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  • 1
    Online Resource
    Online Resource
    Imprint of evolution on protein structures
    Proceedings of the National Academy of Sciences ; 2004
    In:  Proceedings of the National Academy of Sciences Vol. 101, No. 9 ( 2004-03-02), p. 2846-2851
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 101, No. 9 ( 2004-03-02), p. 2846-2851
    Abstract: We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence duplication and subsequent point mutations. A new gene's ability to fold into a stable and unique structure is tested each time through direct kinetic folding simulations. Where possible, the algorithm accepts the new sequence and structure and thus a “new protein structure” is born. During the course of each run, this model evolutionary algorithm provides several thousand new proteins with diverse structures. Analysis of evolved structures shows that later evolved structures are more designable than seed structures as judged by recently developed structural determinant of protein designability, as well as direct estimate of designability for selected structures by thermodynamic sampling of their sequence space. We test the significance of this trend predicted on lattice models on real proteins and show that protein domains that are found in eukaryotic organisms only feature statistically significant higher designability than their prokaryotic counterparts. These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0306638101
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2004
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 2
    Online Resource
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    The network of stabilizing contacts in proteins studied by coevolutionary data
    AIP Publishing ; 2013
    In:  The Journal of Chemical Physics Vol. 139, No. 15 ( 2013-10-21)
    Details
    In: The Journal of Chemical Physics, AIP Publishing, Vol. 139, No. 15 ( 2013-10-21)
    Abstract: The primary structure of proteins, that is their sequence, represents one of the most abundant sets of experimental data concerning biomolecules. The study of correlations in families of co-evolving proteins by means of an inverse Ising-model approach allows to obtain information on their native conformation. Following up on a recent development along this line, we optimize the algorithm to calculate effective energies between the residues, validating the approach both back-calculating interaction energies in a model system, and predicting the free energies associated to mutations in real systems. Making use of these effective energies, we study the network of interactions which stabilizes the native conformation of some well-studied proteins, showing that it displays different properties than the associated contact network.
    Type of Medium: Online Resource
    ISSN: 0021-9606 , 1089-7690
    URL: Article
    DOI: 10.1063/1.4826096
    Language: English
    Publisher: AIP Publishing
    Publication Date: 2013
    detail.hit.zdb_id: 3113-6
    detail.hit.zdb_id: 1473050-9
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  • 3
    Online Resource
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    The evolution dynamics of model proteins
    AIP Publishing ; 2004
    In:  The Journal of Chemical Physics Vol. 121, No. 5 ( 2004-08-01), p. 2381-2389
    Details
    In: The Journal of Chemical Physics, AIP Publishing, Vol. 121, No. 5 ( 2004-08-01), p. 2381-2389
    Abstract: Explicit simulations of protein evolution, where protein chains are described at a molecular, although simplified, level provide important information to understand the similarities found to exist between known proteins. The results of such simulations suggest that a number of evolutionary-related quantities, such as the distribution of sequence similarity for structurally similar proteins, are controlled by evolutionary kinetics and do not reflect an equilibrium state. An important result for phylogeny is that a subset of the residues of each protein evolve on a much larger time scale than the other residues.
    Type of Medium: Online Resource
    ISSN: 0021-9606 , 1089-7690
    URL: Article
    DOI: 10.1063/1.1768513
    Language: English
    Publisher: AIP Publishing
    Publication Date: 2004
    detail.hit.zdb_id: 3113-6
    detail.hit.zdb_id: 1473050-9
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  • 4
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    Online Resource
    Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding
    AIP Publishing ; 2012
    In:  The Journal of Chemical Physics Vol. 137, No. 23 ( 2012-12-21)
    Details
    In: The Journal of Chemical Physics, AIP Publishing, Vol. 137, No. 23 ( 2012-12-21)
    Abstract: The atomistic characterization of the transition state (TS) is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations that build out the transition state is particularly cumbersome, mainly because of the large computational cost of generating a statistically sound set of folding trajectories. Here we show that a biasing algorithm, based on the physics of the ratchet-and-pawl, can be used to approximate efficiently the transition state. The basic idea is that the algorithmic ratchet exerts a force on the protein when it is climbing the free-energy barrier, while it is inactive when it is descending. The transition state can be identified as the point of the trajectory where the ratchet changes regime. Besides discussing this strategy in general terms, we test it within a protein model whose transition state can be studied independently by plain molecular dynamics simulations. Finally, we show its power in explicit-solvent simulations, obtaining and characterizing a set of transition-state conformations for Acyl-Coenzyme A-Binding Protein (ACBP) and Chymotrypsin Inhibitor 2 (CI2).
