Criteria for selecting PEGylation sites on proteins for higher thermodynamic and proteolytic stability.
- P. B. Lawrence, Y. Gavrilov, J. Price
- Biology, ChemistryJournal of the American Chemical Society
- 4 December 2014
A structure-based method for predicting which sites within WW are most likely to experience PEG-based stabilization, and it is shown that this method correctly predicts the location of a stabilizing PEGylation site within the chicken Src SH3 domain.
Mapping fast protein folding with multiple-site fluorescent probes
- M. Prigozhin, Shu-Han Chao, Shahar Sukenik, T. Pogorelov, M. Gruebele
- BiologyProceedings of the National Academy of Sciences
- 15 June 2015
Comparing fast–protein-folding experiments and molecular-dynamics simulations can nowadays be compared on the same timescale and this work demonstrates that comparison between experiment and simulation can be extended to several order parameters, providing a stronger mechanistic test.
The fast and the slow: folding and trapping of λ6-85.
- M. Prigozhin, M. Gruebele
- BiologyJournal of the American Chemical Society
- 7 December 2011
The experimental data and computational modeling suggest the following hypothesis: λ(6-85) is not only thermodynamically but also kinetically protected from reaching such "intramolecular amyloids" while folding, while the latter takes milliseconds to reach compact β-rich traps.
Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides.
- S. Ebbinghaus, K. Meister, M. Gruebele
- Biology, ChemistryBiophysical Journal
- 18 July 2012
Microsecond folding experiments and simulations: a match is made.
- M. Prigozhin, M. Gruebele
- PhysicsPhysical Chemistry, Chemical Physics - PCCP
- 13 February 2013
In this perspective, recent experiments and simulations on the microsecond time scale are compared, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulation to provide more quantitative underlying mechanisms, and tackling the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.
Misplaced helix slows down ultrafast pressure-jump protein folding
- M. Prigozhin, Yanxin Liu, M. Gruebele
- BiologyProceedings of the National Academy of Sciences
- 25 April 2013
The overall conclusion from experiment and simulation is that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast P-drop, at least some λ-YA forms misplaced helical structure within microseconds.
Impact of site-specific PEGylation on the conformational stability and folding rate of the Pin WW domain depends strongly on PEG oligomer length.
- B. K. Pandey, Mason S. Smith, J. Price
- Biology, ChemistryBioconjugate chemistry
- 26 April 2013
It is shown that appending a short PEG oligomer to a single Asn side chain within a reverse turn in the WW domain of the human protein Pin 1 increases WW conformational stability in a manner that depends strongly on the length of the P EG oligomer: shorter oligomers increase folding rate, whereas longer oligomers increased folding rate and reduce unfolding rate.
Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.
- A. Wirth, Yanxin Liu, M. Prigozhin, K. Schulten, M. Gruebele
- Biology, EngineeringJournal of the American Chemical Society
- 2 June 2015
Experimental and computational data highlight FiP35's position at the boundary where activated intermediates and downhill folding meet, and it is shown that this model protein is an excellent candidate for further pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.
Studying IDP stability and dynamics by fast relaxation imaging in living cells.
- A. Dhar, M. Prigozhin, H. Gelman, M. Gruebele
- BiologyMethods in molecular biology
- 2012
Fast relaxation imaging (FReI) temperature-tunes living cells and applies small temperature jumps to them, to monitor biomolecular stability and kinetics in vivo, to measure IDP stability and folding inside the cell.
Bright sub-20-nm cathodoluminescent nanoprobes for electron microscopy
- M. Prigozhin, Peter C. Maurer, S. Chu
- Biology, ChemistryNature Nanotechnology
- 30 May 2018
This work synthesizes small lanthanide-doped nanoparticles and measures the absolute photon emission rate of individual nanoparticles resulting from a given electron excitation flux (cathodoluminescence) to suggest that the optimization of nanoparticle composition, synthesis protocols and electron imaging conditions can lead to sub-20-nm nanolabels that would enable high signal-to-noise localization of individual biomolecules within a cellular context.
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