Publications

2019
M. B. Prigozhin, P. C. Maurer, A. M. Courtis, M. D. Wisser N. Liu, C. Siefe, B. Tian, E. Chan, G. Song, S. Fischer, S. Aloni, D. F. Ogletree, E. S. Barnard, L.-M. Joubert, J. Rao, A. P. Alivisatos, R. M. Macfarlane, B. E. Cohen, Y. Cui, J. A. Dionne, and S. Chu. 2019. “Bright sub-20-nm cathodoluminescent nanoprobes for electron microscopy.” Nature Nanotechnology, 14, Pp. 420-425. Publisher's VersionAbstract
Electron microscopy has been instrumental in our understanding of complex biological systems. Although electron microscopy reveals cellular morphology with nanoscale resolution, it does not provide information on the location of different types of proteins. An electron-microscopy-based bioimaging technology capable of localizing individual proteins and resolving protein–protein interactions with respect to cellular ultrastructure would provide important insights into the molecular biology of a cell. Here, we synthesize small lanthanide-doped nanoparticles and measure the absolute photon emission rate of individual nanoparticles resulting from a given electron excitation flux (cathodoluminescence). Our results 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. In ensemble measurements, these labels exhibit narrow spectra of nine distinct colours, so the imaging of biomolecules in a multicolour electron microscopy modality may be possible.
prigozhin_naturenano_2019.pdf prigozhin_naturenano_2019_si.pdf
M. B. Prigozhin, Y. Zhang, K. Schulten, M. Gruebele, and T. V. Pogorelov. 2019. “Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.” Proc. Natl. Acad. Sci. USA, 116, 12, Pp. 5356-5361. Publisher's VersionAbstract
As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.
prigozhin_pnas_2019.pdf
2015
A. J. Wirth, Y. Liu, M. B. Prigozhin, K. Schulten, and M. Gruebele. 2015. “Comparing fast pressure jump and temperature jump protein folding experiments and simulations.” J. Am. Chem. Soc., 137, 22, Pp. 7152-7159. Publisher's VersionAbstract
The unimolecular folding reaction of small proteins is now amenable to a very direct mechanistic comparison between experiment and simulation. We present such a comparison of microsecond pressure and temperature jump refolding kinetics of the engineered WW domain FiP35, a model system for β-sheet folding. Both perturbations produce experimentally a faster and a slower kinetic phase, and the “slow” microsecond phase is activated. The fast phase shows differences between perturbation methods and is closer to the downhill limit by temperature jump, but closer to the transiently populated intermediate limit by pressure jump. These observations make more demands on simulations of the folding process than just a rough comparison of time scales. To complement experiments, we carried out several pressure jump and temperature jump all-atom molecular dynamics trajectories in explicit solvent, where FiP35 folded in five of the six simulations. We analyzed our pressure jump simulations by kinetic modeling and found that the pressure jump experiments and MD simulations are most consistent with a 4-state kinetic mechanism. Together, our experimental and computational data highlight FiP35’s position at the boundary where activated intermediates and downhill folding meet, and we show 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.
wirth_jacs_2015.pdf
M. B. Prigozhin, S.-H. Chao, S. Sukenik, T. V. Pogorelov, and M. Gruebele. 2015. “Mapping fast protein folding with multiple-site uorescent probes.” Proc. Natl. Acad. Sci. USA, 112, 26, Pp. 7966-7971. Publisher's Version prigozhin_pnas_2015.pdf
2014
P. B. Lawrence, Y. Gavrilov, S. S. Matthews, M. I. Langlois, D. Shental-Bechor, H. M. Greenblatt, B. K. Pandey, M. S. Smith, R. Paxman, C. B. Torgerson, J. P. Merrell, C. Ritz, M. B. Prigozhin, Y. Levy, and J. L. Price. 2014. “Criteria for selecting PEGylation sites on proteins for higher thermodynamic and proteolytic stability.” J. Am. Chem. Soc., 136, 50, Pp. 17547-17560. Publisher's VersionAbstract
PEGylation of protein side chains has been used for more than 30 years to enhance the pharmacokinetic properties of protein drugs. However, there are no structure- or sequence-based guidelines for selecting sites that provide optimal PEG-based pharmacokinetic enhancement with minimal losses to biological activity. We hypothesize that globally optimal PEGylation sites are characterized by the ability of the PEG oligomer to increase protein conformational stability; however, the current understanding of how PEG influences the conformational stability of proteins is incomplete. Here we use the WW domain of the human protein Pin 1 (WW) as a model system to probe the impact of PEG on protein conformational stability. Using a combination of experimental and theoretical approaches, we develop a structure-based method for predicting which sites within WW are most likely to experience PEG-based stabilization, and we show that this method correctly predicts the location of a stabilizing PEGylation site within the chicken Src SH3 domain. PEG-based stabilization in WW is associated with enhanced resistance to proteolysis, is entropic in origin, and likely involves disruption by PEG of the network of hydrogen-bound solvent molecules that surround the protein. Our results highlight the possibility of using modern site-specific PEGylation techniques to install PEG oligomers at predetermined locations where PEG will provide optimal increases in conformational and proteolytic stability.
