Construction of ultra-coarse-grained model of protein with a Gō-like potential

Zhang, Yuwei; Cao, Zexing; Xia, Fei

doi:10.1016/j.cplett.2017.05.039

Cited by 10 publications

(12 citation statements)

References 36 publications

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“…Critically, inherent to the CG mapping is the definition of the elemental units composing the newly-introduced representation: in particle-based CG pictures ( Noid, 2013 ; Kmiecik et al, 2016 ), such units are the effective interaction sites, or “beads”, obtained by lumping together subsets of the system’s constituent atoms. Depending on the chosen resolution level, each site can be representative of small to medium-sized chemical moieties ( Monticelli et al, 2008 ; Bereau and Deserno, 2009 ; Darrè et al, 2015 ), single or groups of amino acids ( Clementi et al, 2000 ; Atilgan et al, 2001 ; Micheletti et al, 2004 ; Zhang et al, 2017 ), up to entire molecular structures ( Chu and Voth, 2006 ; Sept and MacKintosh, 2010 ; Dama et al, 2013 ). In all these cases, the mapping is formally expressed as the functional relation

between the effective sites’ coordinates R and the atomistic ones r ( Noid et al, 2008a ; Rudzinski and Noid, 2011 ).…”

Section: Coarse-grained Modeling: General Frameworkmentioning

confidence: 99%

“…To push the applicability of particle-based CG models to the investigation of phenomena occurring at even larger time and length scales, one possibility is that of resorting to ultra coarse-graining (UCG) methods. Here, each CG site becomes representative of larger chemical entities, be that few residues, whole proteins or even entire molecular complexes ( Chu and Voth, 2006 ; Sept and MacKintosh, 2010 ; Zhang et al, 2017 ). Several examples of UCG models, ranging from more “chemically accurate” to more heuristic ones, have been presented in the literature.…”

Section: Coarse-grained Modeling: Resolution Levelmentioning

confidence: 99%

“…Several examples of UCG models, ranging from more “chemically accurate” to more heuristic ones, have been presented in the literature. While more traditional applications typically focus on single proteins ( Zhang et al, 2017 ; Zhang et al, 2020 ), UCG methods have provided impressive insights into the behavior of overwhelmingly complicated macromolecular structures ( Saunders and Voth, 2012 ; Hagan and Zandi, 2016 ), including actin filaments ( Chu and Voth, 2006 ), bacterial flagella ( Arkhipov et al, 2006a ), and viral capsids ( Arkhipov et al, 2006b ; Nguyen et al, 2009 ; Grime et al, 2016 ).…”

Section: Coarse-grained Modeling: Resolution Levelmentioning

confidence: 99%

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From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Giulini

Rigoli

Mattiotti

et al. 2021

Front. Mol. Biosci.

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The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.

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between the effective sites’ coordinates R and the atomistic ones r ( Noid et al, 2008a ; Rudzinski and Noid, 2011 ).…”

Section: Coarse-grained Modeling: General Frameworkmentioning

confidence: 99%

Section: Coarse-grained Modeling: Resolution Levelmentioning

confidence: 99%

Section: Coarse-grained Modeling: Resolution Levelmentioning

confidence: 99%

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From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Giulini

Rigoli

Mattiotti

et al. 2021

Front. Mol. Biosci.

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“…However, our UCG model is not suitable for being used in a direct simulation of bending deformation, since the MVP-ANM potential used in our model is harmonic and invalid in large deformation. A simulation of the complicated process such as the dissociation and association of tubulins from microtubule requires a more complex potential such as a Gō-like potential ( Zhang et al, 2017a ; Poma et al, 2017 ; Poma et al, 2018 ; Zhang et al, 2020 ).…”

Section: Computational and Simulation Detailsmentioning

confidence: 99%

“…Ultra-coarse-grained (UCG) models ( Dama et al, 2013 ; Davtyan et al, 2014 ; Dama et al, 2017 ; Zhang et al, 2017a ; Jin et al, 2018 ; Jin and Voth, 2018 ) have been rapidly developed in recent years and applied to simulate the functions of biomolecular complexes such as the mechanical properties of F-actin ( Katkar et al, 2018 ), the assembly of HIV capsids ( Grime et al, 2016 ), and two-state conformational changes of proteins ( Zhang et al, 2020 ). The bead resolution of UCG models is lower than the high-resolution models, with one UCG bead usually representing more than a few residues or even secondary structure elements.…”

Section: Introductionmentioning

confidence: 99%

Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length

Zha

Zhang

Xia

et al. 2021

Front. Mol. Biosci.

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Microtubules are one of the most important components in the cytoskeleton and play a vital role in maintaining the shape and function of cells. Because single microtubules are some micrometers long, it is difficult to simulate such a large system using an all-atom model. In this work, we use the newly developed convolutional and K-means coarse-graining (CK-CG) method to establish an ultra-coarse-grained (UCG) model of a single microtubule, on the basis of the low electron microscopy density data of microtubules. We discuss the rationale of the micro-coarse-grained microtubule models of different resolutions and explore microtubule models up to 12-micron length. We use the devised microtubule model to quantify mechanical properties of microtubules of different lengths. Our model allows mesoscopic simulations of micrometer-level biomaterials and can be further used to study important biological processes related to microtubule function.

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Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

Zhang

et al. 2019

J Comput Chem

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The development of ultracoarse‐grained models for large biomolecules needs to derive the optimal number of coarse‐grained (CG) sites to represent the targets. In this work, we propose to use the statistical internal cluster validation indexes to determine the optimal number of CG sites that are optimized based on the essential dynamics coarse‐graining method. The calculated curves of Calinski‐Harabasz and Silhouette Coefficient indexes exhibit the extrema corresponding to the similar CG numbers. The calculated ratios of the optimal CG numbers to the residue numbers of fine‐grained models are in the range from 4 to 2. The comparison of the stability of index results indicates that Calinski‐Harabasz index is the better choice to determine the optimal CG representation in coarse‐graining. © 2019 Wiley Periodicals, Inc.

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Construction of ultra-coarse-grained model of protein with a Gō-like potential

Cited by 10 publications

References 36 publications

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

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