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1. chinaXiv:201605.01808 [pdf]

Significant Expansion of Fluorescent Protein Sensing Ability through the Genetic Incorporation of Superior Photo-Induced Electron-Transfer Quenchers

Liu, Xiaohong; Jiang, Li; Li, Jiasong; Wang, Li; Zhou, Qing; Lv, Xiaoxuan; Gong, Weimin; Wang, Jiangyun; Lu, Yi; Lu, Yi; Yu, Yang
Subjects: Biology >> Biophysics

Photo-induced electron transfer (PET) is ubiquitous for photosynthesis and fluorescent sensor design. However, genetically coded PET sensors are underdeveloped, due to the lack of methods to site-specifically install PET probes on proteins. Here we describe a family of acid and Mn(III) turn-on fluorescent protein (FP) sensors, named iLovU, based on PET and the genetic incorporation of superior PET quenchers in the fluorescent flavoprotein iLov. Using the iLovU PET sensors, we monitored the cytoplasmic acidification process, and achieved Mn(III) fluorescence sensing for the first time. The iLovU sensors should be applicable for studying pH changes in living cells, monitoring biogentic Mn(III) in the environment, and screening for efficient manganese peroxidase, which is highly desirable for lignin degradation and biomass conversion. Our work establishes a platform for many more protein PET sensors, facilitates the de novo design of metalloenzymes harboring redox active residues, and expands our ability to probe protein conformational dynamics.

submitted time 2016-05-18 Hits3250Downloads1447 Comment 0

2. chinaXiv:201605.01465 [pdf]

Structural basis of the substrate specificity of the FPOD/FAOD family revealed by fructosyl peptide oxidase from Eupenicillium terrenum

Gan, Weiqiong; Gao, Feng; Jia, Minze; Gong, Weimin; Gan, Weiqiong; Xing, Keke; Liu, Haiping; Gong, Weimin
Subjects: Biology >> Biophysics

The FAOD/FPOD family of proteins has the potential to be useful for the longterm detection of blood glucose levels in diabetes patients. A bottleneck for this application is to find or engineer a FAOD/FPOD family enzyme that is specifically active towards alpha-fructosyl peptides but is inactive towards other types of glycated peptides. Here, the crystal structure of fructosyl peptide oxidase from Eupenicillium terrenum (EtFPOX) is reported at 1.9 angstrom resolution. In contrast to the previously reported structure of amadoriase II, EtFPOX has an open substrate entrance to accommodate the large peptide substrate. The functions of residues critical for substrate selection are discussed based on structure comparison and sequence alignment. This study reveals the first structural details of group I FPODs that prefer alpha-fructosyl substrates and could provide significant useful information for uncovering the mechanism of substrate specificity of FAOD/FPODs and guidance towards future enzyme engineering for diagnostic purposes.

submitted time 2016-05-12 Hits938Downloads508 Comment 0

3. chinaXiv:201605.01453 [pdf]

Crystal structure of the catalytic subunit of magnesium chelatase

Chen, Xuemin; Pu, Hua; Fang, Ying; Wang, Xiao; Zhao, Shun; Dai, Huai-En; Liu, Lin; Chen, Xuemin; Pu, Hua; Fang, Ying; Wang, Xiao; Zhao, Shun; Lin, Yajing; Gong, Weimin; Zhang, Min; Gong, Weimin
Subjects: Biology >> Biophysics

Tetrapyrroles, including haem and chlorophyll, play vital roles for various biological processes, such as respiration and photosynthesis, and their biosynthesis is critical for virtually all organisms. In photosynthetic organisms, magnesium chelatase (MgCh) catalyses insertion of magnesium into the centre of protoporphyrin IX, the branch-point precursor for both haem and chlorophyll, leading tetrapyrrole biosynthesis into the magnesium branch1,2. This reaction needs a cooperated action of the three subunits of MgCh: the catalytic subunit ChlH and two AAA(+) subunits, ChlI and ChlD ( refs 3-5). To date, the mechanism of MgCh awaits further elucidation due to a lack of high-resolution structures, especially for the similar to 150 kDa catalytic subunit. Here we report the crystal structure of ChlH from the photosynthetic cyanobacterium Synechocystis PCC 6803, solved at 2.5 angstrom resolution. The active site is buried deeply inside the protein interior, and the surrounding residues are conserved throughout evolution. This structure helps to explain the loss of function reported for the cch and gun5 mutations of the ChlH subunit, and to provide the molecular basis of substrate channelling during the magnesium-chelating process. The structure advances our understanding of the holoenzyme of MgCh, a metal chelating enzyme other than ferrochelatase.

submitted time 2016-05-12 Hits1373Downloads723 Comment 0

4. chinaXiv:201605.01369 [pdf]

Subcellular localization and RNAs determine FUS architecture in different cellular compartments

