Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring

2005 ◽  
Vol 33 (4) ◽  
pp. 845-850 ◽  
Author(s):  
A.Y. Mulkidjanian ◽  
M.A. Kozlova ◽  
D.A. Cherepanov
Keyword(s):  
Molecular Dynamics ◽  
Electron Transfer ◽  
Rhodobacter Sphaeroides ◽  
Structural Information ◽  
Binding Pocket ◽  
Initial Position ◽  
Reaction Centre ◽  
Gate Control ◽  
Dynamics Simulations ◽  
Photosynthetic Reaction Centre

This review is focused on reactions that gate (control) the electron transfer between the primary quinone QA and secondary quinone QB in the photosynthetic reaction centre of Rhodobacter sphaeroides. The results on electron and proton transfer are discussed in relation to structural information and to the steered molecular dynamics simulations of the QB ring flip in its binding pocket. Depending on the initial position of QB in the pocket and on certain conditions, the rate of electron transfer is suggested to be limited either by the quinone ring flip or by the charge-compensating proton equilibration between the surface and the buried QB site.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

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