Coarse-grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin

2011 ◽  
Vol 79 (7) ◽  
pp. 2291-2305 ◽  
Author(s):  
Wenjun Zheng
Keyword(s):  
Conformational Transitions ◽  
Coarse Grained ◽  
Filamentous Actin ◽  
Myosin V ◽  
Processive Stepping

Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions

2020 ◽  
Vol 16 (10) ◽  
pp. 6678-6689
Author(s):  
Yuwei Zhang ◽  
Zexing Cao ◽  
John Zenghui Zhang ◽  
Fei Xia
Keyword(s):  
Conformational Transitions ◽  
Coarse Grained ◽  
Coarse Grained Model

scholarly journals Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

2018 ◽  
Vol 19 (11) ◽  
pp. 3496 ◽  
Author(s):  
Sebastian Kmiecik ◽  
Maksim Kouza ◽  
Aleksandra Badaczewska-Dawid ◽  
Andrzej Kloczkowski ◽  
Andrzej Kolinski
Keyword(s):  
Structure Prediction ◽  
Large Scale ◽  
Dynamic Properties ◽  
Experimental Studies ◽  
Network Models ◽  
Conformational Transitions ◽  
Conformational Space ◽  
Coarse Grained ◽  
Elastic Network ◽  
Elastic Network Models

Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.

scholarly journals Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

2009 ◽  
Vol 106 (37) ◽  
pp. 15673-15678 ◽  
Author(s):  
Anil Korkut ◽  
Wayne A. Hendrickson
Keyword(s):  
Molecular Mechanics ◽  
Conformational Changes ◽  
Adenylate Kinase ◽  
Normal Modes ◽  
Conformational Transitions ◽  
The Other ◽  
Coarse Grained ◽  
Knowledge Based ◽  
Comprehensive Knowledge ◽  
Transition Pathways

Many proteins function through conformational transitions between structurally disparate states, and there is a need to explore transition pathways between experimentally accessible states by computation. The sizes of systems of interest and the scale of conformational changes are often beyond the scope of full atomic models, but appropriate coarse-grained approaches can capture significant features. We have designed a comprehensive knowledge-based potential function based on a Cα representation for proteins that we call the virtual atom molecular mechanics (VAMM) force field. Here, we describe an algorithm for using the VAMM potential to describe conformational transitions, and we validate this algorithm in application to a transition between open and closed states of adenylate kinase (ADK). The VAMM algorithm computes normal modes for each state and iteratively moves each structure toward the other through a series of intermediates. The move from each side at each step is taken along that normal mode showing greatest engagement with the other state. The process continues to convergence of terminal intermediates to within a defined limit—here, a root-mean-square deviation of 1 Å. Validations show that the VAMM algorithm is highly effective, and the transition pathways examined for ADK are compatible with other structural and biophysical information. We expect that the VAMM algorithm can address many biological systems.

scholarly journals Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

2020 ◽  
Vol 117 (11) ◽  
pp. 5861-5872 ◽  
Author(s):  
Carsten F. E. Schroer ◽  
Lucia Baldauf ◽  
Lennard van Buren ◽  
Tsjerk A. Wassenaar ◽  
Manuel N. Melo ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Actin Filaments ◽  
Mammalian Cells ◽  
Mechanical Stability ◽  
Coarse Grained ◽  
Lipid Bilayer Membranes ◽  
Filamentous Actin ◽  
Divalent Ions

The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin–membrane interaction.

scholarly journals Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-grained Simulations and Elastic Network Models

2018 ◽  
Author(s):  
Sebastian Kmiecik ◽  
Maksim Kouza ◽  
Aleksandra Elzbieta Badaczewska-Dawid ◽  
Andrzej Kloczkowski ◽  
Andrzej Kolinski
Keyword(s):  
Structure Prediction ◽  
Large Scale ◽  
Dynamic Properties ◽  
Experimental Studies ◽  
Network Models ◽  
Conformational Transitions ◽  
Conformational Space ◽  
Coarse Grained ◽  
Elastic Network ◽  
Elastic Network Models

Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this mini-review, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow quite accurate modeling of much larger systems and longer time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.

Sign in / Sign up

Export Citation Format

Share Document