lawrence_jacs_2014.pdf
M. B. Prigozhin, G. E. Scott, and S. Denos. 2014. “Mechanical modeling and computer simulation of protein folding.” J. Chem. Ed., 91, 11, Pp. 1939-1942. Publisher's VersionAbstract
In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic biological molecules in the heterogeneous environment inside the living cell. Simple mechanical models and computer simulations that evolve in their complexity as the instruction progresses are at the core of this lesson. Methods of statistics and physical chemistry (thermodynamics and kinetics) are employed to investigate a flexible version of a peptide that can sample various conformations within the folded ensemble and ultimately unfold into a random coil.
prigozhin_jchemed_2014.pdf
Y. Liu, M. B. Prigozhin, K. Schulten, and M. Gruebele. 2014. “Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.” J. Am. Chem. Soc., 136, 11, Pp. 4265-4272. Publisher's VersionAbstract
Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, pressure-jump (P-jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-jump is not necessarily faster than that after a temperature jump. Recent P-jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ∼1.5 ms “slow” phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.
liu_jacs_2014.pdf
2013
S. P. Boulos, M. B. Prigozhin, Y. Liu, A. J. Wirth, S. A. Boppart, M. Gruebele, and C. J. Murphy. 2013. “The gold nanorod-biology interface: from proteins to cells to tissue.” Curr. Phys. Chem., 3, 2. Publisher's VersionAbstract
Gold nanorods absorb and scatter light strongly in the near-infrared portion of the electromagnetic spectrum, making them ideal tissue contrast agents for imaging techniques such as optical coherence tomography (OCT). Strong interactions occur at the nano-bio interface, such as proteins binding to gold nanorods forming a 'corona.' To fulfill the promise of nanorods for applications such as contrast agents, we must better understand the intrinsic interactions of these nanomaterials with biological systems at the molecular, cellular and tissue level. In this paper, we briefly review the nanorod-protein interface. We then present some new fast relaxation imaging (FReI) measurements of how the presence of strongly-absorbing gold nanorods affects protein binding and folding, taking into account inner filter effects and the strong quenching effect of nanorods on fluorescent-labeled proteins. Next we show that two-photon photoluminescence of the gold nanorods can be used to image the nanorods in tissue constructs, allowing us to independently study their tissue distribution so they can be used successfully as contrast agents in optical coherence microscopy.
boulos_currphyschem_2013.pdf
B. K. Pandey, M. Smith, C. Torgerson, P. Lawrence, S. S. Matthews, E. Watkins, M. L. Groves, M. B. Prigozhin, and J. L. Price. 2013. “Impact of site-specific PEGylation on the conformational stability and folding rate of the Pin WW domain depends strongly on PEG oligomer length.” Bioconj. Chem., 24, 5, Pp. 796-802. Publisher's VersionAbstract
Protein PEGylation is an effective method for reducing the proteolytic susceptibility, aggregation propensity, and immunogenicity of protein drugs. These pharmacokinetic challenges are fundamentally related to protein conformational stability, and become much worse for proteins that populate the unfolded state under ambient conditions. If PEGylation consistently led to increased conformational stability, its beneficial pharmacokinetic effects could be extended and enhanced. However, the impact of PEGylation on protein conformational stability is currently unpredictable. Here we show 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 PEG oligomer: shorter oligomers increase folding rate, whereas longer oligomers increase folding rate and reduce unfolding rate. This strong length dependence is consistent with the possibility that the PEG oligomer stabilizes the transition and folded states of WW relative to the unfolded state by interacting favorably with side-chain or backbone groups on the WW surface.
pandey_bioconjchem_2013.pdf
M. B. Prigozhin and M. Gruebele. 2013. “Microsecond folding experiments and simulations: a match is made.” Phys. Chem. Chem. Phys., 15, 10, Pp. 3372-3388. Publisher's VersionAbstract
For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. In this perspective we compare recent experiments and simulations on the microsecond time scale, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulations 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.
