Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and<i>ab initio</i>structure determination

Chen, Chung De; Huang, Yen‐Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun‐Jung

doi:10.1107/s1399004714013868

Cited by 5 publications

(5 citation statements)

References 39 publications

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“…According to the structure of lysozyme, − the Arg, Lys, and Asn amino acids are mainly located on the surface of lysozyme (Figure ). The CH groups of the three amino acids are dominant in all of the CH groups of the amino residues.…”

Section: Resultsmentioning

confidence: 99%

Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra

Xing¹,

Lin

Zhou³

et al. 2016

J. Phys. Chem. B

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The denaturation mechanism of hen egg lysozyme is still controversial. In this study, Raman spectroscopy was employed to study the thermal and chemical denaturation mechanisms of lysozyme. All of the Raman bands were synchronously recorded and analyzed during the denaturation process. It was found that the Raman bands of the side groups changed before the bands of skeleton groups. This directly reveals the three-state mechanism of thermal denaturation of lysozyme. The preferential change of the side groups was also observed in the chemical denaturation of lysozyme by guanidine hydrochloride. Moreover, it was found that the Raman bands of the groups on the surface of lysozyme changed before those of the other groups. This indicates that the chemical denaturants interact with the protein surface before the protein core in each step and the chemical denaturation of lysozyme conforms to the multistate and outside-in mechanisms. The synchronous Raman study not only reveals the multistate mechanism of lysozyme denaturation but also demonstrates that this synchronous Raman analysis is a powerful method to study the denaturation mechanisms of other proteins.

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Section: Resultsmentioning

confidence: 99%

Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra

Xing¹,

Lin

Zhou³

et al. 2016

J. Phys. Chem. B

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“…Model refinement based on known FHA domains was also unfeasible because of the variation in loop regions among FHA domains. Finally, the recently developed direct phase selection method 29 effectively resolved the ambiguity of SAD phases and generated optimized initial phases for structure determination. The new algorithm is particularly helpful in cases where only SAD data are available.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…The selenium sites of SeMet tTIFA 1−150 were located with SHELX C/D/E, 26 and the initial phase was calculated by Phaser 27 followed by density modification with DM. 28 Then the optimal initial phases were determined by the direct phase selection method to reduce the phase ambiguity, 29 and subsequently, automated model building was performed with Buccaneer. 30 The model was further improved by conventional two-wavelength MAD data sets collected from optimized crystals.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses

et al. 2015

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Forkhead-associated (FHA) domain is the only signaling domain that recognizes phosphothreonine (pThr) specifically. TRAF-interacting protein with an FHA domain (TIFA) was shown to be involved in immune responses by binding with TRAF2 and TRAF6. We recently reported that TIFA is a dimer in solution and that, upon stimulation by TNF-α, TIFA is phosphorylated at Thr9, which triggers TIFA oligomerization via pThr9-FHA domain binding and activates nuclear factor κB (NF-κB). However, the structural mechanism for the functionally important TIFA oligomerization remains to be established. While FHA domain-pThr binding is known to mediate protein dimerization, its role in oligomerization has not been demonstrated at the structural level. Here we report the crystal structures of TIFA (residues 1-150, with the unstructured C-terminal tail truncated) and its complex with the N-terminal pThr9 peptide (residues 1-15), which show unique features in the FHA structure (intrinsic dimer and extra β-strand) and in its interaction with the pThr peptide (with residues preceding rather than following pThr). These structural features support previous and additional functional analyses. Furthermore, the structure of the complex suggests that the pThr9-FHA domain interaction can occur only between different sets of dimers rather than between the two protomers within a dimer, providing the structural mechanism for TIFA oligomerization. Our results uncover the mechanism of FHA domain-mediated oligomerization in a key step of immune responses and expand the paradigm of FHA domain structure and function.

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“…By introducing a SAD likelihood function to rank possible solutions from phenix.hyss, a study showed that in the case of CysZ multicrystal data (Bunkó czi et al, 2014) SAD likelihood ranking significantly improved the rate of success in finding the correct anomalous substructure in terms of both the strength of the anomalous signal and the number of crystals used to produce the merged data set. Another study introduces a direct phaseselection step prior to density modification (using RESOLVE or DM) that significantly improved the final experimental phases and the quality of the resulting electron-density maps (Chen et al, 2014).…”

Section: Phasing and Structure Solutionmentioning

confidence: 99%

Native SAD is maturing

Rose

Wang

Weiss

2015

IUCrJ

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Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density andab initiostructure determination

Cited by 5 publications

References 39 publications

Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra

Multistate Mechanism of Lysozyme Denaturation through Synchronous Analysis of Raman Spectra

Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses

Native SAD is maturing

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