Yang, Liuqing; Zhang, Jiayu; Gal, Jozsef; Zhu, Haining; Kamelgarn, Marisa; Zhu, Haining; Niu, Chunyan; Gong, Weimin; Gong, Weimin
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Mutations in Fused in sarcoma (FUS) gene cause a subset of familial amyotrophic lateral sclerosis (ALS), a fatal motor neuron degenerative disease. Wild-type FUS is largely localized in the nucleus, but mutant FUS accumulates in the cytoplasm and forms inclusions. It is unclear whether FUS depletion from the nucleus or FUS inclusions in the cytoplasm triggers motor neuron degeneration. In this study, we revealed that the nuclear and cytoplasmic FUS proteins form distinct local distribution patterns. The nuclear FUS forms oligomers and appears granular under confocal microscope. In contrast, the cytoplasmic FUS forms inclusions with no oligomers detected. These patterns are determined by the subcellular localization of FUS, regardless of wild-type or mutant protein. Moreover, mutant FUS remained or re-directed in the nucleus can oligomerize and behave similarly to the wild-type FUS protein. We further found that nuclear RNAs are critical to its oligomerization. Interestingly, the formation of cytoplasmic FUS inclusions is also dependent on RNA binding. Since the ALS mutations disrupt the nuclear localization sequence, mutant FUS is likely retained in the cytoplasm after translation and interacts with cytoplasmic RNAs. We therefore propose that local RNA molecules interacting with the FUS protein in different subcellular compartments play a fundamental role in determining FUS protein architecture and function.

submitted time 2016-05-12 Hits1152Downloads690 Comment 0

5. chinaXiv:201605.01273 [pdf]

Ultrafast Photoinduced Electron Transfer in Green Fluorescent Protein Bearing a Genetically Encoded Electron Acceptor

Lv, Xiaoxuan; Hu, Cheng; Gao, Feng; Li, Jiasong; Liu, Xiaohong; Deng, Kai; Zheng, Peng; Gong, Weimin; Wang, Jiangyun; Lv, Xiaoxuan; Hu, Cheng; Gao, Feng; Li, Jiasong; Liu, Xiaohong; Deng, Kai; Zheng, Peng; Gong, Weimin; Wang, Jiangyun; Zhou, Meng; Xia, Andong
Subjects: Biology >> Biophysics

Electron transfer (ET) is widely used for driving the processes that underlie the chemistry of life. However, our abilities to probe electron transfer mechanisms in proteins and design redox enzymes are limited, due to :the lack of methods to site-specifically insert electron acceptors into proteins in vivo. Here we describe the synthesis and genetic incorporation of 4-fluoro-3-nitrophenylalanine (FNO(2)Phe), which has similar reduction potentials to NAD(P)H and ferredoxin, the most important biological reductants. Through the genetic incorporation of FNO2Phe into green fluorescent:protein (GFP) and femtosecond transient absorption measurement, we show that photoinduced electron transfer (PET) from the GFP chromophore to FNO2Phe occurs very fast (within 11 ps), which is comparable to that of the first electron transfer step in photosystem I, from P700* to A(0). This genetically encoded, low-reduction potential unnatural amino acid (UAA) can significantly in-Trove our ability to investigate electron transfer mechanisms in complex reductases and facilitate the design of miniature proteins that mimic their functions.

submitted time 2016-05-11 Hits1149Downloads634 Comment 0

6. chinaXiv:201605.01192 [pdf]

A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells

Li, Fahui; Dong, Jianshu; Gong, Weimin; Li, Jiasong; Wang, Jiangyun; Li, Fahui; Dong, Jianshu; Gong, Weimin; Li, Jiasong; Wang, Jiangyun; Wang, Jiangyun; Hu, Xiaosong; Shen, Jing; Tian, Huifang
Subjects: Biology >> Biophysics

Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both invitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site- and sequence-specific covalent labeling of RNAs in mammalian cells by using tRNA(Ile2)-agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide-bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site-specific transfer of azide/alkyne groups to an RNA molecule of interest invitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.

submitted time 2016-05-11 Hits1098Downloads636 Comment 0

7. chinaXiv:201605.01190 [pdf]

Crystallization and preliminary X-ray analysis of Rv1674c from Mycobacterium tuberculosis

Li, Jincheng; Zhang, Min; Wang, Xudong; Gong, Weimin; Niu, Chunyan
Subjects: Biology >> Biophysics

Adaptations to hypoxia play an important role in Mycobacterium tuberculosis pathogenesis. Rv0324, which contains an HTH DNA-binding domain and a rhodanese domain, is one of the key transcription regulators in response to hypoxia. M. tuberculosis Rv1674c is a homologue of Rv0324. To understand the interdomain interaction and regulation of the HTH domain and the rhodanese domain, recombinant Rv1674c protein was purified and crystallized by the vapour-diffusion method. The crystals diffracted to 2.25 angstrom resolution. Preliminary diffraction analysis suggests that the crystals belonged to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 67.8, c = 174.5 angstrom, alpha = beta = 90, gamma = 120 degrees. The Matthews coefficient was calculated to be 2.44 angstrom(3) Da(-1), assuming that the crystallographic asymmetric unit contains two protein molecules.

submitted time 2016-05-11 Hits1054Downloads520 Comment 0

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