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  1. Article ; Online: Topology of molecular deformations induces triphasic catch bonding in selectin-ligand bonds.

    Barkan, Casey O / Bruinsma, Robijn F

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

    2024  Volume 121, Issue 6, Page(s) e2315866121

    Abstract: Among the long-standing efforts to elucidate the physical mechanisms of protein-ligand catch bonding, particular attention has been directed at the family of selectin proteins. Selectins exhibit slip, catch-slip, and slip-catch-slip bonding, with minor ... ...

    Abstract Among the long-standing efforts to elucidate the physical mechanisms of protein-ligand catch bonding, particular attention has been directed at the family of selectin proteins. Selectins exhibit slip, catch-slip, and slip-catch-slip bonding, with minor structural modifications causing major changes in selectins' response to force. How can a single structural mechanism allow interconversion between these various behaviors? We present a unifying theory of selectin-ligand catch bonding, using a structurally motivated free energy landscape to show how the topology of force-induced deformations of the molecular system produces the full range of observed behaviors. We find that the pathway of bond rupture deforms in non-trivial ways, such that unbinding dynamics depend sensitively on force. This implies a severe breakdown of Bell's theory-a paradigmatic theory used widely in catch bond modeling-raising questions about the suitability of Bell's theory in modeling other catch bonds. Our approach can be applied broadly to other protein-ligand systems.
    MeSH term(s) Ligands ; Selectins/chemistry ; Proteins ; Protein Binding
    Chemical Substances Ligands ; Selectins ; Proteins
    Language English
    Publishing date 2024-01-31
    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.2315866121
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    In stock of ZB MED Cologne/Königswinter

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  2. Book ; Online: Geometric Signatures of Switching Behavior in Mechanobiology

    Barkan, Casey O. / Bruinsma, Robijn F.

    2022  

    Abstract: The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve important functions ... ...

    Abstract The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve important functions in cell adhesion, mechano-sensing and signaling, and protein folding. We show that these switching behaviors are generated by singularities in the flow field that describes force-induced deformation of bound and transition states. These singularities allow for a complete characterization of switching mechanisms in 2-dimensional (2D) free energy landscapes, and provide a path toward elucidating novel forms of switching in higher dimensional models. Remarkably, the singularity that generates a catch-slip switch occurs in almost every 2D free energy landscape, implying that almost any bond admitting a 2D model will exhibit catch-slip behavior under appropriate force. We apply our analysis to models of P-selectin and antigen extraction to illustrate how these singularities provide an intuitive framework for explaining known behaviors and predicting new behaviors.

    Comment: 6 pages, 3 figures
    Keywords Quantitative Biology - Biomolecules
    Subject code 612
    Publishing date 2022-09-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Physics of viral dynamics.

    Bruinsma, Robijn F / Wuite, Gijs J L / Roos, Wouter H

    Nature reviews. Physics

    2021  Volume 3, Issue 2, Page(s) 76–91

    Abstract: Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible ... ...

    Abstract Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
    Language English
    Publishing date 2021-01-12
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2522-5820
    ISSN (online) 2522-5820
    DOI 10.1038/s42254-020-00267-1
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  4. Article ; Online: Kirigami and the Caspar-Klug construction for viral shells with negative Gauss curvature.

    Perotti, Luigi E / Zhang, Kevin / Rudnick, Joseph / Bruinsma, Robijn F

    Physical review. E

    2019  Volume 99, Issue 2-1, Page(s) 22413

    Abstract: In this work we extend the Caspar-Klug construction to the archaeal viruses, which in recent years have captured the attention of many researchers for their ability to thrive in extreme environments. We assume that the shells of archaeal viruses are ... ...

