The role of solvent viscosity in the dynamics of protein conformational changes

Science ◽  
1992 ◽  
Vol 256 (5065) ◽  
pp. 1796-1798 ◽  
Author(s):  
A Ansari ◽  
C. Jones ◽  
E. Henry ◽  
J Hofrichter ◽  
W. Eaton
ChemInform ◽  
2010 ◽  
Vol 24 (6) ◽  
pp. no-no
Author(s):  
A. ANSARI ◽  
C. M. JONES ◽  
E. R. HENRY ◽  
J. HOFRICHTER ◽  
W. A. EATON

2014 ◽  
Vol 191 ◽  
pp. 356-363 ◽  
Author(s):  
Gelsomina Longobucco ◽  
Gianluca Fasano ◽  
Michael Zharnikov ◽  
Luca Bergamini ◽  
Stefano Corni ◽  
...  

1995 ◽  
Vol 270 (22) ◽  
pp. 13112-13117 ◽  
Author(s):  
Matthew J. Ryle ◽  
William N. Lanzilotta ◽  
Leonard E. Mortenson ◽  
Gerald D. Watt ◽  
Lance C. Seefeldt

2019 ◽  
Author(s):  
Chandrabose Selvaraj ◽  
Gurudeeban Selvaraj ◽  
Satyavani Kaliamurthi ◽  
Dong-Qing Wei ◽  
Sanjeev Kumar Singh

AbstractThe present study clearly explains the dependency of inhibitory activities in SrtA inhibitors is closely related to protein conformational changes of SrtA from Bacillus anthracis B. anthracisSortase A (SrtA) protein anchors proteins by recognizing a cell wall sorting signal containing the amino acid sequence LPXTG In order to analyze conformational changes and the role of SrtA enzyme, especially the loop motions which situated proximal to the active site molecular dynamic simulation was carried out for 100ns. Particular loop is examined for its various conformations from the MD trajectories and the open/close lid conformations are considered for the enzyme activity validations. Experimentally verified SrtA inhibitors activity was analyzed through 3D-QSAR and Molecular docking approaches. Results indicate that, biological activity of SrtA inhibitors is closely related to the closed lid conformation of SrtA from Bacillus anthracis. This work may lead to a better understanding of the mechanism of action and aid to design a novel and more potent SrtA inhibitors.


Author(s):  
Xiaoyu Wang ◽  
Olga Boudker

ABSTRACTGlutamate transporters are essential players in glutamatergic neurotransmission in the brain, where they maintain extracellular glutamate below cytotoxic levels and allow for rounds of transmission. The structural bases of their function are well established, particularly within a model archaeal homologue, sodium and aspartate symporter GltPh. However, the mechanism of gating on the cytoplasmic side of the membrane remains ambiguous. We report Cryo-EM structures of GltPh reconstituted into nanodiscs, including those structurally constrained in the cytoplasm-facing state and either apo, bound to sodium ions only, substrate, or blockers. The structures show that both substrate translocation and release involve movements of the bulky transport domain through the lipid bilayer. They further reveal a novel mode of inhibitor binding and show how solutes release is coupled to protein conformational changes. Finally, we describe how domain movements are associated with the displacement of bound lipids and significant membrane deformations, highlighting the potential regulatory role of the bilayer.


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xiaoyu Wang ◽  
Olga Boudker

Glutamate transporters are essential players in glutamatergic neurotransmission in the brain, where they maintain extracellular glutamate below cytotoxic levels and allow for rounds of transmission. The structural bases of their function are well established, particularly within a model archaeal homolog, sodium, and aspartate symporter GltPh. However, the mechanism of gating on the cytoplasmic side of the membrane remains ambiguous. We report Cryo-EM structures of GltPh reconstituted into nanodiscs, including those structurally constrained in the cytoplasm-facing state and either apo, bound to sodium ions only, substrate, or blockers. The structures show that both substrate translocation and release involve movements of the bulky transport domain through the lipid bilayer. They further reveal a novel mode of inhibitor binding and show how solutes release is coupled to protein conformational changes. Finally, we describe how domain movements are associated with the displacement of bound lipids and significant membrane deformations, highlighting the potential regulatory role of the bilayer.


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