Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding

2014 ◽  
Vol 16 (14) ◽  
pp. 6460-6479 ◽  
Author(s):  
Tao Chen ◽  
Hue Sun Chan
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Protein Chain ◽  
Nonlocal Coupling

Coarse-grained protein chain models with desolvation barriers or sidechains lead to stronger local–nonlocal coupling and more linear chevron plots.

scholarly journals Evolving cellular automata schemes for protein folding modeling using the Rosetta atomic representation

2022 ◽  
Author(s):  
Daniel Varela ◽  
José Santos
Keyword(s):  
Protein Folding ◽  
Cellular Automata ◽  
Cellular Automaton ◽  
Structure Refinement ◽  
Coarse Grained ◽  
Connectionist Model ◽  
Protein Chain ◽  
Folding Process ◽  
Folded Structure ◽  
Protein Components

AbstractProtein folding is the dynamic process by which a protein folds into its final native structure. This is different to the traditional problem of the prediction of the final protein structure, since it requires a modeling of how protein components interact over time to obtain the final folded structure. In this study we test whether a model of the folding process can be obtained exclusively through machine learning. To this end, protein folding is considered as an emergent process and the cellular automata tool is used to model the folding process. A neural cellular automaton is defined, using a connectionist model that acts as a cellular automaton through the protein chain to define the dynamic folding. Differential evolution is used to automatically obtain the optimized neural cellular automata that provide protein folding. We tested the methods with the Rosetta coarse-grained atomic model of protein representation, using different proteins to analyze the modeling of folding and the structure refinement that the modeling can provide, showing the potential advantages that such methods offer, but also difficulties that arise.

scholarly journals Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model

2022 ◽  
Author(s):  
Xun Chen ◽  
Wei Lu ◽  
Min-Yeh Tsai ◽  
Shikai Jin ◽  
Peter G. Wolynes
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Hybrid Model ◽  
Structure Prediction ◽  
Heme Proteins ◽  
Coarse Grained ◽  
Protein Chain ◽  
Folding Energy ◽  
Covalent Bonds ◽  
Ligand Interactions

AbstractHeme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the protein and the heme. The types of protein–ligand interactions in the hybrid model include thioester covalent bonds, coordinated covalent bonds, hydrogen bonds, and electrostatics. We explore the influence of different types of hemes (heme b and heme c) on folding and structure prediction. Including both types of heme improves the quality of protein structure predictions. The free energy landscape shows that both types of heme can act as nucleation sites for protein folding and stabilize the protein folded state. In binding the heme, coordinated covalent bonds and thioester covalent bonds for heme c drive the heme toward the native pocket. The electrostatics also facilitates the search for the binding site.

Self-Similarity of Protein Folding Flows

2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev
Keyword(s):  
Protein Folding ◽  
Sh3 Domain ◽  
Atomic Level ◽  
The Self ◽  
Coarse Grained ◽  
Folding Kinetics ◽  
Native State ◽  
Self Similarity ◽  
Folding Dynamics ◽  
Fractal Character

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Parallel Molecular Dynamics

Coarse Grained Modeling and Approaches to Protein Folding

2010 ◽  
Vol 5 (3) ◽  
pp. 217-240 ◽  
Author(s):  
Carlo Guardiani ◽  
Roberto Livi ◽  
Fabio Ce cconi
Keyword(s):  
Protein Folding ◽  
Coarse Grained

scholarly journals Correction: A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (27) ◽  
pp. 18102-18102
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Chem Phys ◽  
Coarse Grained ◽  
Critical Comparison ◽  
Atomic Models ◽  
Phys Chem Chem Phys

Correction for ‘A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding’ by Jie Hu et al., Phys. Chem. Chem. Phys., 2017, 19, 13629–13639.

scholarly journals Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models

Small ◽  
2017 ◽  
Vol 13 (18) ◽  
pp. 1603748 ◽  
Author(s):  
Shuai Wei ◽  
Logan S. Ahlstrom ◽  
Charles L. Brooks
Keyword(s):  
Protein Folding ◽  
Coarse Grained ◽  
Nanoparticle Interactions
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