Abstract：
:We have studied the statistical constraints on synonymous codon choice to evaluate various proposals regarding the origin of the bias in synonymous codon usage observed by Fiers et al. (1975), Air et al. (1976), Grantham et al. (1980) and others. We have determined the statistical dependence of the degenerate third base on either of its nearest neighbors in mitochondrial, prokaryotic, and eukaryotic coding sequences. We noted an increasing dependence of the third base on its nearest neighbors in moving from mitochondria to prokaryotes to eukaryotes. A statistical model assuming random equiprobable selection of synonymous codons was found grossly adequate for the mitochondria, but totally inadequate for prokaryotes and eukaryotes. A model assuming selection of synonymous codons reflecting a genomic strategy, i.e. the genome hypothesis of Grantham et al. (1980), gave a good approximation of the mitochondrial sequences. A statistical model which exactly maintains codon frequency, but allows the position of corresponding synonymous codons to vary was only grossly adequate for prokaryotes and totally inadequate for eukaryotes. The results of these simulations are consistent with the measures on experimental sequences and suggest that a "frequency constraint" model such as that of Grantham et al. (1980) may be an adequate explanation of the codon usage in mitochondria. However, in addition to this frequency constraint, there may be constraints on synonymous codon choice in prokaryotes due to codon context. Furthermore, any proposal to explain codon usage in eukaryotes must involve a constraint on the context of a codon in the sequence.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Lipman DJ,Wilbur WJdoi
10.1016/0022-2836(83)90063-3subject
Has Abstractpub_date
1983-01-25 00:00:00pages
363-76issue
3eissn
0022-2836issn
1089-8638pii
0022-2836(83)90063-3journal_volume
163pub_type
杂志文章abstract：:We have been able to observe the first step in bacteriophage infection, the docking of phage lambda to its membrane receptor maltoporin, at the single-particle level. High-resolution conductance recording from a single trimeric maltoporin channel reconstituted into a planar lipid bilayer has allowed detection of the s...
journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
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doi：10.1016/0022-2836(86)90485-7
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abstract：:A novel virus, ATV, of the hyperthermophilic archaeal genus Acidianus has the unique property of undergoing a major morphological development outside of, and independently of, the host cell. Virions are extruded from host cells as lemon-shaped tail-less particles, after which they develop long tails at each pointed en...
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pub_type： 杂志文章
doi：10.1006/jmbi.2001.4719
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journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
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doi：10.1006/jmbi.1995.0303
更新日期：1995-06-02 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2000.3551
更新日期：2000-03-17 00:00:00
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pub_type： 杂志文章
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更新日期：2020-05-15 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2001.4802
更新日期：2001-07-27 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(83)80275-7
更新日期：1983-04-25 00:00:00
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pub_type： 杂志文章
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更新日期：2002-11-15 00:00:00
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更新日期：2003-08-29 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：1984-05-05 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0200
更新日期：1996-04-12 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2014-10-23 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0267
更新日期：1996-05-17 00:00:00
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pub_type： 杂志文章
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更新日期：2003-03-21 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.2001.5289
更新日期：2002-01-25 00:00:00
abstract：:The Escherichia coli lac operon provides a classic paradigm for understanding regulation of gene transcription. It is now appreciated that lac promoter repression involves cooperative binding of the bidentate lac repressor tetramer to pairs of lac operators via DNA looping. We have adapted components of this system to...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.04.035
更新日期：2005-06-17 00:00:00
abstract：:DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groov...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：1996-02-09 00:00:00
