From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes

Heath, Allison P.; Kavraki, Lydia E.; Clementi, Cecilia

doi:10.1002/prot.21371

Cited by 116 publications

(131 citation statements)

References 92 publications

(142 reference statements)

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“…Recently, schemes like reconstruction algorithm for coarse-grained structures 65 have been developed for constructing low-energy all-atom protein structures form configurations with only C α atoms. In the present context, this could facilitate SIMNANOWORLD simulations starting from low resolution structures (e.g., electron cryomicroscopic models 66 ) via reconstructing all-atom input structures.…”

Section: Discussionmentioning

confidence: 99%

Order parameters for macromolecules: Application to multiscale simulation

Singharoy

Cheluvaraja

Ortoleva

2011

The Journal of Chemical Physics

175

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Order parameters (OPs) characterizing the nanoscale features of macromolecules are presented. They are generated in a general fashion so that they do not need to be redesigned with each new application. They evolve on time scales much longer than 10 −14 s typical for individual atomic collisions/vibrations. The list of OPs can be automatically increased, and completeness can be determined via a correlation analysis. They serve as the basis of a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Smoluchowski/Langevin equations of stochastic OP dynamics. Such OPs and the multiscale analysis imply computational algorithms that we demonstrate in an application to ribonucleic acid structural dynamics for 50 ns.

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Section: Discussionmentioning

confidence: 99%

Order parameters for macromolecules: Application to multiscale simulation

Singharoy

Cheluvaraja

Ortoleva

2011

The Journal of Chemical Physics

175

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“…[34][35][36][37][38] Several approaches have been developed to derive and optimize CG forcefields. [39][40][41][42][43][44][45] Among these, the iterative Boltzmann inversion (IBI) method 39 has become a popular choice due to its straightforward nature, general applicability to a wide range of systems, and basis in structural properties.…”

Section: Introductionmentioning

confidence: 99%

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

Moore

Iacovella

McCabe

2014

The Journal of Chemical Physics

172

192

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In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems.

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“…Indeed, several of such hybrid schemes have recently been proposed, falling into four classes: back-mapping methods, interface methods, ''constant l'' techniques and fixed resolution methods. Back mapping methods [9][10][11][12][13][14][15][16][17] allow switching between the different levels of resolution, i.e. reconstruct the atomistic structural ensemble that underlies a CG representation for interesting configurations.…”

Section: Introductionmentioning

confidence: 99%

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

191

198

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Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1 : 1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein, together with the solvent, is coarse-grained.

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From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes

Cited by 116 publications

References 92 publications

Order parameters for macromolecules: Application to multiscale simulation

Order parameters for macromolecules: Application to multiscale simulation

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

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