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Literature DB >> 23345711

Structure based sequence dependent stiffness scale for trinucleotides: a direct method.

Abstract

A new set of stiffness parameters for all the 32trinucleotide units has been set up directly from thethree dimensional structures of DNA molecules. It wasobserved that GAC/GTC is the stiffest trinucleotideand ACC/GGT is the most flexible one. The averagestiffness values computed for a set of operatorsequences using the new parameters correlate very wellwith the protein-DNA binding specificity and bindingfree energy change of 434 repressor and Cro repressor,respectively. The new structure based stiffness scalecan explain the protein-DNA binding specificity to thelevel of 0.92.

Entities: Chemical

Keywords: DNA structure; Young's modulus; protein-DNA binding; sequence dependent; stiffness scale

Year: 2000 PMID： 23345711 PMCID： PMC3456187 DOI： 10.1023/A:1005250718139

Source DB: PubMed Journal: J Biol Phys ISSN： 0092-0606 Impact factor: 1.365

30 in total

Review 1. Modeling supercoiled DNA.

Authors: A V Vologodskii; M D Frank-Kamenetskii
Journal: Methods Enzymol Date: 1992 Impact factor: 1.600

2. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.

Authors: S B Smith; L Finzi; C Bustamante
Journal: Science Date: 1992-11-13 Impact factor: 47.728

3. Static and statistical bending of DNA evaluated by Monte Carlo simulations.

Authors: V B Zhurkin; N B Ulyanov; A A Gorin; R L Jernigan
Journal: Proc Natl Acad Sci U S A Date: 1991-08-15 Impact factor: 11.205

4. Protein secondary structure prediction in different structural classes.

Authors: M M Gromiha; S Selvaraj
Journal: Protein Eng Date: 1998-04

5. The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors: F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal: J Mol Biol Date: 1977-05-25 Impact factor: 5.469

6. Importance of DNA stiffness in protein-DNA binding specificity.

Authors: M E Hogan; R H Austin
Journal: Nature Date: 1987 Sep 17-23 Impact factor: 49.962

7. Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments.

Authors: Y Takeda; A Sarai; V M Rivera
Journal: Proc Natl Acad Sci U S A Date: 1989-01 Impact factor: 11.205

Structure based sequence dependent stiffness scale for trinucleotides: a direct method.

Review 1. Modeling supercoiled DNA.

2. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.

3. Static and statistical bending of DNA evaluated by Monte Carlo simulations.

4. Protein secondary structure prediction in different structural classes.

5. The Protein Data Bank: a computer-based archival file for macromolecular structures.

6. Importance of DNA stiffness in protein-DNA binding specificity.

7. Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments.

8. Twist and writhe of a DNA loop containing intrinsic bends.

9. The elasticity of a single supercoiled DNA molecule.

10. Hydrophobic character of amino acid residues in globular proteins.

Review 1. DNA curvature and flexibility in vitro and in vivo.

2. An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites.

3. Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins.