Browsing by Author "Hsu, Yen-Chu"

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Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques
(2010-10-14)
Chu, Chia-Han
;
Lo, Wei-Cheng
;
Wang, Hsin-Wei
;
Hsu, Yen-Chu
;
Hwang, Jenn-Kang
This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened'' their "closed'' structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8 angstrom for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications.
Rotationally resolved ultrahigh-resolution laser spectroscopy of the S(2) (1)A(1)<- S(0) (1)A(1) transition of azulene
(2009-07-14)
Semba, Yosuke
;
Yoshida, Kazuto
;
Kasahara, Shunji
;
Ni, Chi-Kung
;
Hsu, Yen-Chu
We have observed rotationally resolved ultrahigh-resolution fluorescence excitation spectra of the 0(0)(0) (a-type) and 0(0)(0)+467 cm(-1) (b-type) bands of the S(2) (1)A(1)<- S(0) (1)A(1) transition of jet-cooled azulene. The observed linewidth is 0.0017 cm(-1), which corresponds to the lifetime of 3.1 ns in the S(2) state. Zeeman splitting of rotational lines is very small so that intersystem crossing to the triplet state is considered to be very slow. Inertial defect is very small and the molecule is considered to be planar in the S(0) and S(2) states (C(2 upsilon) symmetry). Rotational constants of the S(2) state are almost identical to those of the S(0) state, indicating that geometrical structure is similar in both electronic states. In this case, internal conversion (IC) by vibronic coupling is thought to be inactive. Therefore, the main radiationless transition process in the S(2) (1)A(1) state of azulene was identified to be IC to the S(1) (1)B(2) state. However, this S(2)-> S(1) IC is still slower than that of conventional polycyclic aromatic hydrocarbons. We consider it to be due to the shallower potential energy curve in the S(1) (1)B(2) state, which is also responsible for the extraordinarily fast S(1)-> S(0) IC in the isolated azulene molecule. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3168394]
Rotationally resolved ultrahigh-resolution laser spectroscopy of the S-2 (1)A(1)<- S-0 (1)A(1) transition of azulene
(2009-07-14)
Semba, Yosuke
;
Yoshida, Kazuto
;
Kasahara, Shunji
;
Ni, Chi-Kung
;
Hsu, Yen-Chu
We have observed rotationally resolved ultrahigh-resolution fluorescence excitation spectra of the 0(0)(0) (a-type) and 0(0)(0)+467 cm(-1) (b-type) bands of the S-2 (1)A(1)<- S-0 (1)A(1) transition of jet-cooled azulene. The observed linewidth is 0.0017 cm(-1), which corresponds to the lifetime of 3.1 ns in the S-2 state. Zeeman splitting of rotational lines is very small so that intersystem crossing to the triplet state is considered to be very slow. Inertial defect is very small and the molecule is considered to be planar in the S-0 and S-2 states (C-2 upsilon symmetry). Rotational constants of the S-2 state are almost identical to those of the S-0 state, indicating that geometrical structure is similar in both electronic states. In this case, internal conversion (IC) by vibronic coupling is thought to be inactive. Therefore, the main radiationless transition process in the S-2 (1)A(1) state of azulene was identified to be IC to the S-1 B-1(2) state. However, this S-2 -> S-1 IC is still slower than that of conventional polycyclic aromatic hydrocarbons. We consider it to be due to the shallower potential energy curve in the S-1 B-1(2) state, which is also responsible for the extraordinarily fast S-1 -> S-0 IC in the isolated azulene molecule. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3168394]
Vibrational and rotational structure and excited-state dynamics of pyrene
(1970-01-01)
Baba, Masaaki
;
Saitoh, Motohisa
;
Kowaka, Yasuyuki
;
Taguma, Kunio
;
Yoshida, Kazuto
"Vibrational level structure in the S-0 (1)A(g) and S-1 B-1(3u) states of pyrene was investigated through analysis of fluorescence excitation spectra and dispersed fluorescence spectra for single vibronic level excitation in a supersonic jet and through referring to the results of ab initio theoretical calculation. The vibrational energies are very similar in the both states. We found broad spectral feature in the dispersed fluorescence spectrum for single vibronic level excitation with an excess energy of 730 cm(-1). This indicates that intramolecular vibrational redistribution efficiently occurs at small amounts of excess energy in the S-1 B-1(3u) state of pyrene. We have also observed a rotationally resolved ultrahigh-resolution spectrum of the 0(0)(0) band. Rotational constants have been determined and it has been shown that the pyrene molecule is planar in both the S-0 and S-1 states, and that its geometrical structure does not change significantly upon electronic excitation. Broadening of rotational lines with the magnetic field by the Zeeman splitting of M-J levels was very small, indicating that intersystem crossing to the triplet state is minimal. The long fluorescence lifetime indicates that internal conversion to the S-0 state is also slow. We conclude that the similarity of pyrene's molecular structure and potential energy curve in its S-0 and S-1 states is the main cause of the slow radiationless transitions."