Secondary Structure and Membrane Topology of the Full‐Length Dengue Virus NS4B in Micelles

Li, Yan; Wong, Yiik Diew; Lee, Michelle Yueqi; Li, Qingxin; Wang, Qing Yin; Lescar, Julien; Shi, Pei–Yong; Kang, CongBao

doi:10.1002/anie.201606609

Cited by 30 publications

(32 citation statements)

References 42 publications

(55 reference statements)

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“…The topology of SCN2‐TM in micelles was then evaluated using paramagnetic relaxation enhancement by mixing the sample with different probes which can be used to determine the topology of a membrane protein . When the water soluble paramagnetic probe‐Gd(III)‐DTPA and lipid‐soluble probe‐16DSA were added into SCN2‐TM, the intensity changes of the cross peaks induced by paramagnet reagents were observed for different amino acids.…”

Section: Resultsmentioning

confidence: 99%

“…SDC2‐TM was purified in the presence of DPC micelles using the method described previously . Briefly, the cells were broken in the buffer with 1% DPC by sonication.…”

Section: Methodsmentioning

confidence: 99%

“…Paramagnetic relaxation enhancement (PRE) experiment of SDC2‐TM in the presence of different probes was conducted to identify amino acids that are buried in micelles or exposed to solvent. All the experiments were carried out using the same method as the described previously . Briefly, 1 H‐ 15 N‐HSQC spectra of SDC2‐TM in DPC micelles in the absence and presence of 2 m m gadolinium‐DTPA or 16‐DOXYL‐stearic acid (16DSA) were collected and compared.…”

Section: Methodsmentioning

confidence: 99%

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Secondary structure and topology of the transmembrane domain of Syndecan‐2 in detergent micelles

Kang

2019

FEBS Letters

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Syndecans are single‐span membrane proteins playing important roles in cell–cell and cell–matrix interactions. The transmembrane domain of syndecans is critical for signal transduction across the cell membrane. Here, the structure of the transmembrane domain of syndecan‐2 in detergent micelles was investigated using solution NMR spectroscopy. Backbone resonance assignment was obtained, and NMR studies show that the transmembrane domain forms a helix in detergent micelles, which is also supported by the hydrogen and deuterium exchange experiment. A study of the dynamics revealed the rigid structure of the transmembrane domain formed in solution, and paramagnetic relaxation enhancement defined the topology of the transmembrane domain in detergent micelles. This structural analysis may facilitate a better understanding of the role of the syndecan‐2 transmembrane domain in signal transduction.

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Section: Resultsmentioning

confidence: 99%

“…SDC2‐TM was purified in the presence of DPC micelles using the method described previously . Briefly, the cells were broken in the buffer with 1% DPC by sonication.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Secondary structure and topology of the transmembrane domain of Syndecan‐2 in detergent micelles

Kang

2019

FEBS Letters

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“…NS4B is the largest membrane protein found in the flavivirus genome. It consists of nine helices with helices 2, 3, 5, 7 and 9 forming transmembrane domains 1–5, respectively [ 99 , 100 , 101 ]. DENV accumulation at ER-derived membranes is mediated by the transmembrane domains 3–5 [ 100 ].…”

Section: Nonstructural Proteinsmentioning

confidence: 99%

Molecular Insights into the Flavivirus Replication Complex

Elsen

Quek

Luo

2021

Viruses

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Flaviviruses are vector-borne RNA viruses, many of which are clinically relevant human viral pathogens, such as dengue, Zika, Japanese encephalitis, West Nile and yellow fever viruses. Millions of people are infected with these viruses around the world each year. Vaccines are only available for some members of this large virus family, and there are no effective antiviral drugs to treat flavivirus infections. The unmet need for vaccines and therapies against these flaviviral infections drives research towards a better understanding of the epidemiology, biology and immunology of flaviviruses. In this review, we discuss the basic biology of the flavivirus replication process and focus on the molecular aspects of viral genome replication. Within the virus-induced intracellular membranous compartments, flaviviral RNA genome replication takes place, starting from viral poly protein expression and processing to the assembly of the virus RNA replication complex, followed by the delivery of the progeny viral RNA to the viral particle assembly sites. We attempt to update the latest understanding of the key molecular events during this process and highlight knowledge gaps for future studies.

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“…Several proteins with molecular weights over 100 kDa have been characterized using NMR spectroscopy. To increase signal sensitivity, TROSY-based [ 126 ] experiments are often required for achieving assignment for proteins [ 73 , 127 , 128 , 129 ] with size less than 30 kDa. In the backbone resonance assignment of the SET domain of NSD3, 13 C, 15 N and 2 H-labeled sample and TROSY-based experiments [ 126 , 130 ] are essential to obtain the backbone assignment while this construct contains 256 residues ( Figure 3 a) [ 131 ].…”

Section: Nmr Experiments Used For Protein-ligand Interactionsmentioning

confidence: 99%

Solution NMR Spectroscopy in Target-Based Drug Discovery

Kang

2017

Molecules

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Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

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Secondary Structure and Membrane Topology of the Full‐Length Dengue Virus NS4B in Micelles

Cited by 30 publications

References 42 publications

Secondary structure and topology of the transmembrane domain of Syndecan‐2 in detergent micelles

Secondary structure and topology of the transmembrane domain of Syndecan‐2 in detergent micelles

Molecular Insights into the Flavivirus Replication Complex

Solution NMR Spectroscopy in Target-Based Drug Discovery

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