Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin

Goyal, Venuka Durani; Yadav, Pooja; Kumar, Ashwani; Ghosh, Biplab; Makde, Ravindra D.

doi:10.1107/s2053230x14020755

Cited by 3 publications

(1 citation statement)

References 27 publications

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“…PX-BL21 is primarily aimed to cater for the needs of more than 100 independent research groups in India working in the area of structural biology. The first diffraction data on single crystals of the lysozyme protein were recorded during mid-2012 and since then the beamline has been used by several users (Goyal et al, 2014;Arif et al, 2015;Sonani et al, 2015;Agarwal et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron

et al. 2016

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The protein crystallography beamline (PX-BL21), installed at the 1.5 T bending-magnet port at the Indian synchrotron (Indus-2), is now available to users. The beamline can be used for X-ray diffraction measurements on a single crystal of macromolecules such as proteins, nucleic acids and their complexes. PX-BL21 has a working energy range of 5-20 keV for accessing the absorption edges of heavy elements commonly used for phasing. A double-crystal monochromator [Si(111) and Si(220)] and a pair of rhodium-coated X-ray mirrors are used for beam monochromatization and manipulation, respectively. This beamline is equipped with a single-axis goniometer, Rayonix MX225 CCD detector, fluorescence detector, cryogenic sample cooler and automated sample changer. Additional user facilities include a workstation for on-site data processing and a biochemistry laboratory for sample preparation. In this article the beamline, other facilities and some recent scientific results are briefly described.

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Section: Introductionmentioning

confidence: 99%

Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron

et al. 2016

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De novodesign of triosephosphate isomerases using generative language models

Romero-Romero,

Braun,

Kossendey

et al. 2024

Preprint

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The design of proteins with tailored functions is of immense interest to biotechnology, medicine, and the chemical industry. While protein design is rapidly evolving with the use of AI techniques, the design of complex enzymes remains a challenge. Here, we present the use of two large language models (LLMs), ZymCTRL and ProtGPT2, for the generation of de novo enzymes that catalyze the triosephosphate isomerase (TIM) reaction. Natural TIM enzymes are obligatory oligomers that catalyze a multi-step isomerization reaction near the diffusion limit. This makes TIM an ideal target to assess the generative ability of protein language models. Newly generated sequences were filtered to obtain a set of twelve candidates from each approach for experimental validation. Multiple constructs from both language models exhibit the intended function in vivo through their ability to complement a TIM-deficient E. coli strain. In-depth characterization of the best-behaving artificial enzyme reveals behavior and catalytic efficiency close to its natural counterparts. These findings support the use of conditional and fine-tuned unconditional LLMs for the generation of complex enzymes.

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