Abstract：
:We have used gel electrophoresis to measure the progress of local denaturation in closed circular pBR322 DNA as a function of temperature and linking deficiency, delta Lk. Local denaturation is closely coupled to supercoiling in closed DNA, requiring statistical mechanical methods for analysis. We have applied these methods to the experimental data to evaluate the free energies for three associated molecular processes. These processes are changes in the residual linking deficiency, delta Lkr, initiation of local denaturation, and twisting of denatured strands about one another. Our results confirm the quadratic dependence of the supercoiling free energy upon delta Lk, with a free energy coefficient of 740/N kcal/mol at 37 degrees C, where N is the number of base-pairs. The free energy of initiation of denaturation is 10.2(+/- 0.7) kcal/mol. The free energy of interstrand twisting of denatured regions varies with the square of the twist density, with proportionality coefficient C tau = 1.62 (+/- 0.11) kcal/rad2 at 37 degrees C. We have also calculated the entropy and enthalpy of these three processes, using the temperature dependence of the respective free energies. We find that both the entropy and the enthalpy of supercoiling are positive and vary quadratically with delta Lk. The free energy of initiation of denaturation is independent of temperature, hence arises primarily from a change in enthalpy. The entropy and enthalpy of interstrand twisting of denatured regions are both positive, and the twisting force constant decreases with temperature. These results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Bauer WR,Benham CJdoi
10.1006/jmbi.1993.1669subject
Has Abstractpub_date
1993-12-20 00:00:00pages
1184-96issue
4eissn
0022-2836issn
1089-8638pii
S0022-2836(83)71669-4journal_volume
234pub_type
杂志文章abstract：:Precise regulation of dNTPs within the cellular nucleotide pool is essential for high accuracy of DNA replication and is critical for retaining the genomic integrity. Recently, human dCTPase (deoxycytidine triphosphatase), also known as DCTPP1 (human all-alpha dCTP pyrophosphatase 1), has been revealed to be a key pla...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2020-02-14 00:00:00
abstract：:Four previously isolated mutations in Salmonella phage P22 tailspike protein were used to study the relationship between protein stability, folding, and function. Tailspike protein binds and hydrolyzes the repetitive O-antigen structure in Salmonella lipopolysaccharide. Four mutations (V331G, V331A, A334V, A334I) are ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1999.3165
更新日期：1999-10-29 00:00:00
abstract：:Sleeping Beauty (SB) is the most active Tc1/mariner-type transposable element in vertebrates, and is therefore a valuable vector for transposon mutagenesis in vertebrate models and for human gene therapy. We have analyzed factors affecting target site selection of SB in mammalian cells, by generating transposition eve...
journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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pub_type： 杂志文章
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更新日期：1990-12-05 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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journal_title：Journal of molecular biology
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更新日期：2006-10-13 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0487
更新日期：1996-09-06 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1994.1195
更新日期：1994-02-25 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：2001-01-26 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90274-x
更新日期：1989-09-20 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(89)90476-2
更新日期：1989-06-05 00:00:00
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pub_type： 杂志文章
doi：10.1016/0022-2836(87)90132-x
更新日期：1987-09-20 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：1990-06-05 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1998.1727
更新日期：1998-05-08 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90258-4
更新日期：1984-12-25 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：2006-12-08 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1993.1403
更新日期：1993-07-20 00:00:00
abstract：:Proteorhodopsin (PR) is a recently discovered ubiquitous eubacterial retinal-binding light-driven proton pump. Almost 1000 PR variants are widely distributed in species of marine and freshwater bacteria, suggesting PR's important photobiological role. PR is a typical seven-transmembrane alpha-helical membrane protein ...
journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(92)90637-y
更新日期：1992-08-05 00:00:00
abstract：:Compatible solutes play a decisive role in the defense of microorganisms against changes in temperature and increases in osmolarity in their natural habitats. In Bacillus subtilis, the substrate-binding protein (SBP)-dependent ABC-transporter OpuA serves for the uptake of the compatible solutes glycine betaine (GB) an...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2006-03-24 00:00:00
abstract：:The lumazine synthase/riboflavin synthase complex of Bacillus subtilis consists of an icosahedral capsid of 60 beta subunits enclosing a core of 3 alpha subunits. The preparation of reconstituted hollow capsids consisting of 60 beta subunits and their crystallization in a hexagonal (space group P6(3)22) and in a monoc...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：1992-06-20 00:00:00
abstract：:Polyglutamine (polyQ) amyloid fibrils are observed in disease tissue and have been implicated as toxic agents responsible for neurodegeneration in expanded CAG repeat diseases such as Huntington's disease. Despite intensive efforts, the mechanism of amyloid toxicity remains unknown. As a novel approach to probing poly...
journal_title：Journal of molecular biology
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更新日期：2014-02-20 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.02.074
更新日期：2004-05-07 00:00:00
abstract：:Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein c...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2014.07.018
更新日期：2014-09-23 00:00:00
abstract：:The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, usin...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2007.02.044
更新日期：2007-05-04 00:00:00
