Modulation of the Folding Energy Landscape of Cytochromecwith Salt

2004 ◽  
Vol 126 (43) ◽  
pp. 13934-13935 ◽  
Author(s):  
Shi Zhong ◽  
Denis L. Rousseau ◽  
Syun-Ru Yeh
Keyword(s):  
Energy Landscape ◽  
Folding Energy

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals RNA Pseudoknot Folding Energy Landscape Elucidated with T-Jump Measurements and Kinetic Modeling

2015 ◽  
Vol 108 (2) ◽  
pp. 236a ◽  
Author(s):  
Jorjethe Roca ◽  
Yogambigai Velmurugu ◽  
Ranjani Narayanan ◽  
Prasanth Narayanan ◽  
Serguei Kouznetsov ◽  
...  
Keyword(s):  
Kinetic Modeling ◽  
Energy Landscape ◽  
Folding Energy ◽  
Rna Pseudoknot

Temporal Variation of a Protein Folding Energy Landscape in the Cell

2013 ◽  
Vol 135 (51) ◽  
pp. 19215-19221 ◽  
Author(s):  
Anna Jean Wirth ◽  
Max Platkov ◽  
Martin Gruebele
Keyword(s):  
Protein Folding ◽  
Temporal Variation ◽  
Energy Landscape ◽  
Folding Energy

scholarly journals Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

2010 ◽  
Vol 107 (52) ◽  
pp. 22528-22533 ◽  
Author(s):  
M. M. Chen ◽  
A. I. Bartlett ◽  
P. S. Nerenberg ◽  
C. T. Friel ◽  
C. P. R. Hackenberger ◽  
...  
Keyword(s):  
Energy Landscape ◽  
Folding Energy ◽  
Site Specific ◽  
Immunity Protein

scholarly journals Switching of the folding-energy landscape governs the allosteric activation of protein kinase A

2018 ◽  
Vol 115 (32) ◽  
pp. E7478-E7485 ◽  
Author(s):  
Jeneffer P. England ◽  
Yuxin Hao ◽  
Lihui Bai ◽  
Virginia Glick ◽  
H. Courtney Hodges ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Optical Tweezers ◽  
Energy Landscape ◽  
Interaction Network ◽  
Catalytic Subunit ◽  
Regulatory Subunit ◽  
Folding Energy ◽  
Binding Domains ◽  
Conformational Plasticity ◽  
Apo State

Protein kinases are dynamic molecular switches that sample multiple conformational states. The regulatory subunit of PKA harbors two cAMP-binding domains [cyclic nucleotide-binding (CNB) domains] that oscillate between inactive and active conformations dependent on cAMP binding. The cooperative binding of cAMP to the CNB domains activates an allosteric interaction network that enables PKA to progress from the inactive to active conformation, unleashing the activity of the catalytic subunit. Despite its importance in the regulation of many biological processes, the molecular mechanism responsible for the observed cooperativity during the activation of PKA remains unclear. Here, we use optical tweezers to probe the folding cooperativity and energetics of domain communication between the cAMP-binding domains in the apo state and bound to the catalytic subunit. Our study provides direct evidence of a switch in the folding-energy landscape of the two CNB domains from energetically independent in the apo state to highly cooperative and energetically coupled in the presence of the catalytic subunit. Moreover, we show that destabilizing mutational effects in one CNB domain efficiently propagate to the other and decrease the folding cooperativity between them. Taken together, our results provide a thermodynamic foundation for the conformational plasticity that enables protein kinases to adapt and respond to signaling molecules.

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