scholarly journals Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties

2018 ◽  
Vol 148 (14) ◽  
pp. 145101 ◽  
Author(s):  
Mert Gur ◽  
Elizabeth A. Blackburn ◽  
Jia Ning ◽  
Vikram Narayan ◽  
Kathryn L. Ball ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Mutations ◽  
Enzymatic Properties ◽  
Conformational States ◽  
Dynamics Simulations ◽  
Cyclophilin 40 ◽  
Tpr Domain

scholarly journals Effect of Ca2+ on the promiscuous target-protein binding mechanism of calmodulin

2018 ◽  
Author(s):  
Annie M. Westerlund ◽  
Lucie Delemotte
Keyword(s):  
Molecular Dynamics ◽  
Protein Binding ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Solvent Exposure ◽  
Conformational States ◽  
Hydrophobic Residues ◽  
Target Proteins ◽  
Flexible Mechanism ◽  
Dynamics Simulations

AbstractCalmodulin (CaM) is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling path- ways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question.Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity.This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.Author summaryCalmodulin is a protein involved in the regulation of a variety of cell signaling pathways. It acts by making usually calcium-insensitive proteins sensitive to changes in the calcium concentration inside the cell. Its two lobes bind calcium and allow the energetically unfavorable exposure of hydrophobic residues to the aqueous environment which can then bind target proteins. The mechanisms behind the simultaneous specificity and variation of target protein binding is yet unknown but will aid understanding of the calcium-signaling and regulation that occur in many of our cellular processes.Here, we used molecular dynamics simulations and data analysis techniques to investigate what effect calcium has on the binding modes of calmodulin. The simulations and analyses allow us to observe and differentiate specific states. One domain of calmodulin is shown to be selective with binding involving short- distance interactions between hydrophobic residues, while the other binds target proteins through a more flexible mechanism involving long-distance electrostatic interactions.

Influence of point mutations on the flexibility of cytochrome b5: Molecular dynamics simulations of holoproteins

Biopolymers ◽  
2006 ◽  
Vol 83 (3) ◽  
pp. 297-312 ◽  
Author(s):  
Qinyi Cheng ◽  
David R. Benson ◽  
Mario Rivera ◽  
Krzysztof Kuczera
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cytochrome B5 ◽  
Point Mutations ◽  
Dynamics Simulations
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