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  1. Article ; Online: High index dielectric films on metals: An island of emission.

    Maytin, Andrew / Gruebele, Martin

    The Journal of chemical physics

    2024  Volume 160, Issue 1

    Abstract: Fluorescent emitters are quenched near the surfaces of metals via rapid energy transfer to the metal, via surface plasmons, waveguide modes, and absorption. Commonly, this quenching is reduced by introducing a polymeric or dielectric spacer but requires ... ...

    Abstract Fluorescent emitters are quenched near the surfaces of metals via rapid energy transfer to the metal, via surface plasmons, waveguide modes, and absorption. Commonly, this quenching is reduced by introducing a polymeric or dielectric spacer but requires large distances, at least a fraction of the wavelength, between the metal and chromophore. Using the classical theory for a dipole above a metal/dielectric substrate, we investigate the fluorescent yield for emitters above a wide range of metals and spacers. For metals with low loss and low plasma frequencies, a high index spacer is shown to be advantageous for obtaining higher fluorescent yield in an "island of emission" at finely tuned spacer thickness just 20-30 nm from the metal surface. For such metal-dielectric combinations, fluorophores can be placed surprisingly close to the metal surface while remaining significantly emissive.
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0181874
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Protein folding and surface interaction phase diagrams in vitro and in cells.

    Gruebele, Martin

    FEBS letters

    2021  Volume 595, Issue 9, Page(s) 1267–1274

    Abstract: Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, ... ...

    Abstract Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, interact, and function on the scale from a few molecules to macroscopic ensembles. This review discusses three aspects of protein phase diagrams: first, the relevance of phase diagrams to protein folding and function in vitro and in cells; next, how the evolution of protein surfaces impacts on interaction phase diagrams; and finally, how phase separation plays a role on much larger length-scales than individual proteins or oligomers, when liquid phase-separated regions form to assist protein function and cell homeostasis.
    MeSH term(s) Humans ; Macromolecular Substances/ultrastructure ; Models, Molecular ; Protein Folding ; Protein Stability ; Protein Structure, Quaternary/genetics ; Proteins/genetics ; Proteins/ultrastructure
    Chemical Substances Macromolecular Substances ; Proteins
    Language English
    Publishing date 2021-03-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.14058
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Quantum scrambling across an energy barrier.

    Wolynes, Peter G / Gruebele, Martin

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 52, Page(s) e2319705120

    Language English
    Publishing date 2023-12-18
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2319705120
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  4. Article: Protein folding and surface interaction phase diagrams in vitro and in cells

    Gruebele, Martin

    FEBS letters. 2021 May, v. 595, no. 9

    2021  

    Abstract: Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, ... ...

    Abstract Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, interact, and function on the scale from a few molecules to macroscopic ensembles. This review discusses three aspects of protein phase diagrams: first, the relevance of phase diagrams to protein folding and function in vitro and in cells; next, how the evolution of protein surfaces impacts on interaction phase diagrams; and finally, how phase separation plays a role on much larger length‐scales than individual proteins or oligomers, when liquid phase‐separated regions form to assist protein function and cell homeostasis.
    Keywords homeostasis ; liquids ; separation
    Language English
    Dates of publication 2021-05
    Size p. 1267-1274.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note REVIEW
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.14058
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  5. Article ; Online: Protein Folding Stability and Kinetics in Alginate Hydrogels.

    Chang, Roger / Gruebele, Martin / Leckband, Deborah E

    Biomacromolecules

    2023  Volume 24, Issue 11, Page(s) 5245–5254

    Abstract: Proteins are commonly encapsulated in alginate gels for drug delivery and tissue-engineering applications. However, there is limited knowledge of how encapsulation impacts intrinsic protein properties such as folding stability or unfolding kinetics. Here, ...

    Abstract Proteins are commonly encapsulated in alginate gels for drug delivery and tissue-engineering applications. However, there is limited knowledge of how encapsulation impacts intrinsic protein properties such as folding stability or unfolding kinetics. Here, we use fast relaxation imaging (FReI) to image protein unfolding in situ in alginate hydrogels after applying a temperature jump. Based on changes in the Förster resonance energy transfer (FRET) response of FRET-labeled phosphoglycerate kinase (PGK), we report the quantitative impact of multiple alginate hydrogel concentrations on protein stability and folding dynamics. The gels stabilize PGK by increasing its melting temperature up to 18.4 °C, and the stabilization follows a nonmonotonic dependence on the alginate density. In situ kinetic measurements also reveal that PGK deviates more from two-state folding behavior in denser gels and that the gel decreases the unfolding rate and accelerates the folding rate of PGK, compared to buffer. Phi-value analysis suggests that the folding transition state of an encapsulated protein is structurally similar to that of folded protein. This work reveals both beneficial and negative impacts of gel encapsulation on protein folding, as well as potential mechanisms contributing to altered stability.
    MeSH term(s) Hydrogels ; Protein Folding ; Protein Stability ; Kinetics ; Temperature ; Protein Denaturation
    Chemical Substances Hydrogels
    Language English
    Publishing date 2023-10-31
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ISSN 1526-4602
    ISSN (online) 1526-4602
    DOI 10.1021/acs.biomac.3c00764
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Response to "Comment on 'Thermodiffusion: The physico-chemical mechanics view'" [J. Chem. Phys. 155, 087101 (2021)].

    Kocherginsky, Nikolai / Gruebele, Martin

    The Journal of chemical physics

    2021  Volume 155, Issue 8, Page(s) 87102

    Language English
    Publishing date 2021-09-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0060107
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Thermodiffusion: The physico-chemical mechanics view.

