scholarly journals Distributions of experimental protein structures on coarse-grained free energy landscapes

2015 ◽  
Vol 143 (24) ◽  
pp. 243153 ◽  
Author(s):  
Kannan Sankar ◽  
Jie Liu ◽  
Yuan Wang ◽  
Robert L. Jernigan
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes

scholarly journals Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration

2019 ◽  
Vol 151 (15) ◽  
pp. 154102 ◽  
Author(s):  
Simon Hunkler ◽  
Tobias Lemke ◽  
Christine Peter ◽  
Oleksandra Kukharenko
Keyword(s):  
Free Energy ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes

scholarly journals Simulating and analysing configurational landscapes of protein–protein contact formation

2019 ◽  
Vol 9 (3) ◽  
pp. 20180062 ◽  
Author(s):  
Andrej Berg ◽  
Christine Peter
Keyword(s):  
Free Energy ◽  
Protein Function ◽  
Covalent Bond ◽  
Quantitative Measure ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Dimensional Representation ◽  
Collective Variables ◽  
Contact Formation ◽  
Free Energy Landscapes

Interacting proteins can form aggregates and protein–protein interfaces with multiple patterns and different stabilities. Using molecular simulation one would like to understand the formation of these aggregates and which of the observed states are relevant for protein function and recognition. To characterize the complex configurational ensemble of protein aggregates, one needs a quantitative measure for the similarity of structures. We present well-suited descriptors that capture the essential features of non-covalent protein contact formation and domain motion. This set of collective variables is used with a nonlinear multi-dimensional scaling-based dimensionality reduction technique to obtain a low-dimensional representation of the configurational landscape of two ubiquitin proteins from coarse-grained simulations. We show that this two-dimensional representation is a powerful basis to identify meaningful states in the ensemble of aggregated structures and to calculate distributions and free energy landscapes for different sets of simulations. By using a measure to quantitatively compare free energy landscapes we can show how the introduction of a covalent bond between two ubiquitin proteins at different positions alters the configurational states of these dimers.

scholarly journals Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

2017 ◽  
Vol 114 (28) ◽  
pp. E5494-E5503 ◽  
Author(s):  
Eliodoro Chiavazzo ◽  
Roberto Covino ◽  
Ronald R. Coifman ◽  
C. William Gear ◽  
Anastasia S. Georgiou ◽  
...  
Keyword(s):  
Free Energy ◽  
Added Value ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Computer Assisted ◽  
Energy Landscapes ◽  
Learning Techniques ◽  
Free Energy Landscapes ◽  
Low Dimensional ◽  
Energy Surfaces

We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES.

Rapid Perturbation of Free-Energy Landscapes: From In Vitro to In Vivo

2012 ◽  
Vol 18 (21) ◽  
pp. 6420-6427 ◽  
Author(s):  
Hannah Gelman ◽  
Max Platkov ◽  
Martin Gruebele
Keyword(s):  
Free Energy ◽  
Energy Landscapes ◽  
Free Energy Landscapes
Sign in / Sign up

Export Citation Format

Share Document