A practical method for efficient and optimal production of Seleno‐methionine‐labeled recombinant protein complexes in the insect cells

Wenzel, Sabine; Imasaki, Tsuyoshi; Takagi, Yuichiro

doi:10.1002/pro.3575

Cited by 3 publications

(3 citation statements)

References 39 publications

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“…Selenomethionine is a naturally occurring amino acid, and several bacteria metabolize this compound (Stolz et al, 2006 ). Selenomethionine mimics closely the properties of L‐Met, and selenomethionine‐containing proteins are frequently used to resolve the crystallographic phase problem using multi‐wavelength anomalous diffraction techniques (Wenzel et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Sensing preferences for prokaryotic solute binding protein families

Cerna‐Vargas,

Sánchez‐Romera,

Matilla

et al. 2023

Microbial Biotechnology

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Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three‐dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron‐chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.

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Section: Resultsmentioning

confidence: 99%

Sensing preferences for prokaryotic solute binding protein families

Cerna‐Vargas,

Sánchez‐Romera,

Matilla

et al. 2023

Microbial Biotechnology

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“…However, these approaches can be problematic ( 43 , 48 ). For example, heavy atoms can degrade crystal quality or alter crystal packing so that the resulting crystal is no longer isomorphous ( 49 ), and SeMet incorporation often results in lower protein yield from eukaryotic cells, which can be problematic for proteins that are difficult to produce ( 50 ).…”

Section: Discussionmentioning

confidence: 99%

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

Hsieh

Smallwood

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

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“…Meanwhile, single-wavelength anomalous dispersion (SAD) became the dominant method for de novo protein structure determination; since the year 2007, more deposited PDB coordinates were obtained by SAD than by MAD [ 54 , 55 ]. In addition to this development, the quantitative incorporation of Sem into proteins expressed in yeast, insect and mammalian cells was established for structural biology [ 56 , 57 , 58 ]. Although many atoms can be utilized, even sulfur, phosphorus and other light atoms, Sem-SAD is still the most common approach.…”

Section: Methods For the Incorporation Of Ncaas In Peptides And Proteinsmentioning

confidence: 99%

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

Goettig,

Koch,

Budisa

2023

IJMS

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All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.

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A practical method for efficient and optimal production of Seleno‐methionine‐labeled recombinant protein complexes in the insect cells

Cited by 3 publications

References 39 publications

Sensing preferences for prokaryotic solute binding protein families

Sensing preferences for prokaryotic solute binding protein families

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

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