Disulfide Bonds Are Not Necessary for Intrinsic TNSALP Activity

Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biophysics

Single-molecule studies reveal method for tuning the heterogeneous activity of alkaline phosphatase

Tal Gilboa et al.

Summary: Single-molecule enzymology methods allow for the study of heterogeneous catalytic activities within enzyme populations. This study explores the mechanisms of heterogeneous activity in tissue nonspecific alkaline phosphatase (TNSALP), revealing two subpopulations with different catalytic activities. pH and temperature are shown to influence TNSALP activity, and molecular dynamics simulations provide insight into conformational transitions that align with experimental observations. These findings demonstrate the usefulness of single-molecule enzymology in understanding heterogeneous enzyme activity and provide a simple approach for tuning catalytic activity within enzyme populations using pH and temperature.

BIOPHYSICAL JOURNAL (2022)

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Article Biochemistry & Molecular Biology

Elucidation and control of low and high active populations of alkaline phosphatase molecules for quantitative digital bioassay

Hiroshi Ueno et al.

Summary: This study focuses on the quantitative analysis of single-molecule activities of ALP from Escherichia coli, revealing the static heterogeneity in catalytic activity and showing two distinct populations: half-active and fully-active portions. The research also demonstrated single-molecule Michaelis-Menten kinetics of ALP and found that different origins of ALP exhibit static heterogeneity, suggesting a commonality across species. Cell-free expression of ALP with disulfide bond enhancer and zinc ion resulted in a homogenous population of fully active ALP, indicating a deficiency in correct disulfide bond formation and zinc ion coordination in inactive monomer units. These findings provide insights for further studies on the molecular mechanism and biogenesis of ALP, as well as a potential approach to prepare homogenous and active populations of ALP for highly quantitative and sensitive bioassays.

PROTEIN SCIENCE (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Article Multidisciplinary Sciences