메뉴 건너뛰기




Volumn 40, Issue 18, 2012, Pages 8874-8882

Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEOME; PYRIDINE; PYRIMIDINE;

EID: 84867537613     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks679     Document Type: Article
Times cited : (36)

References (47)
  • 1
    • 0000053031 scopus 로고
    • On the coding of genetic information. Cold spring harbor symp
    • Nirenberg, M. W., Jones, O. W., Leder, P., Clark, F. C., Sly, S. and Petska, S. (1963) On the coding of genetic information. Cold Spring Harbor Symp. Quant. Biol., 28, 549-557.
    • (1963) Quant. Biol. , vol.28 , pp. 549-557
    • Nirenberg, M.1    Jones, O.2    Leder, P.3    Clark, F.4    Sly, S.5    Petska, S.6
  • 2
    • 63449132404 scopus 로고    scopus 로고
    • Origin and evolution of the genetic code: The universal enigma
    • Koonin, E. V. and Novozhilov, A. S. (2009) Origin and evolution of the genetic code: the universal enigma. IUBMB Life, 61, 99-111.
    • (2009) IUBMB Life , vol.61 , pp. 99-111
    • Koonin, E.V.1    Novozhilov, A.S.2
  • 3
    • 0034903851 scopus 로고    scopus 로고
    • Translation: In retrospect and prospect
    • DOI 10.1017/S1355838201010615
    • Woese, C. R. (2001) Translation: in retrospect and prospect. RNA-a Publicat. RNA Soc., 7, 1055-1067. (Pubitemid 32726905)
    • (2001) RNA , vol.7 , Issue.8 , pp. 1055-1067
    • Woese, C.R.1
  • 5
    • 0031940595 scopus 로고    scopus 로고
    • Detection of transmembrane helical segments at the nucleotide level in eukaryotic membrane protein genes
    • Lesnik, T. and Reiss, C. (1998) Detection of transmembrane helical segments at the nucleotide level in eukaryotic membrane protein genes. Biochem. Mol. Biol. Int., 44, 471-479. (Pubitemid 28143812)
    • (1998) Biochemistry and Molecular Biology International , vol.44 , Issue.3 , pp. 471-479
    • Lesnik, T.1    Reiss, C.2
  • 6
    • 66149134063 scopus 로고    scopus 로고
    • Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mrnas
    • Prilusky, J. and Bibi, E. (2009) Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc. Natl Acad. Sci. USA, 106, 6662-6666.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 6662-6666
    • Prilusky, J.1    Bibi, E.2
  • 7
    • 34848918150 scopus 로고    scopus 로고
    • Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function
    • DOI 10.1016/j.cell.2007.08.003, PII S0092867407010227
    • Lecuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P. and Krause, H. M. (2007) Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell, 131, 174-187. (Pubitemid 47498530)
    • (2007) Cell , vol.131 , Issue.1 , pp. 174-187
    • Lecuyer, E.1    Yoshida, H.2    Parthasarathy, N.3    Alm, C.4    Babak, T.5    Cerovina, T.6    Hughes, T.R.7    Tomancak, P.8    Krause, H.M.9
  • 9
    • 79959676389 scopus 로고    scopus 로고
    • The ribosome uses two active mechanisms to unwind messenger rna during translation
    • Qu, X. H., Wen, J. D., Lancaster, L., Noller, H. F., Bustamante, C. and Tinoco, I. (2011) The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature, 475, 118-121.
    • (2011) Nature , vol.475 , pp. 118-121
    • Qu, X.1    Wen, J.2    Lancaster, L.3    Noller, H.4    Bustamante, C.5    Tinoco, I.6
  • 10
    • 77956663124 scopus 로고    scopus 로고
    • Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation
    • Zhang, F. L., Saha, S., Shabalina, S. A. and Kashina, A. (2010) Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science, 329, 1534-1537.
    • (2010) Science , vol.329 , pp. 1534-1537
    • Zhang, F.1    Saha, S.2    Shabalina, S.A.3    Kashina, A.4
  • 11
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick, F. H. C. (1968) The origin of the genetic code. J. Mol. Biol., 38, 367-379.