    Kocherginsky, Nikolai / Gruebele, Martin

    The Journal of chemical physics

    2021  Volume 154, Issue 2, Page(s) 24112

    Abstract: Thermodiffusion in liquids (the Soret effect) has several unusual properties. In particular, transport can occur with or against a temperature gradient depending on the case. Numerous empirical correlations have been proposed with mixed success or range ... ...

    Abstract Thermodiffusion in liquids (the Soret effect) has several unusual properties. In particular, transport can occur with or against a temperature gradient depending on the case. Numerous empirical correlations have been proposed with mixed success or range of applicability. Here, we show that physicochemical mechanics, derived from the Smoluchowski equation as a description of diffusive transport phenomena, is in accord with the experimental and simulated thermodiffusion data from colloidal beads and biomacromolecules to ionic solutions and ultracold fluid mixtures. It yields a simple formula for the Soret coefficient S
    Language English
    Publishing date 2021-01-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0028674
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  8. Article ; Online: Dynamical spectroscopy and microscopy of proteins in cells.

    Gruebele, Martin / Pielak, Gary J

    Current opinion in structural biology

    2021  Volume 70, Page(s) 1–7

    Abstract: With a strong understanding of how proteins fold in hand, it is now possible to ask how in-cell environments modulate their folding, binding and function. Studies accessing fast (ns to s) in-cell dynamics have accelerated over the past few years through ... ...

    Abstract With a strong understanding of how proteins fold in hand, it is now possible to ask how in-cell environments modulate their folding, binding and function. Studies accessing fast (ns to s) in-cell dynamics have accelerated over the past few years through a combination of in-cell NMR spectroscopy and time-resolved fluorescence microscopies. Here, we discuss this recent work and the emerging picture of protein surfaces as not just hydrophilic coats interfacing the solvent to the protein's core and functional regions, but as critical components in cells controlling protein mobility, function and communication with post-translational modifications.
    MeSH term(s) Hydrophobic and Hydrophilic Interactions ; Magnetic Resonance Spectroscopy ; Microscopy ; Protein Folding ; Proteins ; Solvents
    Chemical Substances Proteins ; Solvents
    Language English
    Publishing date 2021-03-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2021.02.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3206: Show issues Location:
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  9. Article ; Online: Cellular Sticking Can Strongly Reduce Complex Binding by Speeding Dissociation.

    Davis, Caitlin M / Gruebele, Martin

    The journal of physical chemistry. B

    2021  Volume 125, Issue 15, Page(s) 3815–3823

    Abstract: While extensive studies have been carried out to determine protein-RNA binding affinities, mechanisms, and dynamics in vitro, such studies do not take into consideration the effect of the many weak nonspecific interactions in a cell filled with potential ...

    Abstract While extensive studies have been carried out to determine protein-RNA binding affinities, mechanisms, and dynamics in vitro, such studies do not take into consideration the effect of the many weak nonspecific interactions in a cell filled with potential binding partners. Here we experimentally tested the role of the cellular environment on affinity and binding dynamics between a protein and RNA in living U-2 OS cells. Our model system is the spliceosomal protein U1A and its binding partner SL2 of the U1 snRNA. The binding equilibrium was perturbed by a laser-induced temperature jump and monitored by Förster resonance energy transfer. The apparent binding affinity in live cells was reduced by up to 2 orders of magnitude compared to in vitro. The measured in-cell dissociation rate coefficients were up to 2 orders of magnitude larger, whereas no change in the measured association rate coefficient was observed. The latter is not what would be anticipated due to macromolecular crowding or nonspecific sticking of the uncomplexed U1A and SL2 in the cell. A quantitative model fits our experimental results, with the major cellular effect being that U1A and SL2 sticking to cellular components are capable of binding, just not as strongly as the free complex. This observation suggests that high binding affinities measured or designed in vitro are necessary for proper binding in vivo, where competition with many nonspecific interactions exists, especially for strongly interacting species with high charge or large hydrophobic surface areas.
    MeSH term(s) Binding Sites ; Dissociative Disorders ; Humans ; Protein Binding ; RNA/metabolism ; RNA, Small Nuclear/metabolism ; Ribonucleoprotein, U1 Small Nuclear/metabolism ; Spliceosomes/metabolism
    Chemical Substances RNA, Small Nuclear ; Ribonucleoprotein, U1 Small Nuclear ; RNA (63231-63-0)
    Language English
    Publishing date 2021-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c00950
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Quantum information scrambling and chemical reactions.

    Zhang, Chenghao / Kundu, Sohang / Makri, Nancy / Gruebele, Martin / Wolynes, Peter G

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 15, Page(s) e2321668121

    Abstract: The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents ... ...

    Abstract The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents that characterize classical chaotic motion. Maldacena, Shenker, and Stanford have suggested a fundamental quantum bound for the rate of information scrambling, which resembles a limit suggested by Herzfeld for chemical reaction rates. Here, we use OTOCs to study model reactions based on a double-well reaction coordinate coupled to anharmonic oscillators or to a continuum oscillator bath. Upon cooling, as one enters the tunneling regime where the reaction rate does not strongly depend on temperature, the quantum Lyapunov exponent can approach the scrambling bound and the effective reaction rate obtained from a population correlation function can approach the Herzfeld limit on reaction rates: Tunneling increases scrambling by expanding the state space available to the system. The coupling of a dissipative continuum bath to the reaction coordinate reduces the scrambling rate obtained from the early-time OTOC, thus making the scrambling bound harder to reach, in the same way that friction is known to lower the temperature at which thermally activated barrier crossing goes over to the low-temperature activationless tunneling regime. Thus, chemical reactions entering the tunneling regime can be information scramblers as powerful as the black holes to which the quantum Lyapunov exponent bound has usually been applied.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2321668121
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