scholarly journals Systematic Interrogation of Protein Refolding Under Cellular-Like Conditions

2021 ◽  
Author(s):  
Philip To ◽  
Sea On Lee ◽  
Yingzi Xia ◽  
Taylor Devlin ◽  
Karen G Fleming ◽  
...  
Keyword(s):  
Isotope Labeling ◽  
Energy Landscape ◽  
Limited Proteolysis ◽  
Energy Landscapes ◽  
E Coli ◽  
Indirect Measures ◽  
Cellular Factors ◽  
Biophysical Techniques ◽  
Acidic Proteins ◽  
Intrinsic Energy

The journey by which proteins navigate their energy landscapes to their native structures is complex, involving (and sometimes requiring) many cellular factors and processes operating in partnership with a given polypeptide chain's intrinsic energy landscape. The cytosolic environment and its complement of chaperones play critical roles in granting proteins safe passage to their native states; however, the complexity of this medium has generally precluded biophysical techniques from interrogating protein folding under cellular-like conditions for single proteins, let alone entire proteomes. Here, we develop a limited-proteolysis mass spectrometry approach paired within an isotope-labeling strategy to globally monitor the structures of refolding E. coli proteins in the cytosolic medium and with the chaperones, GroEL/ES (Hsp60) and DnaK/DnaJ/GrpE (Hsp70/40). GroEL can refold the majority (85%) of the E. coli proteins for which we have data, and is particularly important for restoring acidic proteins and proteins with high molecular weight, trends that come to light because our assay measures the structural outcome of the refolding process itself, rather than indirect measures like binding or aggregation. For the most part, DnaK and GroEL refold a similar set of proteins, supporting the view that despite their vastly different structures, these two chaperones both unfold misfolded states, as one mechanism in common. Finally, we identify a cohort of proteins that are intransigent to being refolded with either chaperone. The data support a model in which chaperone-nonrefolders have evolved to fold efficiently once and only once, co-translationally, and remain kinetically trapped in their native conformations.

scholarly journals Universally bistable shells with nonzero Gaussian curvature for two-way transition waves

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nikolaos Vasios ◽  
Bolei Deng ◽  
Benjamin Gorissen ◽  
Katia Bertoldi
Keyword(s):  
Gaussian Curvature ◽  
Energy Landscape ◽  
Propagation Distance ◽  
Energy Landscapes ◽  
Bending Energy ◽  
Nonlinear Dynamic Response ◽  
One Dimensional ◽  
Doubly Curved Shells ◽  
Doubly Curved ◽  
The Waves

AbstractMulti-welled energy landscapes arising in shells with nonzero Gaussian curvature typically fade away as their thickness becomes larger because of the increased bending energy required for inversion. Motivated by this limitation, we propose a strategy to realize doubly curved shells that are bistable for any thickness. We then study the nonlinear dynamic response of one-dimensional (1D) arrays of our universally bistable shells when coupled by compressible fluid cavities. We find that the system supports the propagation of bidirectional transition waves whose characteristics can be tuned by varying both geometric parameters as well as the amount of energy supplied to initiate the waves. However, since our bistable shells have equal energy minima, the distance traveled by such waves is limited by dissipation. To overcome this limitation, we identify a strategy to realize thick bistable shells with tunable energy landscape and show that their strategic placement within the 1D array can extend the propagation distance of the supported bidirectional transition waves.

scholarly journals Intrinsic Energy Landscapes of Amino Acid Side-Chains

2012 ◽  
Vol 52 (6) ◽  
pp. 1559-1572 ◽  
Author(s):  
Xiao Zhu ◽  
Pedro E.M. Lopes ◽  
Jihyun Shim ◽  
Alexander D. MacKerell
Keyword(s):  
Amino Acid ◽  
Side Chains ◽  
Energy Landscapes ◽  
Amino Acid Side Chains ◽  
Intrinsic Energy

scholarly journals Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein

2021 ◽  
Vol 119 (1) ◽  
pp. e2109169119
Author(s):  
Kristen A. Gaffney ◽  
Ruiqiong Guo ◽  
Michael D. Bridges ◽  
Shaima Muhammednazaar ◽  
Daoyang Chen ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Lipid Bilayer ◽  
Lipid Bilayers ◽  
Limited Proteolysis ◽  
Water Soluble ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Denatured State ◽  
E Coli ◽  
State Ensemble

