Towards functional repertoire of the earliest proteins

References

• Berezovsky, I. N., Grosberg, A. Y., & Trifonov, E. N. (2000). Closed loops of nearly standard size: Common basic element of protein structure. FEBS Letters,466, 283–286.
   PubMed Web of Science ®Google Scholar
• Berezovsky, I. N., Kirzhner, A., Kirzhner, V. M., & Trifonov, E. N. (2003). Spelling protein structure. Journal of Biomolecular Structure & Dynamics,21, 327–339.
   PubMed Web of Science ®Google Scholar
• Berezovsky, I. N., & Trifonov, E. N. (2001). Van der Waals locks: Loop-n-lock structure of globular proteins. Journal of Molecular Biology,307, 1419–1426.
   PubMed Web of Science ®Google Scholar
• Berezovsky, I. N., & Trifonov, E. N. (2002). Flowering buds of globular proteins: Transpiring simplicity of protein organization. Comparative and Functional Genomics,3, 525–534.
   PubMedGoogle Scholar
• Berman, A. L., Kolker, E., & Trifonov, E. N. (1994). Underlying order in protein sequence organization. Proceedings of the National Academy of Sciences USA,91, 4044–4047.
   PubMed Web of Science ®Google Scholar
• Bourne, H. R., Sanders, D. A., & McCormick, F. (1991). The GTPase superfamily: Conserved structure and molecular mechanism. Nature,349, 117–127.
   PubMed Web of Science ®Google Scholar
• Cammer, S., & Carter, C. W., Jr (2010). Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase. Bioinformatics,26, 709–714.
   PubMed Web of Science ®Google Scholar
• Carter, C. W. (1993). Cognition, mechanism, and evolutionary relationships in aminoacyl-transfer RNA-synthetases. Annual review of biochemistry,62, 715–748.
   PubMed Web of Science ®Google Scholar
• Carter, C. W., & Duax, W. L. (2002). Did tRNA synthetase classes arise on opposite strands of the same gene?Molecular Cell,10, 705–708.
   PubMed Web of Science ®Google Scholar
• Chintapalli, S. V., Yew, B. K., Illingworth, C. J. R., Upton, G. J. G., Reeves, P. J., Parkes, K. E. B., & Reynolds, C. A. (2010). Closed loop folding units from structural alignments: Experimental foldons revisited. Journal of Computational Chemistry,31, 2689–2701.
   PubMed Web of Science ®Google Scholar
• Davidson, A. L., & Chen, J. (2004). ATP-binding cassette transporters in bacteria. Annual Reviews in Biochemistry,73, 241–268.
   PubMed Web of Science ®Google Scholar
• Forster, A. C., & Church, G. M. (2006). Towards synthesis of a minimal cell. Molecular Systems Biology, 2, article no. 45.
   Google Scholar
• Frenkel, Z. M., & Trifonov, E. N. (2008). From protein sequence space to elementary protein modules. Gene,408, 64–71.
   PubMed Web of Science ®Google Scholar
• Goncearenco, A., & Berezovsky, I. N. (2010). Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics,26, i497–i503.
   PubMed Web of Science ®Google Scholar
• Goto, N., Kurokawa, K., & Yasunaga, T. (2007). Analysis of invariant sequences in 266 complete genomes. Gene,401, 172–180.
   PubMed Web of Science ®Google Scholar
• Hopfner, K. P., Karcher, A., Shin, D. S., Craig, L., Arthur, L. M., Carney, J. P., & Tainer, J. A. (2000). Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell,101, 789–800.
   PubMed Web of Science ®Google Scholar
• Koonin, E. V. (2003). Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Reviews Microbiology,1, 127–136.
   PubMed Web of Science ®Google Scholar
• Kyrpides, N., Overbeek, R., & Ouzounis, C. (1999). Universal protein families and the functional content of the last universal common ancestor. Journal of Molecular Evolution,49, 413–423.
   PubMed Web of Science ®Google Scholar
• Lamarine, M., Mornon, J. P., Berezovsky, I. N., & Chomilier, J. (2001). Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: Towards an efficient punctuation of protein folding?Cellular and Molecular Life Sciences,58, 492–498.
   PubMed Web of Science ®Google Scholar
• Miller, S. L. (1987). Which organic compounds could have occurred on the prebiotic Earth?Cold Spring Harbour Symposia on Quantitative Biology,52, 17–27.