prigozhin_physchemchemphys_2013.pdf
M. B. Prigozhin, Y. Liu, A. J. Wirth, S. Kapoor, R. Winter, K. Schulten, and M. Gruebele. 2013. “Misplaced helix slows down ultrafast pressure-jump protein folding.” Proc. Natl. Acad. Sci. USA, 110, 20, Pp. 8087-8092. Publisher's VersionAbstract
Using a newly developed microsecond pressure-jump apparatus, we monitor the refolding kinetics of the helix-stabilized five-helix bundle protein λ*YA, the Y22W/Q33Y/G46,48A mutant of λ-repressor fragment 6–85, from 3 μs to 5 ms after a 1,200-bar P-drop. In addition to a microsecond phase, we observe a slower 1.4-ms phase during refolding to the native state. Unlike temperature denaturation, pressure denaturation produces a highly reversible helix-coil-rich state. This difference highlights the importance of the denatured initial condition in folding experiments and leads us to assign a compact nonnative helical trap as the reason for slower P-jump–induced refolding. To complement the experiments, we performed over 50 μs of all-atom molecular dynamics P-drop refolding simulations with four different force fields. Two of the force fields yield compact nonnative states with misplaced α-helix content within a few microseconds of the P-drop. Our 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. We hypothesize that nonnative helix at helix-turn interfaces traps the protein in compact nonnative conformations. These traps delay the folding of at least some of the population for 1.4 ms en route to the native state. Based on molecular dynamics, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state, if this hypothesis is correct.
prigozhin_pnas_2013.pdf
2012
S. Ebbinghaus, K. Meister, M. B. Prigozhin, A. L. DeVries, M. Havenith, J. Dzubiella, and M. Gruebele. 2012. “Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides.” Biophys. J., 103, 2, Pp. L20-L22. Publisher's VersionAbstract
Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Fo¨rster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation.
ebbinghaus_biophysj_2012.pdf
2011
P. L. Walters, M. B. Prigozhin, T. Y. Takeshita, L. Xu, F. M. Olivarez, and M. Gruebele. 2011. “Conformational energy gaps and scaling of conformer density in chain molecules.” Chem. Phys. Lett., 507, 1-3, Pp. 15-18. Publisher's VersionAbstract
We propose three reasons for the simplicity of vibrationally resolved electronic spectra of complex chain molecules: vibr(onic) state localization, insensitivity of chromophores to conformational changes outside the chromophore, and an ‘energy gap law’ for low-lying conformers. Here we use alkanals as simple models of chain molecules to study the third proposal. A disconnectivity tree and scaling analysis reveals an energy gap creating just two ‘special’ conformational minima in the torsional energy landscape of alkanals. We also derive a simple scaling formula to connect the energy spanned by all torsional minima in the alkanal energy landscape with molecular size.
M. B. Prigozhin and M. Gruebele. 2011. “The fast and the slow: folding and trapping of lambda 6-85.” J. Am. Chem. Soc., 133, 48, Pp. 19338-19341. Publisher's VersionAbstract
Molecular dynamics simulations combining many microsecond trajectories have recently predicted that a very fast folding protein like lambda repressor fragment λ6–85 D14A could have a slow millisecond kinetic phase. We investigated this possibility by detecting temperature-jump relaxation to 5 ms. While λ6–85 D14A has no significant slow phase, two even more stable mutants do. A slow phase of λ6–85 D14A does appear in mild denaturant. The experimental data and computational modeling together suggest the following hypothesis: λ6–85 takes only microseconds to reach its native state from an extensively unfolded state, while the latter takes milliseconds to reach compact β-rich traps. λ6–85 is not only thermodynamically but also kinetically protected from reaching such “intramolecular amyloids” while folding.
prigozhin_jacs_2011.pdf
M. B. Prigozhin, K. Sarkar, W. C. Swope, M. Gruebele, and J. Pitera. 2011. “Reducing lambda repressor to the core.” J. Phys. Chem. B, 115, 9, Pp. 2090-2096. Publisher's VersionAbstract
Lambda repressor fragment λ6−85* is one of thefastest folding small protein fragments known to date. We hypothesized that removal of three out of five helices of λ6−85* would further reduce this protein to its smallest folding core. Molecular dynamics simulations singled out two energetically stable reduced structures consisting of only helices 1 and 4 connected by a short glycine/serine linker, as well as a less stable control. We investigated these three polypeptides and their fragments experimentally by using circular dichroism, fluorescence spectroscopy, and temperature jump relaxation spectroscopy to gain insight into their thermodynamic and kinetic properties. Based on the thermal melts, the order of peptide stability was in correspondence with theoretical predictions. The most stable two-helix bundle, λblue1, is a cooperatively folding miniprotein with the same melting temperature and folding rate as the full-length λ6−85* pseudo wild type and a well-defined computed structure.
prigozhin_jpcb_2011.pdf