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On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study
被引:7
作者:

Masone, Diego
论文数: 0 引用数: 0
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机构:
Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina
Univ Nacl Cuyo, Fac Ingn, Mendoza, Argentina Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina

Uhart, Marina
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina

Bustos, Diego M.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina
Univ Nacl Cuyo, Fac Ciencias Exactas & Nat, Mendoza, Argentina Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina
机构:
[1] Univ Nacl Cuyo, CONICET, Inst Histol & Embriol IHEM, CC56, RA-5500 Mendoza, Argentina
[2] Univ Nacl Cuyo, Fac Ingn, Mendoza, Argentina
[3] Univ Nacl Cuyo, Fac Ciencias Exactas & Nat, Mendoza, Argentina
来源:
关键词:
MOLECULAR-DYNAMICS;
CRYSTAL-STRUCTURE;
PROTEIN;
SIMULATIONS;
BINDING;
CHARMM;
GROMACS;
GUI;
DATABASE;
BUILDER;
D O I:
10.1038/srep46114
中图分类号:
O [数理科学和化学];
P [天文学、地球科学];
Q [生物科学];
N [自然科学总论];
学科分类号:
07 ;
0710 ;
09 ;
摘要:
Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-todomain interactions, IDRs follow a 'fly-casting' model including 'induced folding'. Unfortunately, it is only possible to experimentally explore initial and final states. However, the complete movie of conformational changes of protein regions and their characterization can be addressed by in silico experiments. Here, we simulate the binding of two proteins to describe how the phosphorylation of a single residue modulates the entire process. 14-3-3 protein family is considered a master regulator of phosphorylated proteins and from a modern point-of-view, protein phosphorylation is a three component system, with writers (kinases), erasers (phosphatases) and readers. This later biological role is attributed to the 14-3-3 protein family. Our molecular dynamics results show that phosphorylation of the key residue Thr31 in a partner of 14-3-3, the aralkylamine N-acetyltransferase, releases the flycasting mechanism during binding. On the other hand, the non-phosphorylation of the same residue traps the proteins, systematically and repeatedly driving the simulations into wrong protein-protein conformations.
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Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation
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Intrinsic disorder is a key characteristic in partners that bind 14-3-3 proteins
[J].
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;
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.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
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论文数: 0 引用数: 0
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[7]
A model for the interaction between plant GAPN and 14-3-3ζ using protein-protein docking calculations, electrostatic potentials and kinetics
[J].
Bustos, DM
;
Iglesias, AA
.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING,
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h-index: 0
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[8]
Evolutionary conservation in multiple faces of protein interaction
[J].
Choi, Yoon Sup
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Yang, Jae-Seong
;
Choi, Yonghwan
;
Ryu, Sung Ho
;
Kim, Sanguk
.
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[9]
Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding
[J].
Diaz-Moreno, Irene
;
Hollingworth, David
;
Frenkiel, Thomas A.
;
Kelly, Geoff
;
Martin, Stephen
;
Howell, Steven
;
Garcia-Mayoral, MariaFlor
;
Gherzi, Roberto
;
Briata, Paola
;
Ramos, Andres
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NATURE STRUCTURAL & MOLECULAR BIOLOGY,
2009, 16 (03)
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Diaz-Moreno, Irene
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[10]
The binding mechanisms of intrinsically disordered proteins
[J].
Dogan, Jakob
;
Gianni, Stefano
;
Jemth, Per
.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS,
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Dogan, Jakob
论文数: 0 引用数: 0
h-index: 0
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Uppsala Univ, Dept Med Biochem & Microbiol, SE-75123 Uppsala, Sweden Uppsala Univ, Dept Med Biochem & Microbiol, SE-75123 Uppsala, Sweden

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论文数: 0 引用数: 0
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Uppsala Univ, Dept Med Biochem & Microbiol, SE-75123 Uppsala, Sweden Uppsala Univ, Dept Med Biochem & Microbiol, SE-75123 Uppsala, Sweden