Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis

2007 ◽  
pp. 305-339 ◽  
Author(s):  
Irina S. Moreira ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos
Keyword(s):  
Free Energy ◽  
Alanine Scanning Mutagenesis ◽  
Alanine Scanning ◽  
Relative Free Energy ◽  
Free Energy Of Binding

scholarly journals Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

2009 ◽  
Vol 35 (10-11) ◽  
pp. 986-997 ◽  
Author(s):  
Abdallah Sayyed-Ahmad ◽  
Himanshu Khandelia ◽  
Yiannis N. Kaznessis
Keyword(s):  
Free Energy ◽  
Antimicrobial Peptides ◽  
Relative Free Energy ◽  
Free Energy Of Binding

scholarly journals Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Alanine Scanning Mutagenesis ◽  
Angiotensin Converting Enzyme 2 ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Protein Interfaces ◽  
Computational Alanine Scanning ◽  
Entry Receptor

<p>The ability of coronaviruses to infect humans is invariably associated with their binding strengths to human receptor proteins. Both SARS-CoV-2, initially named 2019-nCoV, and SARS-CoV were reported to utilize angiotensin-converting enzyme 2 (ACE2) as an entry receptor in human cells. To better understand the interplay between SARS-CoV-2 and ACE2, we performed computational alanine scanning mutagenesis on the “hotspot” residues at protein-protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on a physical basis, and also provide useful information for the design of antiviral drugs.</p>

Hydration of chloride and bromide anions: determination of relative free energy by computer simulation

1985 ◽  
Vol 107 (25) ◽  
pp. 7793-7794 ◽  
Author(s):  
Terry P. Lybrand ◽  
Indira Ghosh ◽  
J. Andrew McCammon
Keyword(s):  
Computer Simulation ◽  
Free Energy ◽  
Relative Free Energy

scholarly journals Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Alanine Scanning Mutagenesis ◽  
Angiotensin Converting Enzyme 2 ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Protein Interfaces ◽  
Computational Alanine Scanning ◽  
Entry Receptor

<p>The ability of coronaviruses to infect humans is invariably associated with their binding strengths to human receptor proteins. Both SARS-CoV-2, initially named 2019-nCoV, and SARS-CoV were reported to utilize angiotensin-converting enzyme 2 (ACE2) as an entry receptor in human cells. To better understand the interplay between SARS-CoV-2 and ACE2, we performed computational alanine scanning mutagenesis on the “hotspot” residues at protein-protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on a physical basis, and also provide useful information for the design of antiviral drugs.</p>

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

2016 ◽  
Vol 57 (1) ◽  
pp. 60-72 ◽  
Author(s):  
Inês C. M. Simões ◽  
Inês P. D. Costa ◽  
João T. S. Coimbra ◽  
Maria J. Ramos ◽  
Pedro A. Fernandes
Keyword(s):  
Free Energy ◽  
Binding Free Energy ◽  
Alanine Scanning Mutagenesis ◽  
Alanine Scanning ◽  
Protein Interfaces

scholarly journals Noncovalent Interactions of Tiopronin-Protected Gold Nanoparticles with DNA: Two Methods to Quantify Free Energy of Binding

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
R. Prado-Gotor ◽  
E. Grueso
Keyword(s):  
Gold Nanoparticles ◽  
Free Energy ◽  
Conformational Changes ◽  
Noncovalent Interactions ◽  
Binding Free Energy ◽  
Free Energies ◽  
Double Stranded Dna ◽  
Second Procedure ◽  
Free Energy Of Binding

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the “true” free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

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