Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin

Delfino, Francesco; Porozov, Yuri; Stepanov, Eugene; Tamazian, Gaik; Tozzini, Valentina

doi:10.3389/fmolb.2019.00104

Cited by 7 publications

(11 citation statements)

References 34 publications

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“…This distribution is consistent with the extended [43] and compact CaM [63] structures that have been experimentally-observed in the absence of target. Transition path calculations have suggested that the extended CaM formation is slightly more favorable than the compact one with a ∼3-4 kcal/mol theromodynamic advantage and these two CaM states are separated by a ∼10 kcal/mol barrier [64]. Our R G data of the WT linker CaM model qualitatively agree with the transition path results as the integrated extended CaM probability density is greater than that of the compact states.…”

Section: Linker Flexibility Determines the Cam Conformation Ensemblesupporting

confidence: 80%

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Sun

Kekenes‐Huskey

2021

Preprint

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Calmodulin (CaM) is a universal calcium binding protein known to bind at least 300 targets. The selectivity and specificity towards these targets are partially attributed to the protein's flexible alpha-helical linker that connects its N- and C- domains. However, how this flexible linker mediates the driving forces guiding CaM's binding to regulatory targets is not well-established. Therefore, we utilized coarse-grained (CG) Martini molecular dynamics simulations to probe interrelationships between CaM/target assembly and the role of its linker region. As a model system, we simulated the binding of CaM to the CaM binding region (CaMBR) of calcineurin (CaN). The simulations were conducted assuming a 'wild-type' calmodulin with normal flexibility of its linker between the N- and C-terminal domains, as well as a labile, highly flexible linker variant. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a tightly-bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka =6.3×108 M −1 s−1, which is similar to the experimentally-determined rate of 2.2×108 M −1 s−1 (Cook et al 2020). Further, our simulations recapitulated the inverse relationship between the association rate and solution ionic strength reported in the literature. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration and its ionic strength dependence is attenuated. These effects appear to stem from a difference in the ensembles of extended and collapsed states controlled by the linker properties. Specifically, the labile linker variant samples fewer extended states compatible with target peptide binding. Therefore, our simulations suggest that variations in the CaM linker's propensity for alpha-helical secondary structure can modulate the kinetics of target binding. This finding is important, given that some CaM variants found in the human population and post-translational modifications sites fall within this linker region, which may alter the protein's normal regulatory functions.

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Section: Linker Flexibility Determines the Cam Conformation Ensemblesupporting

confidence: 80%

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Sun

Kekenes‐Huskey

2021

Preprint

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“…This distribution was consistent with the extended [ 47 ] and compact CaM [ 68 ] structures that have been experimentally-observed in the absence of a target. Transition path calculations have suggested that the extended CaM formation was slightly more favorable than the compact one with a ∼3–4 kcal/mol theromodynamic advantage and these two CaM states were separated by a ∼10 kcal/mol barrier [ 69 ]. Our

data of the WT linker CaM model qualitatively agreed with these transition path results, as the integrated extended CaM probability density was greater than that of the compact states.…”

Section: Results and Discussionmentioning

confidence: 99%

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Sun

Kekenes‐Huskey

2021

IJMS

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Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet. Insights into this would be invaluable to understanding its regulation of diverse cellular signaling pathways. Therefore, we utilized Martini coarse-grained (CG) molecular dynamics simulations to probe CaM/target assembly for a model system: CaM binding to the calcineurin (CaN) regulatory domain. The simulations were conducted assuming a ‘wild-type’ calmodulin with normal flexibility of its linker, as well as a labile, highly-flexible linker variant to emulate structural changes that could be induced, for instance, by post-translational modifications. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in the experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 × 108 M−1 s−1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 × 108 M−1 s−1. Furthermore, our simulations recapitulated its well-known inverse relationship between the association rate and the solution ionic strength. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration. This effect appears to stem from a difference in the ensembles of extended and collapsed states which are controlled by the linker flexibility. Therefore, our simulations suggest that variations in the CaM linker’s propensity for alpha helical secondary structure can modulate the kinetics of target binding.

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“…Briefly, u h and u u are represented by anharmonic terms accurately describing the secondary structures; the u nb terms both local and nonlocal are represented by a Morse potential, but while the nonlocal part is a generic non-biased, the local contacts-defined through a geometric criterion 1 -have equilibrium distance set at the reference structure. The force constants are previously optimized and are reported together with other details in previous works (Delfino et al, 2019) and in the Supplementary Material.…”

Section: Systems Representations and Ffsmentioning

confidence: 99%

“…Relevant quantities (e.g., energies and RMSD, r values) are evaluated by means of cluster averages. Alternative averaging algorithms are used and compared with the clustering, based on the running averages of r and of the energies (Delfino et al, 2019). Transition paths are also searched for using algorithms exclusively based on the A and B structures.…”

mentioning

confidence: 99%

“…These are PROMPT (PRotein cOnformational Motion PredicTion 3 ) (Tamazian et al, 2015) based on the minimization of a mass transport functional subject to restrains on the bond angles and dihedrals along the chain, and MAP (Minimal Action Path) (Franklin et al, 2007) based on the numerical solution of Euler equations of a simplified Lagrangian including harmonic networks to bias toward A and B states. Both methods are very computationally cheap and parameter free, and return an already cleaned up transition path, with no need of postprocessing (Delfino et al, 2019). Figure 2 reports the LD results at different temperatures and with different FFs (simulation parameters reported in the caption).…”

mentioning

confidence: 99%

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Evolutionary Switches Structural Transitions via Coarse-Grained Models

Delfino

Porozov

Stepanov

et al. 2020

Journal of Computational Biology

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Transitions between different conformational states are ubiquitous in proteins. A vast class of conformation-changing proteins includes evolutionary switches, which vary their conformation as an effect of few mutations or weak environmental variations. However, modeling those processes is extremely difficult due to the need of efficiently exploring a vast conformational space to look for the actual transition path. In this study, we report a strategy that simplifies this task attacking the complexity on several sides. We first apply a minimalist coarse-grained model to the protein, based on an empirical force field with a partial structural bias toward one or both the reference structures. We then explore the transition paths by means of stochastic molecular dynamics and select representative structures by means of a principal path-based clustering algorithm. We finally compare this trajectory with that produced by independent methods adopting a morphing-oriented approach. Our analysis indicates that the minimalist model returns trajectories capable of exploring intermediate states with physical meaning, retaining a very low computational cost, which can allow systematic and extensive exploration of the multistable proteins transition pathways.

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Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin

Cited by 7 publications

References 34 publications

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding

Evolutionary Switches Structural Transitions via Coarse-Grained Models

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