ArticleBiophysical journal2008
Selection of optimal variants of Gō-like models of proteins through studies of stretching.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
- Choosing the right density for a concentrated protein system like gluten in a coarse-grained model.European biophysics journal : EBJ · 2023Article
- Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models.Journal of chemical theory and computation · 2023Article
- Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Viscoelastic properties of wheat gluten in a molecular dynamics study.PLoS computational biology · 2021Article
- Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.Frontiers in molecular biosciences · 2021Article
- Nascent Folding of Proteins Across the Three Domains of Life.Frontiers in molecular biosciences · 2021Article
- GLN: a method to reveal unique properties of lasso type topology in proteins.Scientific reports · 2020Article
- Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2020Article
- Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations.BMC molecular and cell biology · 2020Article
- Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures.International journal of molecular sciences · 2019Article
- Searching the Optimal Folding Routes of a Complex Lasso Protein.Biophysical journal · 2019Article
- Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes.Analytical chemistry · 2019Article
- Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.PloS one · 2019Article
- Mechanical and thermodynamic properties of AβBeilstein journal of nanotechnology · 2019Article
- Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module.Scientific reports · 2018Article
- The exclusive effects of chaperonin on the behavior of proteins with 52 knot.PLoS computational biology · 2018Article
- Self-assembly of model proteins into virus capsids.Journal of physics. Condensed matter : an Institute of Physics journal · 2017Article
- Topological transformations in proteins: effects of heating and proximity of an interface.Scientific reports · 2017Article
- Periodic forces trigger knot untying during translocation of knotted proteins.Scientific reports · 2016Article
- Wang-Landau simulation of Gō model molecules.The European physical journal. E, Soft matter · 2016Article
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2 authors.
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Abstract
The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales--uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching.
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