A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level

DasGupta, Debarati; Mandalaparthy, Varun; Jayaram, B.

doi:10.1002/jcc.25072

Cited by 15 publications

(4 citation statements)

References 141 publications

(202 reference statements)

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“…Salt concentrations did not have important impact on the resulting binding free energies, therefore 0.15 M was used as in the MD simulation. It is well known that MM/PBSA and MM/GBSA usually overestimate the absolute binding free energy, therefore the resulting binding free energies were scaled down using the scaling factor of 2.45 as proposed for the MM/GBSA method by DasGupta et al [ 42 ]. So obtained binding free energy results were used to estimate the qualitative differences between the two COVID viruses, not the absolute values of the binding free energies.…”

Section: Resultsmentioning

confidence: 99%

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A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

et al. 2022

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The pandemic of COVID-19 severe acute respiratory syndrome, which was fatal for millions of people worldwide, triggered the race to understand in detail the molecular mechanisms of this disease. In this work, the differences of interactions between the SARS-CoV/SARS-CoV-2 Receptor binding domain (RBD) and the human Angiotensin Converting Enzyme 2 (ACE2) receptor were studied using in silico tools. Our results show that SARS-CoV-2 RBD is more stable and forms more interactions with ACE2 than SARS-CoV. At its interface, three stable binding patterns are observed and named red-K31, green-K353 and blue-M82 according to the central ACE2 binding residue. In SARS-CoV instead, only the first two binding patches are persistently formed during the MD simulation. Our MM/GBSA calculations indicate the binding free energy difference of about 2.5 kcal/mol between SARS-CoV-2 and SARS-CoV which is compatible with the experiments. The binding free energy decomposition points out that SARS-CoV-2 RBD–ACE2 interactions of the red-K31 ($$-23.5~\pm ~0.2~kcal/mol$$ - 23.5 ± 0.2 k c a l / m o l ) and blue-M82 ($$-9.1~\pm ~0.1~kcal/mol$$ - 9.1 ± 0.1 k c a l / m o l ) patterns contribute more to the binding affinity than in SARS-CoV ($$-1.8~\pm ~0.02~kcal/mol$$ - 1.8 ± 0.02 k c a l / m o l for red-K31), while the contribution of the green-K353 pattern is very similar in the two strains ($$-17.8~\pm ~0.2~kcal/mol$$ - 17.8 ± 0.2 k c a l / m o l and $$-22.7~\pm ~0.1~kcal/mol$$ - 22.7 ± 0.1 k c a l / m o l for SARS-CoV-2 and SARS-CoV, respectively). Five groups of mutations draw our attention at the RBD–ACE2 binding interface, among them, the mutation –PPA469-471/GVEG482-485 has the most important and favorable impact on SARS-CoV-2 binding to the ACE2 receptor. These results, highlighting the molecular differences in the binding between the two viruses, contribute to the common knowledge about the new corona virus and to the development of appropriate antiviral treatments, addressing the necessity of ongoing pandemics.

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Section: Resultsmentioning

confidence: 99%

“…The Molecular mechanics with generalized Born and surface area solvation (MM/GBSA) method was employed using the mmpbsa.py script (Eqs 2 & 3) [40,41]. The resulting binding free energies were scaled down using the scaling factor of 2.45 as proposed for the MM/GBSA method by DasGupta et al [42].…”

Section: Molecular Dynamics (Md) Simulationmentioning

confidence: 99%

A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

et al. 2022

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“…Gas-phase infrared (IR) spectroscopy of small and medium peptides − allows insight into protein folding forces − at the atomic level. Thanks to the development of various techniques to transfer intact biomolecules into the gas phase, IR spectroscopy became a routine tool for studies of biomolecular systems of increasing size and complexity .…”

Section: Introductionmentioning

confidence: 99%

Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches

et al. 2019

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In this article, we report the results of gas-phase IR spectroscopy of neutral glycylglycine (Gly-Gly) in the 700− 1850 cm −1 frequency range. A combination of laser desorption, jet-cooling, and IR multiple-photon dissociation vacuum− ultraviolet (IRMPD-VUV) action spectroscopy is employed, together with extensive quantum chemical calculations that assist in the analysis of the experimental data. As a result, we determined that the most favorable conformer in the lowtemperature environment of the supersonic jet is the nearly planar structure with two C5 hydrogen-bonding interactions. Calculations clearly show that this conformer is favored because of its flexibility (considerable entropy stabilization) as well as efficient conformer relaxation processes in the jet. To gain more understanding into the relative stability of the lowest-energy Gly-Gly conformers, the relative strength of hydrogen bonding and steric interactions is analyzed using the noncovalent interactions (NCI) approach.

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“…The mean square fluctuation of the minimum distances between proteins and ligands was observed in MD (RMSF, Å) [47]. The plots were generated using the Qtrace program.…”

mentioning

confidence: 99%

Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst

Nobre,

Silva,

Menezes

et al. 2023

Compounds

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The scientific community recognizes coffee grounds (Coffea arabica) as an important biological residue, which led to using the Eversa® Transform 2.0 lipase as an in silico enzymatic catalyst for coffee grounds’ free fatty acids (FFA). Molecular modeling studies, including molecular docking, were performed, which revealed the structures of the lipase and showed the primary interactions between the ligands and the amino acid residues in the active site of the enzyme. Of the ligands tested, 6,9-methyl octadienoate had the best free energy of −6.1 kcal/mol, while methyl octadecenoate and methyl eicosanoate had energies of −5.7 kcal/mol. Molecular dynamics confirmed the stability of the bonds with low Root Mean Square Deviation (RMSD) values. The MMGBSA study showed that methyl octadecenoate had the best free energy estimate, and CASTp identified key active sites for potential enzyme immobilization in experimental studies. Overall, this study provides efficient and promising results for future experimental investigations, showing a classification of oils present in coffee grounds and their binding affinity with Eversa.

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A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level

Cited by 15 publications

References 141 publications

A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches

Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst

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