Computing protein dynamics from protein structure with elastic network models

2014 ◽  
Vol 4 (5) ◽  
pp. 488-503 ◽  
Author(s):  
Ugo Bastolla
Keyword(s):  
Protein Structure ◽  
Protein Dynamics ◽  
Network Models ◽  
Elastic Network ◽  
Elastic Network Models

scholarly journals FlexE: Using Elastic Network Models to Compare Models of Protein Structure

2012 ◽  
Vol 8 (10) ◽  
pp. 3985-3991 ◽  
Author(s):  
Alberto Perez ◽  
Zheng Yang ◽  
Ivet Bahar ◽  
Ken A. Dill ◽  
Justin L. MacCallum
Keyword(s):  
Protein Structure ◽  
Network Models ◽  
Elastic Network ◽  
Elastic Network Models

scholarly journals New Mechanistic Insights on Carbon Nanotubes’ Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 171
Author(s):  
Michael González-Durruthy ◽  
Riccardo Concu ◽  
Juan M. Ruso ◽  
M. Natália D. S. Cordeiro
Keyword(s):  
Carbon Nanotubes ◽  
Network Models ◽  
Single Walled Carbon Nanotubes ◽  
Docking Studies ◽  
Fractal Surface ◽  
Submitochondrial Particles ◽  
Elastic Network ◽  
Elastic Network Models ◽  
Walled Carbon Nanotubes

Single-walled carbon nanotubes can induce mitochondrial F0F1-ATPase nanotoxicity through inhibition. To completely characterize the mechanistic effect triggering the toxicity, we have developed a new approach based on the combination of experimental and computational study, since the use of only one or few techniques may not fully describe the phenomena. To this end, the in vitro inhibition responses in submitochondrial particles (SMP) was combined with docking, elastic network models, fractal surface analysis, and Nano-QSTR models. In vitro studies suggest that inhibition responses in SMP of F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/mL) for both pristine and COOH single-walled carbon nanotubes types (SWCNT). Besides, both SWCNTs show an interaction inhibition pattern mimicking the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor blocking the c-ring F0 subunit). Performed docking studies denote the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB) fit well with the in vitro evidence from the thermodynamics point of view, following an affinity order such as: FEB (oligomycin A/F0-ATPase complex) = −9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = −6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = −5.9 kcal/mol, with predominance of van der Waals hydrophobic nano-interactions with key F0-ATPase binding site residues (Phe 55 and Phe 64). Elastic network models and fractal surface analysis were performed to study conformational perturbations induced by SWCNT. Our results suggest that interaction may be triggering abnormal allosteric responses and signals propagation in the inter-residue network, which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). In addition, Nano-QSTR models have been developed to predict toxicity induced by both SWCNTs, using results of in vitro and docking studies. Results show that this method may be used for the fast prediction of the nanotoxicity induced by SWCNT, avoiding time- and money-consuming techniques. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug design-based nanotechnology, and potential biomedical application in precision nanomedicine.

scholarly journals Edge-based formulation of elastic network models

2019 ◽  
Vol 1 (3) ◽  
Author(s):  
Maxwell Hodges ◽  
Sophia N. Yaliraki ◽  
Mauricio Barahona
Keyword(s):  
Network Models ◽  
Elastic Network ◽  
Elastic Network Models ◽  
Edge Based

scholarly journals Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

2008 ◽  
Vol 2 ◽  
pp. BBI.S460 ◽  
Author(s):  
Lee-Wei Yang ◽  
Choon-Peng Chng
Keyword(s):  
Conformational Changes ◽  
Conformational Dynamics ◽  
Computational Cost ◽  
Network Models ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Elastic Network ◽  
Elastic Network Models ◽  
Time Space ◽  
Functional Dynamics

In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series.

scholarly journals Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

2015 ◽  
Vol 11 (10) ◽  
pp. e1004542 ◽  
Author(s):  
Hyuntae Na ◽  
Robert L. Jernigan ◽  
Guang Song
Keyword(s):  
Network Models ◽  
Coarse Grained ◽  
Elastic Network ◽  
Elastic Network Models

scholarly journals Validating and Improving Elastic Network Models Using Molecular Dynamics

2011 ◽  
Vol 100 (3) ◽  
pp. 155a
Author(s):  
Nicholas Leioatts ◽  
Tod D. Romo ◽  
Alan Grossfield
Keyword(s):  
Molecular Dynamics ◽  
Network Models ◽  
Elastic Network ◽  
Elastic Network Models

scholarly journals The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

2006 ◽  
Vol 2 (3) ◽  
pp. 696-704 ◽  
Author(s):  
Taner Z. Sen ◽  
Yaping Feng ◽  
John V. Garcia ◽  
Andrzej Kloczkowski ◽  
Robert L. Jernigan
Keyword(s):  
Network Models ◽  
Elastic Network ◽  
Protein Motions ◽  
Elastic Network Models
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