The Energy Landscape Theory of Protein Folding

1997 ◽  
pp. 61-79 ◽  
Author(s):  
Peter G. Wolynes ◽  
Zan Luthey-Schulten
Keyword(s):  
Protein Folding ◽  
Energy Landscape ◽  
Energy Landscape Theory ◽  
Landscape Theory

scholarly journals Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility

2021 ◽  
Author(s):  
Ryan R. Cheng ◽  
Esteban Dodero-Rojas ◽  
Michele Di Pierro ◽  
José Nelson Onuchic
Keyword(s):  
Protein Folding ◽  
Protein Sequence ◽  
Energy Landscape ◽  
Spike Protein ◽  
Receptor Protein ◽  
Energy Landscape Theory ◽  
Landscape Theory ◽  
Selection Of

We explore the energetic frustration patterns associated with the binding between the SARS-CoV-2 spike protein and the ACE2 receptor protein in a broad selection of animals. Using energy landscape theory and the concept of energy frustration—theoretical tools originally developed to study protein folding—we are able to identify interactions among residues of the spike protein and ACE2 that result in COVID-19 resistance. This allows us to identify whether or not a particular animal is susceptible to COVID-19 from the protein sequence of ACE2 alone. Our analysis predicts a number of experimental observations regarding COVID-19 susceptibility, demonstrating that this feature can be explained, at least partially, on the basis of theoretical means.

The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios

2000 ◽  
pp. 87-152 ◽  
Author(s):  
José Nelson Onuchic ◽  
Hugh Nymeyer ◽  
Angel E. García ◽  
Jorge Chahine ◽  
Nicholas D. Socci
Keyword(s):  
Protein Folding ◽  
Energy Landscape ◽  
Energy Landscape Theory ◽  
Landscape Theory

Recent successes of the energy landscape theory of protein folding and function

2005 ◽  
Vol 38 (4) ◽  
pp. 405-410 ◽  
Author(s):  
P. G. Wolynes
Keyword(s):  
Protein Folding ◽  
Energy Landscape ◽  
Helical Bundles ◽  
Energy Landscape Theory ◽  
Landscape Theory ◽  
Hydrophilic Residues ◽  
And Function ◽  
Quality Of Structure

Protein folding and binding can be understood using energy landscape theory. When seeming deviations from the predictions of the funnel hypothesis are found, landscape theory helps us locate the cause. Sometimes the deviation reflects symmetry effects, allowing extra degeneracies to occur. Such effects seem to explain some kinetic anomalies in helical bundles. When binding processes were found to use apparently non-funneled landscapes this was traced to an inadequate understanding of biomolecular forces. The discrepancy allowed the discovery of new water-mediated forces – some of which act between hydrophilic residues. Introducing such forces into the algorithms greatly improves the quality of structure predictions.

scholarly journals Impact of Conformational Substates and Energy Landscapes on Understanding Hemoglobin Kinetics and Function

2021 ◽  
Author(s):  
William A. Eaton
Keyword(s):  
Protein Folding ◽  
Protein Function ◽  
Energy Landscape ◽  
Rate Theory ◽  
Energy Landscapes ◽  
New Era ◽  
Energy Landscape Theory ◽  
Conformational Substates ◽  
Landscape Theory ◽  
And Function

AbstractHans Frauenfelder’s discovery of conformational substates in studies of myoglobin carbon monoxide geminate rebinding kinetics at cryogenic temperatures (Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, & Gunsalus IC (1975) Dynamics of Ligand Binding to Myoglobin. Biochemistry 14(24):5355–5373) followed by his introduction of energy landscape theory with Peter Wolynes (Frauenfelder H, Sligar SG, & Wolynes PG (1991) The Energy Landscapes and Motions of Proteins. Science 254(5038):1598–1603) marked the beginning of a new era in the physics and physical chemistry of proteins. Their work played a major role in demonstrating the power and importance of dynamics and of Kramers reaction rate theory for understanding protein function. The biggest impact of energy landscape theory has been in the protein folding field, which is well-known and has been documented in numerous articles and reviews, including a recent one of my own (Eaton WA (2021) Modern Kinetics and Mechanism of Protein Folding: a Retrospective. J. Phys. Chem. B. 125(14):3452–3467). Here I will describe the much less well-known impact of their modern view of proteins on both experimental and theoretical studies of hemoglobin kinetics and function. I will first describe how Frauenfelder’s experiments motivated and influenced my own research on myoglobin, which were key ingredients to my work on understanding hemoglobin.

scholarly journals Learning To Fold Proteins Using Energy Landscape Theory

2014 ◽  
Vol 54 (8-9) ◽  
pp. 1311-1337 ◽  
Author(s):  
Nicholas P. Schafer ◽  
Bobby L. Kim ◽  
Weihua Zheng ◽  
Peter G. Wolynes
Keyword(s):  
Energy Landscape ◽  
Energy Landscape Theory ◽  
Landscape Theory

scholarly journals COVID-19: Energy landscape theory of SARS-CoV-2 complexes with Particulate Matter

2020 ◽  
Author(s):  
Gianluigi Zangari del Balzo
Keyword(s):  
Particulate Matter ◽  
Energy Landscape ◽  
The United States ◽  
Deep Penetration ◽  
Energy Landscape Theory ◽  
Landscape Theory ◽  
Italian Regions ◽  
Rapid Spread ◽  
Experimental Laboratory ◽  
Definition Of

In the past few days, the global scientific community has made much progress in research for the COVID-19 pandemic, but the new SARS-CoV-2 coronavirus has not yet been correctly characterized thermodynamically and much is still unknown. In particular, the current SARS-CoV-2 models lack the characterization of the virus system within its environment. This is a serious systematic error, which stands in the way of impeding research into the pandemic.In the present work, therefore, we consider the SARS-CoV-2 system with its environment, and we give a correct thermodynamic definition, through analysis and simulations, from air transport to cellular entry through the mechanism of receptor- mediated endocytosis.In studying the aerosol environment of the SARS-CoV-2 virus, we cannot omit the presence of nanoparticles or dust.Therefore, analyzing and comparing the air environments in China and Italy, we note that the Chinese and Italian regions which were at the beginning the most affected by the pandemic are also the most polluted. The same phenomenon is happening today for the United States and Brazil.We therefore propose an energy landscape theory of synergistic complexes of SARS- CoV-2 with particulate matter (PM).This could explain the optimized strategy of deep penetration of interstitial lung cells and the rapid spread of the pandemic in the most polluted areas of the planet. It could also explain the severity and difficulty of treating the forms of interstitial pneumonia occurred in Italy and worldwide.The energy landscape theory of complexes of SARS-CoV-2 with particulate matter (PM), leads to crucial methodological constraints aimed at containing systematic errors in experimental laboratory procedures and in mathematical modeling, which can allow and accelerate the definition of the mechanism of action of the virus and therefore the realization of the appropriate therapies and health protocols.

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