    Abstract In this work we extend the Caspar-Klug construction to the archaeal viruses, which in recent years have captured the attention of many researchers for their ability to thrive in extreme environments. We assume that the shells of archaeal viruses are composed of hexamers and pentamers-as is true for icosahedral viruses-together with heptamers, necessary to introduce negative Gauss curvature. Following the original work of Caspar and Klug, we first construct models capable of reproducing the shape observed in electron microscopy images of archaeal viruses. Next, using the technique of kirigami, we present a systematic way to formulate archaeal virus templates from regular hexagonal lattices. Finally, we utilize the presented techniques to build finite element models of archaeal virus geometries and investigate their shapes as a function of material properties. In particular, using thin-shell elasticity theory, we describe a buckling transition as a function of a modified Föppl-von Kármán number γ^{★} and we show how changes in γ^{★} may initiate the tail formation in the Acidianus two-tailed archaeal virus.
    MeSH term(s) Elasticity ; Models, Molecular ; Normal Distribution ; Viruses/chemistry
    Language English
    Publishing date 2019-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.99.022413
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  5. Article: Flory theory of the folding of designed RNA molecules.

    Schwab, David / Bruinsma, Robijn F

    The journal of physical chemistry. B

    2009  Volume 113, Issue 12, Page(s) 3880–3893

    Abstract: We construct a Flory theory for the folding of RNA molecules that have a designed, linear ground state. ...

    Abstract We construct a Flory theory for the folding of RNA molecules that have a designed, linear ground state.
    MeSH term(s) Models, Chemical ; Nucleic Acid Conformation ; RNA/chemistry ; Thermodynamics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2009-03-26
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-6106
    ISSN 1520-6106
    DOI 10.1021/jp8068893
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  6. Article ; Online: Assembly of viral capsids, buckling, and the Asaro-Grinfeld-Tiller instability.

    Morozov, Alexander Yu / Bruinsma, Robijn F

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2010  Volume 81, Issue 4 Pt 1, Page(s) 41925

    Abstract: Icosahedral viral shells are characterized by intrinsic elastic stress focused on the 12 structurally required pentamers. We show that, according to thin-shell theory, assembling icosahedral viral shells should be subject to the Asaro-Grinfeld-Tiller ... ...

    Abstract Icosahedral viral shells are characterized by intrinsic elastic stress focused on the 12 structurally required pentamers. We show that, according to thin-shell theory, assembling icosahedral viral shells should be subject to the Asaro-Grinfeld-Tiller instability (AGTI). AGTIs are encountered in growing epitaxial films exposed to extrinsic elastic stress. For viral shells, the AGTI relieves intrinsic elastic stresses by generating corrugation along the perimeter of the assembling shell. The buckling transition of Lidmar, Mirny, and Nelson provides an alternative mechanism for stress release, which in principle would allow for avoidance of AGTIs. For system parameters appropriate for viral shells however, the AGTI appears to be unavoidable. The azimuthal stress condensation produced by the AGTI might actually assist assembly by providing a guiding mechanism for the insertion of pentamers during viral assembly.
    MeSH term(s) Biomechanical Phenomena ; Capsid/chemistry ; Capsid/metabolism ; Elasticity ; Kinetics ; Models, Biological ; Protein Binding ; Stress, Mechanical ; Thermodynamics ; Viruses/chemistry
    Language English
    Publishing date 2010-04
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1550-2376
    ISSN (online) 1550-2376
    DOI 10.1103/PhysRevE.81.041925
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  7. Article ; Online: Ground state instabilities of protein shells are eliminated by buckling.

    Singh, Amit R / Perotti, Luigi E / Bruinsma, Robijn F / Rudnick, Joseph / Klug, William S

    Soft matter

    2017  Volume 13, Issue 44, Page(s) 8300–8308

    Abstract: We propose a hybrid discrete-continuum model to study the ground state of protein shells. The model allows for shape transformation of the shell and buckling transitions as well as the competition between states with different symmetries that ... ...

    Abstract We propose a hybrid discrete-continuum model to study the ground state of protein shells. The model allows for shape transformation of the shell and buckling transitions as well as the competition between states with different symmetries that characterize discrete particle models with radial pair potentials. Our main results are as follows. For large Föppl-von Kármán (FvK) numbers the shells have stable isometric ground states. As the FvK number is reduced, shells undergo a buckling transition resembling that of thin-shell elasticity theory. When the width of the pair potential is reduced below a critical value, then buckling coincides with the onset of structural instability triggered by over-stretched pair potentials. Chiral shells are found to be more prone to structural instability than achiral shells. It is argued that the well-width appropriate for protein shells lies below the structural instability threshold. This means that the self-assembly of protein shells with a well-defined, stable structure is possible only if the bending energy of the shell is sufficiently low so that the FvK number of the assembled shell is above the buckling threshold.
    MeSH term(s) Biomechanical Phenomena ; Mechanical Phenomena ; Models, Molecular ; Protein Stability ; Proteins/chemistry ; Stereoisomerism ; Thermodynamics
    Chemical Substances Proteins
    Language English
    Publishing date 2017-10-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/c7sm01184a
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  8. Article ; Online: DNA condensation by field-induced non-equilibrium noise.

