Folding intermediates of wild-type and mutants of barnase. II. correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate

1998 ◽  
Vol 276 (3) ◽  
pp. 647-656 ◽  
Author(s):  
Paul A. Dalby ◽  
Jane Clarke ◽  
Christopher M. Johnson ◽  
Alan R. Fersht
Keyword(s):  
Folding Intermediate ◽  
Wild Type ◽  
Folding Intermediates ◽  
Amide Exchange ◽  
Exchange Kinetics

scholarly journals Pharmacological inactivation of the prion protein by targeting a folding intermediate

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Giovanni Spagnolli ◽  
Tania Massignan ◽  
Andrea Astolfi ◽  
Silvia Biggi ◽  
Marta Rigoli ◽  
...  
Keyword(s):  
Prion Protein ◽  
Prion Diseases ◽  
Cellular Prion Protein ◽  
Surface Glycoprotein ◽  
Folding Intermediate ◽  
Biological Regulation ◽  
Cell Surface Glycoprotein ◽  
Folding Intermediates ◽  
Protein Levels ◽  
Small Molecule Ligands

AbstractRecent computational advancements in the simulation of biochemical processes allow investigating the mechanisms involved in protein regulation with realistic physics-based models, at an atomistic level of resolution. These techniques allowed us to design a drug discovery approach, named Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT), based on the rationale of negatively regulating protein levels by targeting folding intermediates. Here, PPI-FIT was tested for the first time on the cellular prion protein (PrP), a cell surface glycoprotein playing a key role in fatal and transmissible neurodegenerative pathologies known as prion diseases. We predicted the all-atom structure of an intermediate appearing along the folding pathway of PrP and identified four different small molecule ligands for this conformer, all capable of selectively lowering the load of the protein by promoting its degradation. Our data support the notion that the level of target proteins could be modulated by acting on their folding pathways, implying a previously unappreciated role for folding intermediates in the biological regulation of protein expression.

Structure of a kinetic protein folding intermediate by equilibrium amide exchange

1997 ◽  
Vol 4 (10) ◽  
pp. 801-804 ◽  
Author(s):  
Laszlo L. P. Hosszu ◽  
C. Jeremy Craven ◽  
Martin J. Parker ◽  
Mark Lorch ◽  
James Spencer ◽  
...  
Keyword(s):  
Protein Folding ◽  
Folding Intermediate ◽  
Amide Exchange

Kinetic and equilibrium folding intermediates

1995 ◽  
Vol 348 (1323) ◽  
pp. 35-41 ◽  
Keyword(s):  
Protein Folding ◽  
Molten Globule ◽  
Low Dielectric Constant ◽  
The Novel ◽  
Folding Intermediate ◽  
Molten Globule State ◽  
Folding Intermediates ◽  
First Order ◽  
Low Dielectric ◽  
First Order Phase

Our recent experiments on the molten globule state and other protein folding intermediates lead to following conclusions: (i) the molten globule is separated by intramolecular first-order phase transitions from the native and unfolded states and therefore is a specific thermodynamic state of protein molecules; (ii) the novel equilibrium folding intermediate (the ‘pre-molten globule’ state) exists which can be similar to the ‘burst’ kinetic intermediate of protein folding; (iii) proteins denature and release their non-polar ligands at moderately low pH and moderately low dielectric constant, i.e. under conditions which may be related to those near membranes.

Kinetic and thermodynamic properties of wild-type and engineered mutants of tyrosyl-tRNA synthetase analyzed by pyrophosphate-exchange kinetics

Biochemistry ◽  
1991 ◽  
Vol 30 (21) ◽  
pp. 5151-5156 ◽  
Author(s):  
Tim N. C. Wells ◽  
Jack W. Knill-Jones ◽  
Tamara E. Gray ◽  
Alan R. Fersht
Keyword(s):  
Thermodynamic Properties ◽  
Trna Synthetase ◽  
Wild Type ◽  
Exchange Kinetics

scholarly journals Signal Sequence Mutations as Tools for the Characterization of LamB Folding Intermediates

2002 ◽  
Vol 184 (24) ◽  
pp. 6918-6928 ◽  
Author(s):  
Amy Rizzitello Duguay ◽  
Thomas J. Silhavy
Keyword(s):  
Amino Acid ◽  
Outer Membrane ◽  
Biochemical Analysis ◽  
Positive Charge ◽  
Signal Sequence ◽  
Wild Type ◽  
Inner Membrane ◽  
Folding Intermediates ◽  
Sequence Processing

ABSTRACT lamBA23DA25Y and lamBA23YA25Y tether LamB to the inner membrane by blocking signal sequence processing. We isolated suppressors of lamBA23DA25Y and lamBA23YA25Y, all of which mapped within the LamB signal sequence. Most interesting were mutations that changed an amino acid with a strong positive charge to an amino acid with no charge. Further characterization of two such suppressors revealed that they produce functional LamB that is localized to the outer membrane with its entire signal sequence still attached. Biochemical analysis shows that mutant LamB monomer chases into an oligomeric species with properties different from those of wild-type LamB trimer. Because assembly of mutant LamB is slowed, these mutations provide useful tools for the characterization of LamB folding intermediates.

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