    • (1968) J. Mol. Biol. , vol.38 , pp. 367-379
    • Crick, F.H.C.1
  • 12
    • 17844405021 scopus 로고    scopus 로고
    • Coevolutlon theory of genetic code at age thirty
    • DOI 10.1002/bies.20208
    • Wong, J. T. (2005) Coevolution theory of the genetic code at age thirty. Bioessays, 27, 416-425. (Pubitemid 40592598)
    • (2005) BioEssays , vol.27 , Issue.4 , pp. 416-425
    • Wong, J.T.-F.1
  • 13
    • 0026327996 scopus 로고
    • A quantitative measure of error minimization in the genetiC-code
    • Haig, D. and Hurst, L. D. (1991) A quantitative measure of error minimization in the genetiC-code. J. Mol. Evol., 33, 412-417.
    • (1991) J. Mol. Evol. , vol.33 , pp. 412-417
    • Haig, D.1    Hurst, L.D.2
  • 15
    • 0013824051 scopus 로고
    • On the evolution of the genetic code
    • Woese, C. R. (1965) On the evolution of the genetic code. Proc. Natl Acad. Sci. USA, 54, 1546-1552.
    • (1965) Proc. Natl Acad. Sci. USA , vol.54 , pp. 1546-1552
    • Woese, C.R.1
  • 16
    • 0014228783 scopus 로고
    • Fundamental nature of genetic code: Prebiotic interactions between polynucleotides and polyamino acids or their derivatives
    • Woese, C. R. (1968) Fundamental nature of genetic code: prebiotic interactions between polynucleotides and polyamino acids or their derivatives. Proc. Natl Acad. Sci. USA, 59, 110-117.
    • (1968) Proc. Natl Acad. Sci. USA , vol.59 , pp. 110-117
    • Woese, C.R.1
  • 17
    • 0014674857 scopus 로고
    • Models for the evolution of codon assignments
    • Woese, C. R. (1969) Models for the evolution of codon assignments. J. Mol. Biol., 43, 235-240.
    • (1969) J. Mol. Biol. , vol.43 , pp. 235-240
    • Woese, C.R.1
  • 18
    • 0031799551 scopus 로고    scopus 로고
    • Amino acids as RNA ligands: A direct-RNA-template theory for the code's origin
    • DOI 10.1007/PL00006357
    • Yarus, M. (1998) Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol., 47, 109-117. (Pubitemid 28307578)
    • (1998) Journal of Molecular Evolution , vol.47 , Issue.1 , pp. 109-117
    • Yarus, M.1
  • 19
    • 72449163457 scopus 로고    scopus 로고
    • Rna-amino acid binding: A stereochemical era for the genetic code
    • Yarus, M., Widmann, J. J. and Knight, R. (2009) RNA-amino acid binding: a stereochemical era for the genetic code. J. Mol. Evol., 69, 406-429.
    • (2009) J. Mol. Evol. , vol.69 , pp. 406-429
    • Yarus, M.1    Widmann, J.J.2    Knight, R.3
  • 20
    • 77952335310 scopus 로고    scopus 로고
    • Imprints of the genetic code in the ribosome
    • Johnson, D. B. and Wang, L. (2010) Imprints of the genetic code in the ribosome. Proc. Natl Acad. Sci. USA, 107, 8298-8303.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 8298-8303
    • Johnson, D.B.1    Wang, L.2
  • 22
    • 0015910584 scopus 로고
    • Evolution of the genetic code
    • Woese, C. R. (1973) Evolution of the genetic code. Naturwissenschaften, 60, 447-459.
    • (1973) Naturwissenschaften , vol.60 , pp. 447-459
    • Woese, C.R.1
  • 23
    • 44249087590 scopus 로고    scopus 로고
    • On the physical basis of the amino acid polar requirement
    • Mathew, D. C. and Luthey-Schulten, Z. (2008) On the physical basis of the amino acid polar requirement. J. Mol. Evol., 66, 519-528.
    • (2008) J. Mol. Evol. , vol.66 , pp. 519-528
    • Mathew, D.C.1    Luthey-Schulten, Z.2
  • 24
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the universal protein resource (uniprot)
    • The UniProt Consortium
    • The UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Research, 40, D71-D75.
    • (2012) Nucleic Acids Research , vol.40
  • 26
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite a web server for clustering comparing biological sequences.
    • Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 28
    • 1342310510 scopus 로고    scopus 로고
    • Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
    • DOI 10.1110/ps.03431704
    • Moelbert, S.,-emberly, E. and Tang, C. (2004) Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Protein Sci., 13, 752-762. (Pubitemid 38252572)
    • (2004) Protein Science , vol.13 , Issue.3 , pp. 752-762
    • Moelbert, S.1    Emberly, E.2    Tang, C.3
  • 31
    • 67651204443 scopus 로고    scopus 로고
    • Strong correlation between statistical transmembrane tendency and experimental hydrophobicity scales for identification of transmembrane helices
    • Zhao, G. and London, E. (2009) Strong correlation between statistical transmembrane tendency and experimental hydrophobicity scales for identification of transmembrane helices. J. Membrane. Biol., 229, 165-168.