    Bruinsma, Robijn F / Riehn, Robert

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2009  Volume 10, Issue 16, Page(s) 2871–2875

    Abstract: DNA molecules under good solvent conditions condense when subjected to strong AC electrical fields. It is shown that AC electrical fields couple charge fluctuations to molecular shape fluctuations, which produces a non-equilibrium noise source that can ... ...

    Abstract DNA molecules under good solvent conditions condense when subjected to strong AC electrical fields. It is shown that AC electrical fields couple charge fluctuations to molecular shape fluctuations, which produces a non-equilibrium noise source that can dominate over equilibrium thermal noise in the long-wavelength limit. The field-induced excess charge fluctuations amplify the Asakura-Oosawa fluctuation attraction force between neighboring chains, providing a mechanism for field-induced DNA condensation.
    MeSH term(s) Algorithms ; DNA/chemistry ; Solvents/chemistry ; Static Electricity ; Temperature
    Chemical Substances Solvents ; DNA (9007-49-2)
    Language English
    Publishing date 2009-10-14
    Publishing country Germany
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2025223-7
    ISSN 1439-7641 ; 1439-4235
    ISSN (online) 1439-7641
    ISSN 1439-4235
    DOI 10.1002/cphc.200900525
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  9. Article: Chirality and equilibrium biopolymer bundles.

    Grason, Gregory M / Bruinsma, Robijn F

    Physical review letters

    2007  Volume 99, Issue 9, Page(s) 98101

    Abstract: ... poor solvent conditions, as has been observed in in vitro studies of F actin [O. Pelletier et al., Phys ...

    Abstract We use continuum theory to show that chirality is a key thermodynamic control parameter for the aggregation of biopolymers: chirality produces a stable disperse phase of hexagonal bundles under moderately poor solvent conditions, as has been observed in in vitro studies of F actin [O. Pelletier et al., Phys. Rev. Lett. 91, 148102 (2003)]. The large characteristic radius of these chiral bundles is not determined by a mysterious long-range molecular interaction but by in-plane shear elastic stresses generated by the interplay between a chiral torque and an unusual, but universal, nonlinear gauge term in the strain tensor of ordered chains that is imposed by rotational invariance.
    MeSH term(s) Actins/chemistry ; Biopolymers/chemistry ; Models, Chemical ; Models, Molecular ; Stereoisomerism ; Thermodynamics
    Chemical Substances Actins ; Biopolymers
    Language English
    Publishing date 2007-08-31
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.99.098101
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  10. Article: Phase diagram of chiral biopolymer Wigner crystals.

    Grason, Gregory M / Bruinsma, Robijn F

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2007  Volume 76, Issue 2 Pt 1, Page(s) 21924

    Abstract: We study the statistical mechanics of counterion Wigner crystals associated with hexagonal bundles of chiral biopolymers. We show that, due to spontaneous chiral symmetry breaking induced by frustration, these Wigner crystals would be chiral even if the ... ...

    Abstract We study the statistical mechanics of counterion Wigner crystals associated with hexagonal bundles of chiral biopolymers. We show that, due to spontaneous chiral symmetry breaking induced by frustration, these Wigner crystals would be chiral even if the biopolymers themselves were not chiral. Using a duality transformation of the model onto a "spin-charge" Hamiltonian, we show that melting of the Wigner crystal is due to the unbinding of screw dislocations and that the melting temperature has a singular dependence on the intrinsic chirality of the biopolymers. Finally, we report that, if electrostatic interactions are strongly screened, the counterions can condense in the form of an intermediate achiral Wigner solid phase that melts by the unbinding of fractional topological charges.
    Language English
    Publishing date 2007-08
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.76.021924
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