Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

D’Abramo, Marco; Bešker, Neva; Chillemi, Giovanni; Grottesi, Alessandro

doi:10.3389/fgene.2014.00128

Cited by 15 publications

(12 citation statements)

References 33 publications

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“…The timescale of the molecular dynamics simulations (20 ns) was chosen to see the local structural effects of the substitution of pSer to Asp, especially for what concerns the salt bridges network. Such timescale however prevented us to simulate large movements of the kinase lobes, that happen in the order of microseconds and that would require a much larger computing power, not available with the current technology 59,60 .…”

Section: Discussionmentioning

confidence: 99%

Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints

Somale

Nardo

Blasio

et al. 2020

Sci Rep

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The activation of the majority of AGC kinases is regulated by two phosphorylation events on two conserved serine/threonine residues located on the activation loop and on the hydrophobic motif, respectively. In AGC kinase family, phosphomimetic substitutions with aspartate or glutamate, leading to constitutive activation, have frequently occurred at the hydrophobic motif site. On the contrary, phosphomimetic substitutions in the activation loop are absent across the evolution of AGC kinases. this observation is explained by the failure of aspartate and glutamate to mimic phosphorylatable serine/threonine in this regulatory site. By detailed 3D structural simulations of RSK2 and further biochemical evaluation in cells, we show that the phosphomimetic residue on the activation loop fails to form a critical salt bridge with R114, necessary to reorient the αc-helix and to activate the protein. By a phylogenetic analysis, we point at a possible coevolution of a phosphorylatable activation loop and the presence of a conserved positively charged amino acid on the αC-helix. In sum, our analysis leads to the unfeasibility of phosphomimetic substitution in the activation loop of RSK and, at the same time, highlights the peculiar structural role of activation loop phosphorylation. The 61 human AGC kinases form a monophyletic group of serine/threonine kinases that preferably phosphorylates residues in close proximity of basic amino acids such as Arg (R) and Lys (K) 1,2. The kinase domains (KD) of all the AGC kinases share the same tertiary structure, characterized by an amino-terminal small lobe (N-lobe) and a carboxy-terminal large lobe (C-lobe), as originally described for PKA 3. The two lobes form a pocket that binds one molecule of ATP as phosphate donor during substrate phosphorylation. The transition from inactive to active state in AGC kinases is achieved through conformational rearrangements of key structural elements, such as the activation segment and the αC-helix. The activation segment is a sequence of variable length (from 25 aa of PKAa to 43 aa of MAST1) spanning from Asp-Phe-Gly (DFG) to Ala-Pro-Glu (APE) sequences, and including the activation loop (AL) and the P + 1 loop 4. The DFG sequence is part of the ATP binding site whose orientation defines the active (DFG-in) 3 and the inactive (DFG-out) states of AGC kinases 5. The AL contains, in 43 out of 61 AGC kinases (Fig. 1A), a key phosphorylatable site (consensus sequence S/T-x-x-G-T), found to be substrate of 3-Phosphoinositide-dependent protein kinase-1 (PDK1) 6. The phosphate group added on the AL form a complex set of salt bridges with basic amino acid groups, that in PKA are respectively: R165 in the catalytic loop, H87 in the αC-helix and K189 in the AL, just after the DFG motif 7,8. By connecting these residues, the phosphorylation of the AL promotes the transition in a more ordered conformation, the stabilization of the two lobes in the closed/active conformation and the assembly of a key hydrophobic core, defined R-spine 9-11. Crucial event in the tr...

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Section: Discussionmentioning

confidence: 99%

Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints

Somale

Nardo

Blasio

et al. 2020

Sci Rep

View full text Add to dashboard Cite

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“…More advanced enhanced sampling techniques, such as umbrella sampling [91], metadynamics [92], and replica exchange MD [93], can also be applied to identify protein conformations for docking screening. Indeed, these techniques, which allow exploring a protein conformational landscape far larger with respect to that of standard MD simulations, have already been applied to study protein flexibility and function [94,95,96,97,98,99,100,101] and to identify additional binding pockets that could be exploited for the design of novel inhibitors [102,103]. However, it should be noted that the application of these advanced methods is computationally more demanding with respect to standard MD.…”

Section: Current Rational Design Approaches Including Dockingmentioning

confidence: 99%

Molecular Docking: Shifting Paradigms in Drug Discovery

Pinzi

Rastelli

2019

IJMS

1,418

691

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Molecular docking is an established in silico structure-based method widely used in drug discovery. Docking enables the identification of novel compounds of therapeutic interest, predicting ligand-target interactions at a molecular level, or delineating structure-activity relationships (SAR), without knowing a priori the chemical structure of other target modulators. Although it was originally developed to help understanding the mechanisms of molecular recognition between small and large molecules, uses and applications of docking in drug discovery have heavily changed over the last years. In this review, we describe how molecular docking was firstly applied to assist in drug discovery tasks. Then, we illustrate newer and emergent uses and applications of docking, including prediction of adverse effects, polypharmacology, drug repurposing, and target fishing and profiling, discussing also future applications and further potential of this technique when combined with emergent techniques, such as artificial intelligence.

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“…MD simulations of the Tat/Cyclin T1/CDK9 complex presented the first detailed study of supramolecular assemblies that involve transcriptional CDK, revealing how presence of multiple binding partners may promote structural environment favoring formation of the active state [ 87 , 88 ]. These studies exemplified a considerable progress in characterizing conformational ensembles and transitions in CDK proteins [ 89 ].…”

Section: Introductionmentioning

confidence: 99%

Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone

2017

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The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.

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Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

Cited by 15 publications

References 33 publications

Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints

Activation of RSK by phosphomimetic substitution in the activation loop is prevented by structural constraints

Molecular Docking: Shifting Paradigms in Drug Discovery

Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone

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