Protein folding information in nucleic acids which is not present in the genetic code

Annals of the New York Academy of Sciences

Volumn 1091, Issue , 2006, Pages 399-411

  Biro, Jan C ^a,b  

^a Homulus Foundation   (United States)

^b NONE   (United States)

Author keywords

Anfinsen; Codon; Complementarity; Folding energy; Protein design; Protein folding; Protein structure; RNA folding; Specific protein interaction; Translation

Indexed keywords

MESSENGER RNA; NUCLEIC ACID; PROTEIN; SINGLE STRANDED RNA;

AMINO ACID SEQUENCE; BASE PAIRING; CODON; CONFERENCE PAPER; EXON; GENETIC CODE; INTRON; NUCLEOTIDE SEQUENCE; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA STRUCTURE; STATISTICAL SIGNIFICANCE; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; GENETICS; THERMODYNAMICS;

GENETIC CODE; NUCLEIC ACID CONFORMATION; PROTEIN FOLDING; RNA, MESSENGER; THERMODYNAMICS;

EID: 33947572539     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1196/annals.1378.083     Document Type: Conference Paper

References (34)

1. ANFINSEN, C.B., R.R. REDFIELD, W.I. CHOATE, et al. 1954. Studies on the gross structure, cross-linkages, and terminal sequences in ribonuclease. J. Biol. Chem. 207: 201-210.
2. LEVINTHAL, C. 1969. How to fold graciously in Mossbauer spectroscopy in biological systems. In Proceedings of a Meeting held at Allerton House, Monticello, IL. P. Debrunner, J.C.M. Tsibris, & E. Munck, Eds.: 22-24. University of Illinois Press. Urbana, IL.
3. KLEPEIS, J.L. & A.C. FLOUDAS. 2003. ASTRA-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biochem. J. 85: 2119-2146.
4. WALTER, S. & J. BUCHNER. 2002. Molecular chaperones - cellular machines for protein folding. Angew Chem. Int. Ed. Engl. 41: 1098-1113.
5. KOMAR, A.A., A. KOMMER, I.A. KRASHENINNIKOV & A.S. SPIRIN. 1997. Cotranslational folding of globin. J. Biol. Chem. 272: 10646-10651.
6. THANARAJ, T.A. & P. ARGOS. 1996. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci. 5: 1973-1983.
7. BRUNAK, S. & J. ENGELBRECHT. 1996. Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. Proteins 25: 237-252.
8. GUPTA, S.K., S. MAJUMDAR, T.K. BHATTACHARYA & T.C. GHOSH. 2000. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem. Biophys. Res. Commun. 269: 692-696.
9. CHIUSANO, M.L., F. ALVAREZ-VALIN, M. DI GIULIO, et al. 2000. Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 261: 63-69.
10. GU, W., T. ZHOU, J. MA, X. SUN, Z. LU, et al. 2004. The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems 73: 89-97.
11. ERMOLAEVA, O. 2001. Synonymous codon usage in bacteria. Curr. Issues Mol. Biol. 3: 91-97.
12. BIRO, J.C., J.M. BIRO & A.M. BIRO. 2005. Hidden massages in hidden subsequences: a study on collagens. In 30th FEBS Congress - 9th IUBMB Conference, Budapest, Hungary, 2-7 July 2005 [Abstract].
13. KATZ, L. & C.B. BURGE. 2003. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res. 13: 2042-2051.
14. ZUKER, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.
15. BIRO, J.C. & G. FORDOS. 2005. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. BMC Bioinformatics 6: 170. Available at http://www.janbiro. com/downloads.
16. BIRO, J.C. 2005. SeqForm. Available at http://www.janbiro.com/ downloads.
17. BERMAN, H.M., J. WESTBROOK, Z. FENG, et al. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242. Available at http://www.pdb.org/.
18. BERMAN, H.M., W.K. OLSON, D.L. BEVERIDGE, et al. 1992. The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 63: 751-759. Available at http://ndbserver.rutgers.edu/index.html.
19. ADZHUBEI, I.A. & A.A. ADZHUBEI. 1999. ISSD Version 2.0: taxonomic range extended. Nucleic Acids Res. 27: 268-271. Available at http://www.protein.bio.msu.su/issd/.
20. BIRO, J.C., B. BENYO, C. SANSOM, et al. 2003. A common periodic table of codons and amino acids. Biochem. Biophys. Res. Commun. 306: 408-415.
21. SEFFENS, W. & D. DIGBY. 1999. mRNA has greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27: 1578-1584.
22. ORESIC, M., M. DEHN, D. KORENBLUM & D. SHALLOWAY. 2003. Tracing specific synonymous codon-secondary structure correlations through evolution. J. Mol. Evol. 56: 473-484.
23. D'ONOFRIO, G., T.C. GHOSH & G. BERNARDI. 2002. The base composition of the genes is correlated with the secondary structures of the encoded proteins. Gene 300: 179-187.
24. XIE, T. & D. DING. 1998. The relationship between synonymous codon usage and protein structure. FEBS Lett. 434: 93-96.
25. KUMAREVEL, T.S., M.M. GROMIHA & M.N. PONNUSWAMY. 2001. Distribution of amino acid residues and residue-residue contacts in molecular chaperons. Prep. Biochem. Biotechnol. 31: 163-183.
26. EILERS, M., A.B. PATEL, W. LIU & S.O. SMITH. 2002. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biochem. J. 82: 2720-2736.
27. GLASER, F., D.M. STEINBERG, I.A. VAKSER & N. BEN-TAL. 2001. Residue frequencies at protein-protein interfaces. Proteins Struct. Funct. Genet. 43: 89-102.
28. NAOR, D., D. FISHER, R.L. JERNIGAN, et al. 1996. Amino acid pair interchanges at spatially conserved locations. J. Mol. Biol. 256: 924-938.
29. AZARYA-SPRINZAK, E., D. NAOR, H.J. WOLFSON & R. NUSSINOV. 1997. Interchanges of spatially neighboring residues in structurally conserved environment. Protein Eng. 10: 1109-1122.
30. SINGER, M.S., G. VRIEND & R.P. BYWATER. 2002. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Eng. 15: 721-725.
31. SHAO, Y. & C. BYSTROFF. 2003. Predicting inter-residue contacts using templates and pathways. Proteins Struct. Funct. Genet. 53: 497-502.
32. BIRO, J. 1981. Comparative analysis of specificity in protein-protein interactions. Part II: the complementary coding of some proteins as the possible source of specificity in protein-protein interactions. Med. Hypotheses 7: 981-993.
33. SEGERSTEEN, U., H. NORDGREN & J.C. BIRO. 1986. Frequent occurrence of short complementary sequences in nucleic acids. Biochem. Biophys. Res. Commun. 139: 94-101.
34. HELA, J.R., G.W. ROBERTS, J.G. RAYNES, et al. 2002. Specific interactions between sense and complementary peptides: the basics for the proteomic code. Chembiochem 3: 136-151.