutionary aspects of protein structure and folding,
Curr. Opinion Struct. Biol. 13, 110-114 (2003)

Trifonov, E. N., Kirzhner, A., Kirzhner, V.M., Berezovsky, I. N., An eye-opener to protein structure,
ComPlexUs 1, 29-37 (2003)

Berezovsky I. N., Trifonov, E. N., Protein structure: marriage with polymer physics, In "Protein structures. Kaleidoscope of Structural Properties and Functions", v. 1, Uversky V. N., Editor, Transworld Research Network, Trivandrum, India, pp 1-15 (2003)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A., Rosenfeld, V. R., Trifonov, E. N.,
Closed loops: persistence of the protein chain returns,
Prot. Eng. 15, 955-957 (2002)

Berezovsky, I. N., Trifonov, E. N.,
Flowering buds of globular proteins: transpiring simplicity of protein organization,
Comp Funct Genom 3, 525-534 (2002)

Berezovsky, I. N., Trifonov, E. N., Back to units of protein folding,
J. Biomolec. Str. Dyn. 20, 315-316 (2002)

Trifonov, E. N., Berezovsky, I. N., Molecular evolution from abiotic scratch,
FEBS Letters 527, 1-4 (2002)

Berezovsky, I. N., Trifonov, E. N.,
Loop fold structure of proteins: Resolution of Levinthal's paradox,
J. Biomolec. Str. Dyn. 20, 5-6 (2002)

Trifonov, E. N., Berezovsky, I. N., Proteomic code,
Molecular Biology 36, 239-243 (2002)

Berezovsky, I. N., Trifonov, E. N., Protein structure and folding: a new start.
J. Biomolec. Str. Dyn. 19, 397-403 (2001)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A, Trifonov, E. N.,
Protein folding: looping from hydrophobic nuclei.
Proteins: Structure, Function and Genetics 45, 346-350 (2001)

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)

Berezovsky, I. N., Trifonov, E. N., Loop fold nature of globular proteins.
Protein Engineering 14, 403-407 (2001)

Berezovsky, I. N., Trifonov, E. N.
Van der Waals locks: loop-n-lock structure of globular proteins.
JMB 307, 1419-1426 (2001)

Berezovsky, I. N., Trifonov, E. N., Evolutionary aspects of protein structure and folding.
Molecular Biology 35, 233-239 (English), 278-284 (Russian) (2001)

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)

Trifonov, E. N., Elucidating sequence codes: three codes for evolution.
Annals NY Acad. Sci. 870, 330-338 (1999).
(Title of the volume: Molecular Strategies in Biological Evolution, Ed. L. Caporale).