MEPSA: minimum energy pathway analysis for energy landscapes

Marcos‐Alcalde, Íñigo; Setoaín, Javier; Mendieta‐Moreno, Jesús I.; Mendieta, Jesús; Gómez‐Puertas, Paulino

doi:10.1093/bioinformatics/btv453

Cited by 106 publications

(131 citation statements)

References 9 publications

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“…In each case, the minimum energy pathway along the calculated free-energy surfaces (cyan and red lines on the maps in Fig. 2a) was calculated using the MEPSA algorithm 49 , by extracting the minimum free-energy path of the reaction from the substrate S (the initial ATP molecule) to the product P (final ADP molecule plus inorganic phosphate group), as represented in Fig. 2b.…”

Section: Resultsmentioning

confidence: 99%

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Two-step ATP-driven opening of cohesin head

Marcos‐Alcalde

Mendieta‐Moreno

Puisac³

et al. 2017

Sci Rep

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The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the “head” structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.

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Section: Resultsmentioning

confidence: 99%

“…The partition function was calculated for each group in order to estimate a free-energy surface that was then smoothed via a 3D LOESS local regression. Reaction paths and energy profiles were calculated using MEPSA 49 .…”

Section: Methodsmentioning

confidence: 99%

Two-step ATP-driven opening of cohesin head

Marcos‐Alcalde

Mendieta‐Moreno

Puisac³

et al. 2017

Sci Rep

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“…For validation, POLARIS' results were compared to those obtained with a published energy landscape analysis algorithm entitled MEPSA (Minimum Energy Pathway Analysis) (30), which uses an approach similar to Dijkstra's algorithm (24), with small differences in the sampling and traceback. The metric used to compare the two algorithms is the final integrated energy from a single continuous list of coordinates spanning between any two user-defined points.…”

Section: Mepsa Comparisonmentioning

confidence: 99%

POLARIS: path of least action analysis on energy landscapes

Seitz¹,

Frank²

2019

Preprint

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Free-energy landscapes are a powerful tool for analyzing dynamical processes -capable of providing a complete mapping of a system's configurations in state space while articulating its energetics topologically in the form of sprawling hills and valleys. Within this mapping, the path of least action can be derived -representing the most probable sequence of transitions taken between any two states in the landscape. In this article, POLARIS (Path of Least Action Recursive Survey) is presented as a dynamic, global approach that efficiently automates the discovery of the least action path on 2D energy landscapes. Important built-in features of this program include plotting of landscape trajectories and transition state theory diagrams, generation of text files with least action coordinates and respective energies, and bifurcation analysis tools that provide downstream versatility for comparing most probable paths and reaction rates.

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“…The contour lines are reported with a spacing in energy of 0.01 eV, the color map distinguish more probable areas (blue) from less visited areas (orange-red). The black dots mark the Minimum Energy Pathway (MEP) [104] .…”

Section: Free Energy Landscape For the Lithium Solvation In Eanmentioning

confidence: 99%

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study

et al. 2017

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The understanding of lithium solvation and transport in ionic liquids is important due to the possible applications in electrochemical devices. Using first principles simulations aided with the metadynamics approach we study the free energy landscape for lithium at infinite dilution conditions in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and find a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium solvated either by 3 or 4 nitrates ions with a transition barrier between them of 0.2 eV. Other less probable conformations having a different solvation pattern are also investigated.1

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MEPSA: minimum energy pathway analysis for energy landscapes

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 106 publications

References 9 publications

Two-step ATP-driven opening of cohesin head

Two-step ATP-driven opening of cohesin head

POLARIS: path of least action analysis on energy landscapes

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study

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