Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations-Reference-Cited by-同舟云学术

Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

Published:2019-06-16 Issue:7 Volume:25 Page:
ISSN:1610-2940
Container-title:Journal of Molecular Modeling
language:en
Short-container-title:J Mol Model

Author:

Anan Ryo,Nakamura Toshiya,Shimamura Kanako,Matsushita Yuki,Ohyama Tatsuya,Kurita Noriyuki

Publisher

Springer Science and Business Media LLC

Subject

Inorganic Chemistry,Computational Theory and Mathematics,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Catalysis

Link

http://link.springer.com/content/pdf/10.1007/s00894-019-4087-3.pdf

Reference33 articles.

1. Bell CE, Lewis M (2000) A closer view of the conformation of the lac repressor bound to operator. Nat Struct Biol 7:209–214

2. Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J Mol Biol 357:173–183

3. Pastan I, Crombrugghe BD, Perlman RL, Varmus HE (1970) Regulation of inducible enzyme synthesis in escherichia coli by cyclic adenosine 3′, 5′-monophosphate. Science 169:339–344

4. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356

5. Passner JM, Schullz SC, Steitz TA (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution. J Mol Biol 304:847–859

Cited by 5 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Comparative study of interaction energies between αIIbβ3 integrin and the peptidic, peptidomimetic and non-peptidic ligands by quantum mechanics FMO-PIEDA calculations;Chemical Papers;2023-06-10

2. Molecular Modeling Insights into the Structure and Behavior of Integrins: A Review;Cells;2023-01-14

3. 1,4-Dideoxy-1,4-imino-d- and l-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms;Organic & Biomolecular Chemistry;2022

4. Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding;Journal of Chemical Information and Modeling;2020-10-27

5. How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP3−in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5′ thio galactose substrates;Organic & Biomolecular Chemistry;2020