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 The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Renuka Kudva ◽  
Pengfei Tian ◽  
Fátima Pardo-Avila ◽  
Marta Carroni ◽  
Robert B Best ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Domain ◽  
Coarse Grained ◽  
E Coli ◽  
Folded Structure ◽  
Bacterial Ribosome ◽  
Folded Proteins ◽  
Exit Tunnel ◽  
Ribosome Exit Tunnel ◽  
Dynamics Simulations

The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

scholarly journals The Shape of the Bacterial Ribosome Exit Tunnel Affects Cotranslational Protein Folding

2018 ◽  
Author(s):  
Renuka Kudva ◽  
Pengfei Tian ◽  
Fatima Pardo Avila ◽  
Marta Carroni ◽  
Robert B. Best ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Domain ◽  
Coarse Grained ◽  
E Coli ◽  
Folded Structure ◽  
Bacterial Ribosome ◽  
Folded Proteins ◽  
Exit Tunnel ◽  
Ribosome Exit Tunnel ◽  
Dynamics Simulations

AbstractThe E.coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. It remains unclear, however, to what extent the geometry of the tunnel influences protein folding. Here, using E. coli ribosomes with deletions in loops in proteins uL23 and uL24 that protrude into the tunnel, we investigate how tunnel geometry determines where proteins of different sizes fold. We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~100-residue protein normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. This supports the idea that cotranslational folding commences once a protein domain reaches a location in the exit tunnel where there is sufficient space to house the folded structure.

scholarly journals Unfolding the chaperone story

2017 ◽  
Vol 28 (22) ◽  
pp. 2919-2923 ◽  
Author(s):  
F. Ulrich Hartl
Keyword(s):  
Protein Folding ◽  
Molecular Chaperones ◽  
Current Concept ◽  
Cellular Process ◽  
Protein Chain ◽  
Native State ◽  
Folding Process ◽  
Spontaneous Process ◽  
Short Essay

Protein folding in the cell was originally assumed to be a spontaneous process, based on Anfinsen’s discovery that purified proteins can fold on their own after removal from denaturant. Consequently cell biologists showed little interest in the protein folding process. This changed only in the mid and late 1980s, when the chaperone story began to unfold. As a result, we now know that in vivo, protein folding requires assistance by a complex machinery of molecular chaperones. To ensure efficient folding, members of different chaperone classes receive the nascent protein chain emerging from the ribosome and guide it along an ordered pathway toward the native state. I was fortunate to contribute to these developments early on. In this short essay, I will describe some of the critical steps leading to the current concept of protein folding as a highly organized cellular process.

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 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.

Simulating Self-Regeneration and Self-Replication Processes Using Movable Cellular Automata with a Mutual Equilibrium Neighborhood

2020 ◽  
Vol 29 (4) ◽  
pp. 741-757
Author(s):  
Kateryna Hazdiuk ◽  
◽  
Volodymyr Zhikharevich ◽  
Serhiy Ostapov ◽  
◽  
...  
Keyword(s):  
Cellular Automata ◽  
Cellular Automaton ◽  
Three Dimensional ◽  
Computer Models ◽  
The Self ◽  
Model Construction ◽  
Natural Phenomena ◽  
Different Types ◽  
Movable Cellular Automata ◽  
Self Replication

This paper deals with the issue of model construction of the self-regeneration and self-replication processes using movable cellular automata (MCAs). The rules of cellular automaton (CA) interactions are found according to the concept of equilibrium neighborhood. The method is implemented by establishing these rules between different types of cellular automata (CAs). Several models for two- and three-dimensional cases are described, which depict both stable and unstable structures. As a result, computer models imitating such natural phenomena as self-replication and self-regeneration are obtained and graphically presented.

A STUDY OF BIFURCATIONS IN A CIRCULAR REAL CELLULAR AUTOMATON

1993 ◽  
Vol 03 (02) ◽  
pp. 293-321 ◽  
Author(s):  
JÜRGEN WEITKÄMPER
Keyword(s):  
Hopf Bifurcation ◽  
Dynamical Systems ◽  
Cellular Automata ◽  
Cellular Automaton ◽  
Parallel Computers ◽  
Discrete Dynamical Systems ◽  
Two Dimensional ◽  
Bifurcation Structure ◽  
Logistic Mapping ◽  
Henon Mapping

Real cellular automata (RCA) are time-discrete dynamical systems on ℝN. Like cellular automata they can be obtained from discretizing partial differential equations. Due to their structure RCA are ideally suited to implementation on parallel computers with a large number of processors. In a way similar to the Hénon mapping, the system we consider here embeds the logistic mapping in a system on ℝN, N>1. But in contrast to the Hénon system an RCA in general is not invertible. We present some results about the bifurcation structure of such systems, mostly restricting ourselves, due to the complexity of the problem, to the two-dimensional case. Among others we observe cascades of cusp bifurcations forming generalized crossroad areas and crossroad areas with the flip curves replaced by Hopf bifurcation curves.

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