scholarly journals Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

Nanoscale ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 5422-5434 ◽  
Author(s):  
David Winogradoff ◽  
Shalini John ◽  
Aleksei Aksimentiev
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Anionic Surfactant ◽  
Protein Unfolding ◽  
Protein Assembly ◽  
Full Length ◽  
Dynamics Simulations

Molecular dynamics simulations reveal how anionic surfactant SDS and heat unfold full-length proteins.

scholarly journals The flexibility of ACE2 in the context of SARS-CoV-2 infection

2020 ◽  
Author(s):  
E. P. Barros ◽  
L. Casalino ◽  
Z. Gaieb ◽  
A. C. Dommer ◽  
Y. Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Receptor Binding ◽  
Rational Design ◽  
Binding Domain ◽  
Full Length ◽  
Receptor Binding Domain ◽  
Spike Glycoprotein ◽  
Linker Region ◽  
Dynamics Simulations

AbstractThe COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.Statement of SignificanceAs the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.

Targeted Molecular Dynamics Simulations of Protein Unfolding

2000 ◽  
Vol 104 (18) ◽  
pp. 4511-4518 ◽  
Author(s):  
Philippe Ferrara ◽  
Joannis Apostolakis ◽  
Amedeo Caflisch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Unfolding ◽  
Targeted Molecular Dynamics ◽  
Dynamics Simulations

Validation of protein-unfolding transition states identified in molecular dynamics simulations

2001 ◽  
Vol 68 ◽  
pp. 83-93 ◽  
Author(s):  
Valerie Daggett
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Protein Unfolding ◽  
Molecular Structures ◽  
Simulation Studies ◽  
Molecular Models ◽  
Chymotrypsin Inhibitor 2 ◽  
Combined Use ◽  
Dynamics Simulations

Experimental and simulation studies can complement each other nicely in the area of protein folding. Experiment reports on the average properties of a large ensemble (approx. 10(17)-10(19) molecules), typically over time. Molecular dynamics simulations, on the other hand, provide detailed information for a single molecule, a component of the ensemble. By combining these approaches we can obtain not only a more complete picture of folding, but we can also take advantage of the strengths of different methods. For example, experiment cannot provide molecular structures. Molecular dynamics simulations can provide such information, but the simulations are meaningless without a linked experiment. Thus, the interrelated nature of simulation in assessing experimental assumptions and in providing structures to augment energetic descriptions, and experiment in judging whether the simulations are reasonable, provides more confidence in the resulting information about folding. This combination yields tested and testable molecular models of states that evade characterization by conventional methods. Therefore, we have explored the combined use of these methods to map folding/unfolding pathways at atomic resolution, in collaboration with Alan Fersht. Here we focus on chymotrypsin inhibitor 2, a small single-domain, two-state folding protein.

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