Defining the denatured state ensemble (DSE) and disordered proteins is essential to understanding folding, chaperone action, degradation, and translocation. As compared with water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we measure the DSE of the helical membrane protein GlpG of Escherichia coli (E. coli) in native-like lipid bilayers. The DSE was obtained using our steric trapping method, which couples denaturation of doubly biotinylated GlpG to binding of two streptavidin molecules. The helices and loops are probed using limited proteolysis and mass spectrometry, while the dimensions are determined using our paramagnetic biotin derivative and double electron–electron resonance spectroscopy. These data, along with our Upside simulations, identify the DSE as being highly dynamic, involving the topology changes and unfolding of some of the transmembrane (TM) helices. The DSE is expanded relative to the native state but only to 15 to 75% of the fully expanded condition. The degree of expansion depends on the local protein packing and the lipid composition. E. coli’s lipid bilayer promotes the association of TM helices in the DSE and, probably in general, facilitates interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.

Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules

2015 ◽  
Vol 14 (10) ◽  
pp. 4179-4193 ◽  
Author(s):  
Michela Di Michele ◽  
Elisabeth Stes ◽  
Elien Vandermarliere ◽  
Rohit Arora ◽  
Juan Astorga-Wells ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Small Molecules ◽  
Conformational Changes ◽  
Isotope Labeling ◽  
Limited Proteolysis ◽  
Stable Isotope Labeling

scholarly journals Graphene and novel graphitic ZnO and ZnS nanofilms: the energy landscape, non-stoichiometry and water dissociation

2019 ◽  
Vol 1 (5) ◽  
pp. 1924-1935
Author(s):  
Sergio Conejeros ◽  
Neil L. Allan ◽  
Frederik Claeyssens ◽  
Judy N. Hart
Keyword(s):  
Ab Initio ◽  
Energy Landscape ◽  
Adsorbed Water ◽  
Water Dissociation ◽  
Energy Landscapes ◽  
Zns Films

Ab initio energy landscapes of thin ZnO and ZnS films reveal new structures, non-stoichiometry and different behaviour of adsorbed water.

The energy landscape concept and its implications for synthesis planning

2014 ◽  
Vol 86 (6) ◽  
pp. 883-898 ◽  
Author(s):  
Martin Jansen
Keyword(s):  
Energy Landscape ◽  
Chemical Compounds ◽  
Materials Chemistry ◽  
Energy Landscapes ◽  
Free Energies ◽  
Lack Of Control ◽  
Synthesis Planning ◽  
Materials Research ◽  
Potential Energy Landscapes ◽  
Almost All

AbstractSynthesis of novel solids, in a chemical sense, is one of the spearheads of innovation in materials research. However, such an undertaking is substantially impaired by lack of control and predictability. We present a concept that points the way towards rational planning of syntheses in solid state and materials chemistry. The foundation of our approach is the representation of the whole material world, i.e., the known and not-yet-known chemical compounds, on an energy landscape, which implies information about the free energies of these configurations. From this it follows at once that all chemical compounds capable of existence (both thermodynamically stable and metastable ones) are already present in virtuo in this landscape. For the first step of synthesis planning, i.e., the identification of candidates that are capable of existence, we computationally search the respective potential energy landscapes for (meta)stable structure candidates. Recently we have extended our techniques to finite temperatures and pressures and calculated phase diagrams, including metastable manifestations of matter, without resorting to any experimental pre-information. The conception developed is physically consistent, and its feasibility has been proven. Applying appropriate experimental tools has enabled us to realize, e.g., elusive Na3 N, including almost all of its predicted polymorphs, many years after the predictions were published.

Energy landscapes for cooperative processes: nearly ideal glass transitions, liquid–liquid transitions and folding transitions

2004 ◽  
Vol 363 (1827) ◽  
pp. 415-432 ◽  
Author(s):  
C. Austen Angell
Keyword(s):  
Phase Transitions ◽  
Liquid Phase ◽  
Point Defects ◽  
Laboratory Experiments ◽  
Constant Pressure ◽  
Energy Landscape ◽  
Experimental Methods ◽  
Glass Transitions ◽  
Energy Landscapes ◽  
Cooperative Processes

We describe basic phenomenology in the physics of supercooling liquids at constant volume (most simulations), and at constant pressure (most laboratory experiments) before focusing attention on the exceptional cases that exhibit liquid–liquid phase transitions on constant–pressure cooling. We give evidence for point defects in glasses and liquids near T g . Models based on defects predict transitions with density gaps in constant–pressure systems. We describe the energy landscape representation of such systems. Water, in these terms, is post–critical, and its nearly ideal glass formation can be related to nucleation–free protein ‘funnel–folding’. For nucleated folding of proteins, a pseudo–gap should be present. Experimental methods of distinguishing between alternative folding scenarios are described.

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