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Showing 1–15 of 15 results
Advanced filters: Author: Shina C.L. Kamerlin Clear advanced filters

  • Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.

    • Gloria Gamiz-Arco
    • Luis I. Gutierrez-Rus
    • Jose M. Sanchez-Ruiz
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-16

  • We present a computational approach to the design of high-efficiency enzymes with catalytic parameters comparable to natural enzymes, enabling programming of stable, high-efficiency, new-to-nature Kemp elimination enzymes through minimal experimental effort.

    • Dina Listov
    • Eva Vos
    • Sarel J. Fleishman
    ResearchOpen Access
    Nature
    Volume: 643, P: 1421-1427

  • The emergence of novel catalytic functions in ancient proteins likely played a role in the evolution of modern enzymes. Here, the authors use protein sequences from Precambrian beta-lactamases and demonstrate that a single hydrophobic-to-ionizable amino acid mutation can lead to substantial Kemp eliminase activity.

    • Valeria A. Risso
    • Sergio Martinez-Rodriguez
    • Jose M. Sanchez-Ruiz
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-13

  • ATPPRT is a multi-protein allosteric enzyme where the regulatory protein HisZ enhances catalysis by HisGs. Here, the authors report catalytically impaired active site mutants of HisGs that are allosterically rescued by HisZ despite the HisZ:HisGs interface lying ~20 Å away from the active site.

    • Gemma Fisher
    • Marina Corbella
    • Rafael G. da Silva
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-15

  • Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization.

    • Nan-Sook Hong
    • Dušan Petrović
    • Colin J. Jackson
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-10

  • Enzyme conformational plasticity plays an important part in expanding the functional diversity of a limited repertoire of sequences. This Review discusses the role of flexible loops in enzyme evolution, focusing on both examples from natural evolution and engineering success stories.

    • Marina Corbella
    • Gaspar P. Pinto
    • Shina C. L. Kamerlin
    Reviews
    Nature Reviews Chemistry
    Volume: 7, P: 536-547

  • Ribosomal protein synthesis is driven by the hydrolysis of GTP. Wallin and colleagues employ molecular dynamics and computer simulations to show that a universally conserved histidine promotes GTP hydrolysis in its protonated form, and is driven into the active conformation by interactions with the ribosome.

    • Göran Wallin
    • Shina C. L. Kamerlin
    • Johan Åqvist
    Research
    Nature Communications
    Volume: 4, P: 1-10

  • Ancestral sequence inference, directed evolution, structural analysis, NMR, and molecular dynamics simulations illuminate how enantioselective activity arises during the evolutionary trajectory of chalcone isomerase from a noncatalytic ancestor.

    • Miriam Kaltenbach
    • Jason R. Burke
    • Dan S. Tawfik
    Research
    Nature Chemical Biology
    Volume: 14, P: 548-555

  • Ancestral protein reconstruction followed by biochemical and structural analyses characterizes the evolutionary trajectory of methyl-parathion hydrolase from an ancestral dihydrocoumarin hydrolase through the accumulation of five key mutations.

    • Gloria Yang
    • Dave W Anderson
    • Nobuhiko Tokuriki
    Research
    Nature Chemical Biology
    Volume: 15, P: 1120-1128

  • In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.

    • Rommie E. Amaro
    • Johan Åqvist
    • Modesto Orozco
    Comments & Opinion
    Nature Methods
    Volume: 22, P: 641-645