Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers

Lee, Cheng Chung; Maestre-Reyna, M.; Hsu, Kai Cheng; Wang, Hao Ching; Liu, Chia I.; Jeng, W.Y.; Lin, Li-Hung; Wood, Richard M.; Chou, Chia Cheng; Yang, Jinn-Moon; Wang, Andrew H.J.

doi:10.1002/anie.201405664

Cited by 50 publications

(54 citation statements)

References 25 publications

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“…Both K20 side chains of the wild-type protein are stabilized by electrostatic interactions with sulfates and E5′ side chains from the neighboring protein (symmetry-related molecules) in the crystal (Fig 2B). The K24 side chain is more ordered in chain A, which is stabilized by polyethylene glycol 400 (PEG 400) (Fig 1B), similar to the stabilization observed in crown ether binding mode [39]. On the other hand, the K24 side chain in chain B forms electrostatic interactions with the E39′ side chain of the neighboring protein (Fig 2C).…”

Section: Resultssupporting

confidence: 54%

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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

et al. 2017

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The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22′ and R11′/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.

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Section: Resultssupporting

confidence: 54%

“…The extended N- or C-terminal tails of DNA-binding domains often increase the affinity for the target DNA and thus represent crucial segments for gene activation or repression [39]. Based on the FP, EM, and FRET analyses, the basic and flexible C-termini of Sso7c4 may act as two hands that grasp the DNA molecule, further inducing DNA bending.…”

Section: Resultsmentioning

confidence: 99%

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

et al. 2017

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“…As noted earlier, the Neisseria DMP19 dimer was first determined to be a transcriptional regulator (12). However, in a subsequent study, another conformation of DMP19 was found (39). In this newly determined structure, helices α1 and 2 of DMP19, which are both involved in the dimer formation in the original dimeric DMP19 structure, were rotated by 180 to make two DMP19 monomers that were unable to assemble into a dimer.…”

Section: Dmps That Target Bacterial Histone-like Proteinsmentioning

confidence: 79%

New paradigm of functional regulation by DNA mimic proteins: Recent updates

et al. 2018

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For many, “DNA mimic protein” (DMP) remains an unfamiliar term. The key feature of these proteins is their DNA‐like shape and charge distribution, and they affect the activity of DNA‐binding proteins by occupying their DNA‐binding domains. Functionally, DMPs regulate mechanisms such as gene expression, restriction, and DNA repair as well as the nucleosome package. Although a few DMPs, such as phage uracil DNA glycosylase inhibitor (UGI) and overcome classical restriction (Ocr), were reported about 20 years ago, only a small number of DMPs have been studied to date. In 2014, we reviewed the functional and structural features of 16 DMPs that were known at the time. Now, seven new DMPs, namely anti‐CRISPR suppressors AcrF2, AcrF10 and AcrIIA4, human immunodeficiency virus essential factor VPR, multi‐functional inhibitor anti‐restriction nuclease (Arn), translational regulator AbbA, and putative Z‐DNA mimic MBD3, have been reported. In addition, further study of two previously known DMPs, DMP19 and SAUGI, increased our knowledge of their importance and function. Here, we discuss these updated results and address how several characteristics of the structure/sequence of DMPs (e.g. the DNA‐like charge distribution and structural D/E‐rich repeats) might someday be used to identify new DMPs using bioinformatic approach. © 2018 IUBMB Life, 71(5):539–548, 2019

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“…In this study,w ef irst crystallized the apo form of PigA and then the FADc omplex by adding crowne ther. [9] The XRD resolution was improved from 2.55 to 1.3 .I naddition to clearly elucidating the FAD-binding mode, the crystal structure also allows model construction of the substrate, which is carried by PigG. Based on the model, ac atalytic mechanism is proposed, in which Glu244 on the Re side of FADs tarts the reactionb y a-proton abstraction from the proline.W ea lso found ap lausible oxygen-binding site near the Si face of FAD, at which hydride transfer may be mediated by Thr160.…”

Section: Resultsmentioning

confidence: 99%

“…The crown ether can stabilize crystal packing by binding to surface lysine side chains and providing hydrophobic interactions. [9] In the end, as econd crystal form was obtained that diffracted X-rays more effectively to 1.8 and 1.3 .Itbelongstospace group I222 and contains one molecule of PigA in the asymmetric unit. The structures were refined to R/R free values of 0.143/0.174 at 1.8 and 0.114/ 0.127 at 1.3 .E ach model comprises 383 amino acid residues; one FAD; severals maller ligands, such as crown ether and ethylene glycol;a nd an umber of water molecules.T he C-terminal residues,i ncluding the His 8 -tag, were not seen.…”

Section: Introductionmentioning

confidence: 98%

Crystal structure of PigA, a proline-oxidizing enzyme in prodigiosin biosynthesis

Lee¹,

Ko²,

Hsiao³

et al. 2018

Acta Cryst Sect A

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because the fatty acids are covalently bound to coenzyme A and ACP. [5] Despite extensive research into the biosynthetic pathways for prodigiosin,s of ar the structures of only two proteins,P igG and PigE, have been determined. [6,7] Recently,t he structure of AnaB, ah omologue with 41 %s equence identity to that of PigA, which catalyzes prolineo xidization in anatoxin biosynthesis, has been solved. [8] Unlike PigA, however,A naB makes only one doubleb ond. To understand the mechanism of catalysis by PigA that forms two double bonds in proline, we have determined the crystal structure of the enzyme in the apo form and in complexw ith FADa nd proline. We then constructed ac omplex model of PigA and prolyl-PigG to elucidate possible enzyme-substrate interactions. Results Crystal structures, apo and FADb oundThe PigA-coding gene was expressed in Escherichia coli with a His 8 -tag. The recombinantp rotein was purified in as ingle step by using aN i-NTA column. As an apoenzyme, it was first crystallizedi ns pace group C222 1 with two protein molecules in an asymmetricu nit. By using this crystal form,a nX RD data set was collected to 2.55 resolution. The structure wass olved by molecular replacement, as described in the Experimental Section. Subsequentr efinement yielded R and R free values of 0.18 and 0.23, respectively.H owever,t he completeness was 69 and 53 %f or the two outer shells beyond2 .73 (Table 1). To obtain better crystals for structurala nalysiso fP igA at ah igherr esolu-Scheme1.Biosynthetic pathways of prodigiosin. A) The production of MBCstarts with attachmentofp hosphopantetheine( PNS;designated with atilde~) and l-proline to PigG. After oxidation by PigA, the A-ring moiety reacts with malonyl-PigH and l-serine to generate the Br ing. The skeletono fMAP comes from pyruvate and 2-octenal. MAP then combines with MBC to form the final product. B) PigL and PigI initiate the biosynthesis by makingt he PNS linkage between PigG and proline. PigG then carries the substrate to PigA for two-stepo xidation.C)Both chemical structures of coenzymeAand prolyl-PigG contain aP NS moiety.PIG:phosphatidylinositol N-acetylglucosaminyltransferase.

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Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers

Cited by 50 publications

References 25 publications

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

New paradigm of functional regulation by DNA mimic proteins: Recent updates

Crystal structure of PigA, a proline-oxidizing enzyme in prodigiosin biosynthesis

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