   PubMedGoogle Scholar
• Prakash, T., Ramakrishnan, C., Dash, D., & Brahmachari, S. K. (2005). Conformational analysis of invariant peptide sequences in bacterial genomes. Journal of Molecular Biology,345, 937–955.
   PubMed Web of Science ®Google Scholar
• Pupov, D. V., Barinova, N. A., & Kulbachinskiy, A. V. (2008). Analysis of RNA Cleavage by RNA Polymerases from Escherichia coli and Deinococcus radiodurans. Biochemistry (Moscow),73, 725–729.
   PubMed Web of Science ®Google Scholar
• Rossmann, M. G., Moras, D., & Olsen, K. W. (1974). Chemical and biological evolution of nucleotide-binding protein. Nature,250, 194–199.
   PubMed Web of Science ®Google Scholar
• Saladino, R., Crestini, C., Pino, S., Costanzo, G., & Di Mauro, E. (2012). Formamide and origin of life. Physics of Life Reviews,9, 84–104.
   PubMed Web of Science ®Google Scholar
• Smith, C. A., & Rayment, I. (1996). Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophysical Journal,70, 1590–1602.
   PubMed Web of Science ®Google Scholar
• Sobolevsky, Y., Frenkel, Z. M., & Trifonov, E. N. (2007). Combinations of ancestral modules in proteins. Journal of Molecular Evolution,65, 640–650.
   PubMed Web of Science ®Google Scholar
• Sobolevsky, Y., & Trifonov, E. N. (2005). Conserved sequences of prokaryotic proteomes and their compositional age. Journal of Molecular Evolution,61, 591–596.
   PubMed Web of Science ®Google Scholar
• Sobolevsky, Y., & Trifonov, E. N. (2006). Protein modules conserved since LUCA. Journal of Molecular Evolution,63, 622–634.
   PubMed Web of Science ®Google Scholar
• Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Hutchison, C. A., 3rd (1999). E-CELL: Software environment for whole-cell simulation. Bioinformatics,15, 72–74.
   PubMed Web of Science ®Google Scholar
• Tomoyasu, T., Yuki, T., Morimura, S., Mori, H., Yamanaka, K., Niki, H., & Ogura, T. (1993). The Escherichia coli FtsH Protein Is a Prokaryotic member of a Protein Family of Putative ATPases Involved in Membrane Functions, Cell Cycle Control, and Gene Expression. Journal of Bacteriology,175, 1344–1351.
   PubMed Web of Science ®Google Scholar
• Trifonov, E. N. (2002). Segmented genome: Elementary units of genome structure. Russian Journal of Genetics,38, 659–663.
   Web of Science ®Google Scholar
• Trifonov, E. N. (2004). The triplet code from first principles. Journal of Biomolecular Structure & Dynamics,22, 1–11.
   PubMed Web of Science ®Google Scholar
• Trifonov, E. N. (2009). Origin of the genetic code and of the earliest oligopeptides. Research in Microbiology,160, 481–486.
   PubMed Web of Science ®Google Scholar
• Trifonov, E. N., & Berezovsky, I. N. (2003). Evolutionary aspects of protein structure and folding. Current Opinion in Structural Biology,13, 110–114.
   PubMed Web of Science ®Google Scholar
• Trifonov, E. N., & Frenkel, Z. M. (2009). Evolution of protein modularity. Current Opinion in Structural Biology,19, 335–340.
   PubMed Web of Science ®Google Scholar
• Walker, J. E., Saraste, M., Runswick, M. J., & Gay, N. J. (1982). Distantly related sequences in the alpha-subunits and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO Journal,1, 945–951.
   PubMed Web of Science ®Google Scholar
• Wheelan, S. J., Marchler-Bauer, A., & Bryant, S. H. (2000). Domain size distributions can predict domain boundaries. Bioinformatics,16, 613–618.
   PubMed Web of Science ®Google Scholar
• Zaychikov, E., Martin, E., Denissova, L., Kozlov, M., Markovtsov, V., Kashlev, M., & Mustaev, A. (1996). Mapping of catalytic residues in the RNA polymerase active center. Science,273, 107–109.
   PubMed Web of Science ®Google Scholar