The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes.

Point mutations play a vital role in the conformational transformation of HRAS. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of free energy landscapes (FELs) were adopted to explore the effect of mutations D33K, A59T and L120A on conformation states of the GDP-bound HRAS. The results from the post-processing analyses on GaMD trajectories suggest that mutations alter the flexibility and motion modes of the switch domains from HRAS. The analyses from FELs show that mutations induce more disordered states of the switch domains and affect interactions of GDP with HRAS, implying that mutations yield a vital effect on the binding of HRAS to effectors. The GDP-residue interaction network revealed by our current work indicates that salt bridges and hydrogen bonding interactions (HBIs) play key roles in the binding of GDP to HRAS. Furthermore, instability in the interactions of magnesium ions and GDP with the switch SI leads to the extreme disorder of the switch domains. This study is expected to provide the energetic basis and molecular mechanism for further understanding the function of HRAS.Communicated by Ramaswamy H. Sarma.

Exploring conformation changes of Janus kinase 2 pseudokinase mediated by mutations through Gaussian accelerated molecular dynamics and principal component analysis.

The pseudokinase domain (JH2) of the protein tyrosine kinase (Janus kinase 2, JAK2) regulates the activity of a tyrosine kinase domain (JH1) in JAK2, which is further affected by mutations in the JH2. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by construction of free energy landscapes (FELs) and principal component analysis (PCA) were performed to study effect of two mutations V617F and V617F/E596A on the conformations of the ATP-bound JH2. The dynamic analyses reveal that mutations affect the structural flexibility and correlated motions of the JH2, meanwhile also change the dynamics behavior of the P-loop and αC-helix of the JH2. The information from FELs unveils that mutations induce less energy states than the free JH2 and the WT one. The analyses of interaction networks uncover that mutations affect the salt bridge interactions of ATP with K581, K677 and R715 and alter hydrogen bonding interactions (HBIs) of ATP with the JH2. The changes in conformations of the JH2 and ATP-JH2 interaction networks caused by mutations in turn generate effect on the activity regulations of the JH2 on the JH1. This work is expected to provide significant theoretical helps for deeply understanding the function of the JH2 and drug design toward JAK2.Communicated by Ramaswamy H. Sarma.

Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.

Mutations highly affect the structural flexibility of two switch domains in M-RAS considered an important target of anticancer drug design. Gaussian accelerated molecular dynamics (GaMD) simulations were applied to probe the effect of mutations P40D, D41E, and P40D/D41E/L51R on the conformational transition of the switch domains from the GTP-bound M-RAS. The analyses of free energy landscapes (FELs) not only reveal that three mutations induce less energetic states than the wild-type (WT) M-RAS but also verify that the switch domains are extremely disordered. Principal component analysis (PCA) and dynamics analysis suggest that three mutations greatly affect collective motions and structural flexibility of the switch domains that mostly overlap with binding regions of M-RAS to its effectors, which in turn disturbs the activity of M-RAS. The analyses of the interaction network between GTP and M-RAS show that the high instability in hydrogen bonding interactions (HBIs) of GTP with residue 41 and Y42 in the switch domain I drives the disordered states of the switch domains. This work is expected to provide a molecular mechanism for deeply understanding the function of M-RAS and future drug design towards the treatment of cancers.

Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes.

Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode the effect of Q61A, Q61H and Q61L on the activity of KRAS. Dynamics analyses based on MR-GaMD trajectory reveal that motion modes and dynamics behavior of the switch domain in KRAS are heavily affected by the three Q61 mutants. Information of free energy landscapes (FELs) shows that Q61A, Q61H and Q61L induce structural disorder of the switch domain and disturb the activity of KRAS. Analysis of the interaction network uncovers that the decrease in the stability of hydrogen bonding interactions (HBIs) of GTP with residues V29 and D30 induced by Q61A, Q61H and Q61L is responsible for the structural disorder of the switch-I and that in the occupancy of the hydrogen bond between GTP and residue G60 leads to the structural disorder of the switch-II. Thus, the high disorder of the switch domain caused by three current Q61 mutants produces a significant effect on binding of KRAS to its effectors. This work is expected to provide useful information for further understanding function and target roles of KRAS in anti-cancer drug development.

Conformational transformation of switch domains in GDP/K-Ras induced by G13 mutants: An investigation through Gaussian accelerated molecular dynamics simulations and principal component analysis.

Mutations in K-Ras are involved in a large number of all human cancers, thus, K-Ras is regarded as a promising target for anticancer drug design. Understanding the target roles of K-Ras is important for providing insights on the molecular mechanism underlying the conformational transformation of the switch domains in K-Ras due to mutations. In this study, multiple replica Gaussian accelerated molecular (MR-GaMD) simulations and principal component analysis (PCA) were applied to probe the effect of G13A, G13D and G13I mutations on conformational transformations of the switch domains in GDP-associated K-Ras. The results suggest that G13A, G13D and G13I enhance the structural flexibility of the switch domains, change the correlated motion modes of the switch domains and strengthen the total motion strength of K-Ras compared with the wild-type (WT) K-Ras. Free energy landscape analyses not only show that the switch domains of the GDP-bound inactive K-Ras mainly exist as a closed state but also indicate that mutations evidently alter the free energy profile of K-Ras and affect the conformational transformation of the switch domains between the closed and open states. Analyses of hydrophobic interaction contacts and hydrogen bonding interactions show that the mutations scarcely change the interaction network of GDP with K-Ras and only disturb the interaction of GDP with the switch (SW1). In summary, two newly introduced mutations, G13A and G13I, play similar adjustment roles in the conformational transformations of two switch domains to G13D and are possibly utilized to tune the activity of K-Ras and the binding of guanine nucleotide exchange factors.

Binding mechanism of inhibitors to p38α MAP kinase deciphered by using multiple replica Gaussian accelerated molecular dynamics and calculations of binding free energies.

The p38α MAP Kinase has been an important target of drug design for treatment of inflammatory diseases and cancers. This work applies multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics generalized Born surface area (MM-GBSA) method to probe the binding mechanism of inhibitors L51, R24 and 1AU to p38α. Dynamics analyses show that inhibitor bindings exert significant effect on conformational changes of the active helix α2 and the conserved DFG loop. The rank of binding free energies calculated with MM-GBSA not only agrees well with that determined by the experimental IC50 values but also suggests that mutual compensation between the enthalpy and entropy changes can improve binding of inhibitors to p38α. The analyses of free energy landscapes indicate that the L51, R24 and 1AU bound p38α display a DFG-out conformation. The residue-based free energy decomposition method is used to evaluate contributions of separate residues to the inhibitor-p38α binding and the results imply that residues V30, V38, L74, L75, I84, T106, H107, L108, M109, L167, F169 and D168 can be utilized as efficient targets of potent inhibitors toward p38α.