    • (2009) J. Membrane. Biol. , vol.229 , pp. 165-168
    • Zhao, G.1    London, E.2
  • 32
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • DOI 10.1093/bioinformatics/bti541
    • Dosztá nyi, Z., Csizmó k, V., Tompa, P. and Simon, I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434. (Pubitemid 41222453)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 33
    • 0034736513 scopus 로고    scopus 로고
    • Consensus temporal order of amino acids and evolution of the triplet code
    • DOI 10.1016/S0378-1119(00)00476-5, PII S0378111900004765
    • Trifonov, E. N. (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene, 261, 139-151. (Pubitemid 32103531)
    • (2000) Gene , vol.261 , Issue.1 , pp. 139-151
    • Trifonov, E.N.1
  • 36
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino-acids - Side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution
    • Radzicka, A. and Wolfenden, R. (1988) Comparing the polarities of the amino-acids - side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry, 27, 1664-1670.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 37
    • 0015217634 scopus 로고
    • Solubility of amino acids and 2 glycine peptides in aqueous ethanol and dioxane solutions - Establishment of a hydrophobicity scale
    • Nozaki, Y. and Tanford, C. (1971) Solubility of amino acids and 2 glycine peptides in aqueous ethanol and dioxane solutions - establishment of a hydrophobicity scale. J. Biol. Chem., 246, 2211-2217.
    • (1971) J. Biol. Chem. , vol.246 , pp. 2211-2217
    • Nozaki, Y.1    Tanford, C.2
  • 38
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino-acid-sequences of membrane-proteins
    • Engelman, D. M., Steitz, T. A. and Goldman, A. (1986) Identifying nonpolar transbilayer helices in amino-acid-sequences of membrane-proteins. Annu. Rev. Biophys. Bio., 15, 321-353.
    • (1986) Annu. Rev. Biophys. Bio. , vol.15 , pp. 321-353
    • Engelman, D.1    Steitz, T.A.2    Goldman, A.3
  • 39
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D. and Mclachlan, A. D. (1986) Solvation energy in protein folding and binding. Nature, 319, 199-203. (Pubitemid 16128783)
    • (1986) Nature , vol.319 , Issue.6050 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 40
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 41
    • 84863967724 scopus 로고    scopus 로고
    • Evolution of protein synthesis from an rna world
    • Noller, H. F. (2012) Evolution of protein synthesis from an RNA world. Cold Spring Harb Perspect Biol., 4, 1-U20.
    • (2012) Cold Spring Harb Perspect Biol. , vol.4
    • Noller, H.F.1
  • 42
    • 22244445209 scopus 로고    scopus 로고
    • Origins of the genetic code: The escaped triplet theory
    • DOI 10.1146/annurev.biochem.74.082803.133119
    • Yarus, M., Caporaso, J. G. and Knight, R. (2005) Origins of the genetic code: the escaped triplet theory. Annu. Rev. Biochem., 74, 179-198. (Pubitemid 40995505)
    • (2005) Annual Review of Biochemistry , vol.74 , pp. 179-198
    • Yarus, M.1    Caporaso, J.G.2    Knight, R.3
  • 43
    • 67649992002 scopus 로고    scopus 로고
    • Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
    • Butler, T., Goldenfeld, N., Mathew, D. and Luthey-Schulten, Z. (2009) Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys. Rev. E, 79, 060901.
    • (2009) Phys. Rev. E , vol.79 , pp. 060901
    • Butler, T.1    Goldenfeld, N.2    Mathew, D.3    Luthey-Schulten, Z.4
  • 45
    • 20344381944 scopus 로고    scopus 로고
    • Translational autoregulation of thymidylate synthase and dihydrofolate reductase
    • Tai, N., Schmitz, J. C., Liu, J., Lin, X., Bailly, M., Chen, T. and Chu, E. (2004) Translational autoregulation of thymidylate synthase and dihydrofolate reductase. Front. Biosci., 9, 2521-2526.
    • (2004) Front. Biosci. , vol.9 , pp. 2521-2526
    • Tai, N.1    Schmitz, J.2    Liu, J.3    Lin, X.4    Bailly, M.5    Chen, T.6    Chu, E.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.