    Type of Medium: Online Resource
    ISSN: 0021-9606 , 1089-7690
    URL: Article
    DOI: 10.1063/1.4769085
    Language: English
    Publisher: AIP Publishing
    Publication Date: 2012
    detail.hit.zdb_id: 3113-6
    detail.hit.zdb_id: 1473050-9
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  • 5
    Online Resource
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    Optical Absorption of a Green Fluorescent Protein Variant:  Environment Effects in a Density Functional Study
    American Chemical Society (ACS) ; 2007
    In:  The Journal of Physical Chemistry B Vol. 111, No. 36 ( 2007-09-01), p. 10807-10812
    Details
    In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 111, No. 36 ( 2007-09-01), p. 10807-10812
    Type of Medium: Online Resource
    ISSN: 1520-6106 , 1520-5207
    URL: Article
    DOI: 10.1021/jp072511e
    RVK:
    VA5430.B
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2007
    detail.hit.zdb_id: 1357799-2
    detail.hit.zdb_id: 2006039-7
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  • 6
    Online Resource
    Online Resource
    Cold Denaturation of the HIV1 Protease Monomer
    American Chemical Society (ACS) ; 2017
    In:  Biochemistry Vol. 56, No. 8 ( 2017-02-28), p. 1029-1032
    Details
    In: Biochemistry, American Chemical Society (ACS), Vol. 56, No. 8 ( 2017-02-28), p. 1029-1032
    Type of Medium: Online Resource
    ISSN: 0006-2960 , 1520-4995
    URL: Article
    URL: Article
    DOI: 10.1021/acs.biochem.6b01141
    DOI: 10.1021/acs.biochem.6b01141.s001
    RVK:
    WA 15000
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2017
    detail.hit.zdb_id: 1108-3
    detail.hit.zdb_id: 1472258-6
    SSG: 12
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  • 7
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    Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential
    American Chemical Society (ACS) ; 2020
    In:  The Journal of Physical Chemistry B Vol. 124, No. 20 ( 2020-05-21), p. 4079-4088
    Details
    In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 124, No. 20 ( 2020-05-21), p. 4079-4088
    Type of Medium: Online Resource
    ISSN: 1520-6106 , 1520-5207
    URL: Article
    URL: Article
    DOI: 10.1021/acs.jpcb.0c01671
    DOI: 10.1021/acs.jpcb.0c01671.s001
    RVK:
    VA5430.B
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2020
    detail.hit.zdb_id: 1357799-2
    detail.hit.zdb_id: 2006039-7
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  • 8
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    Cohesin and CTCF control the dynamics of chromosome folding
    Springer Science and Business Media LLC ; 2022
    In:  Nature Genetics Vol. 54, No. 12 ( 2022-12), p. 1907-1918
    Details
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 54, No. 12 ( 2022-12), p. 1907-1918
    Abstract: In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
    URL: Article
    DOI: 10.1038/s41588-022-01232-7
    RVK:
    XA 10000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1494946-5
    detail.hit.zdb_id: 1108734-1
    SSG: 12
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  • 9
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    Sequence of events in folding mechanism: Beyond the Gō model
    Wiley ; 2006
    In:  Protein Science Vol. 15, No. 7 ( 2006-07), p. 1638-1652
    Details
    In: Protein Science, Wiley, Vol. 15, No. 7 ( 2006-07), p. 1638-1652
    Abstract: Simplified Gō models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a C α ‐based Gō model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src‐SH3, and CI2) and the effect of mutations (ΔΔ G U‐N , ΔΔ G ‡‐N , ΔΔ G ‡‐ U , and φ‐values) on the wild‐type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.
    Type of Medium: Online Resource
    ISSN: 0961-8368 , 1469-896X
    URL: Article
    DOI: 10.1110/ps.052056006
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 2000025-X
    detail.hit.zdb_id: 1106283-6
    SSG: 12
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  • 10
    Online Resource
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    Design of HIV‐1‐PR inhibitors that do not create resistance: Blocking the folding of single monomers
    Wiley ; 2005
    In:  Protein Science Vol. 14, No. 10 ( 2005-10), p. 2668-2681
    Details
    In: Protein Science, Wiley, Vol. 14, No. 10 ( 2005-10), p. 2668-2681
    Abstract: The main problems found in designing drugs are those of optimizing the drug–target interaction and of avoiding the insurgence of resistance. We suggest a scheme for the design of inhibitors that can be used as leads for the development of a drug and that do not face either of these problems, and then apply it to the case of HIV‐1‐PR. It is based on the knowledge that the folding of single‐domain proteins, such as each of the monomers forming the HIV‐1‐PR homodimer, is controlled by local elementary structures (LES), stabilized by local contacts among hydrophobic, strongly interacting, and highly conserved amino acids that play a central role in the folding process. Because LES have evolved over many generations to recognize and strongly interact with each other so as to make the protein fold fast and avoid aggregation with other proteins, highly specific (and thus little toxic) as well as effective folding‐inhibitor molecules suggest themselves: short peptides (or eventually their mimetic molecules) displaying the same amino acid sequence of that of LES (p‐LES). Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV‐1‐PR that successfully avoid the action of p‐LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Monte Carlo simulations, we first identify the LES of the HIV‐1‐PR and then show that the corresponding p‐LES peptides act as effective inhibitors of the folding of the protease.
    Type of Medium: Online Resource
    ISSN: 0961-8368 , 1469-896X
    URL: Article
    DOI: 10.1110/ps.051670905
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2005
    detail.hit.zdb_id: 2000025-X
    detail.hit.zdb_id: 1106283-6
    SSG: 12
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