Browsing by Author "Lyu, Ping-Chiang"

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Circular Permutation Prediction Reveals a Viable Backbone Disconnection for Split Proteins: An Approach in Identifying a New Functional Split Intein
(2012-08-24)
Lee, Yun-Tzai
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Su, Tz-Hsiang
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Lo, Wei-Cheng
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Lyu, Ping-Chiang
;
Sue, Shih-Che
Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS) activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)
(2012-01-17)
Wang, Nai-Jyuan
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Lee, Chi-Ching
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Cheng, Chao-Sheng
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Lo, Wei-Cheng
;
Yang, Ya-Fen
Background: Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. Methods: In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database - nsLTPDB - which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/. Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X-2 V X5-7 C [V, L, I] x Y [L, A, V] X8-13 CC x G X-12 D x [Q, K, R] X-2 CXC X16-21 P X-2 C X13-15C, and that of Type II is C X-4 L X-2 C X9-11 P [S, T] X-2 CC X-5 Q X2-4 C[L, F] C X-2 [A, L, I] x [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs. Conclusions: Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.
CPred: a web server for predicting viable circular permutations in proteins
(2012-07-01)
Lo, Wei-Cheng
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Wang, Li-Fen
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Liu, Yen-Yi
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Dai, Tian
;
Hwang, Jenn-Kang
"Circular permutation (CP) is a protein structural rearrangement phenomenon, through which nature allows structural homologs to have different locations of termini and thus varied activities, stabilities and functional properties. It can be applied in many fields of protein research and bioengineering. The limitation of applying CP lies in its technical complexity, high cost and uncertainty of the viability of the resulting protein variants. Not every position in a protein can be used to create a viable circular permutant, but there is still a lack of practical computational tools for evaluating the positional feasibility of CP before costly experiments are carried out. We have previously designed a comprehensive method for predicting viable CP cleavage sites in proteins. In this work, we implement that method into an efficient and user-friendly web server named CPred (CP site predictor), which is supposed to be helpful to promote fundamental researches and biotechnological applications of CP. The CPred is accessible at http://sarst.life.nthu.edu.tw/CPred."
Deciphering the Preference and Predicting the Viability of Circular Permutations in Proteins
(2012-02-16)
Lo, Wei-Cheng
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Dai, Tian
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Liu, Yen-Yi
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Wang, Li-Fen
;
Hwang, Jenn-Kang
Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e. g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology.
Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques
(2010-10-14)
Chu, Chia-Han
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Lo, Wei-Cheng
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Wang, Hsin-Wei
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Hsu, Yen-Chu
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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.
GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects
(2013-04-10)
Lee, Chi-Ching
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Chen, Yi-Ping Phoebe
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Yao, Tzu-Jung
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Ma, Cheng-Yu
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Lo, Wei-Cheng
Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. (c) 2012 Elsevier B.V. All rights reserved.
High performance electric-double-layer amorphous IGZO thin-film transistors gated with hydrated bovine serum albumin protein
(2015-09-01)
Chen, Shih-Han
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Liu, Hung-Chuan
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Lee, Chun-Yi
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Gan, Jon-Yiew
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Zan, Hsiao-Wen
Device performance of amorphous indium gallium zinc oxide (a-IGZO) thin film transistors (TFTs) has been improved greatly by using bovine serum albumin (BSA) as the top gate dielectric. BSA is a natural protein with acidic and basic amino acid residues, which is easily hydrated in air ambient. A typical a-IGZO TFT with hydrated BSA as the top gate dielectric exhibits a field-effect mobility (mu(FE)) value of 113.5 cm(2) V-1 s(-1) in saturation regime and a threshold voltage (V-TH) value of 0.25 V in air ambient. The excellent device performance can be well explained by the formation of electric double layers (EDLs) near the interfaces of a-IGZO/hydrated BSA and hydrated BSA/gate electrode. The reliability issue of a-IGZO TFTs gated with hydrated BSA has been also investigated by using the life time test without encapsulation. The V-TH value increases and mu(FE,sat) value reduces slightly for the a-IGZO TFT and remain stabilized over 60 days. (C) 2015 Elsevier B.V. All rights reserved.
Novel Water-Soluble Cyclodextrin-Based Conjugated Polymer for Selective Host-Guest Interactions of Cationic Surfactant CTAB and Reverse FRET with Rhodamine B Tagged Adamantyl Guest
(2016-08-09)
Dwivedi, Atul Kumar
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Singh, Ravinder
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Singh, Ashutosh
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Wei, Kung-Hwa
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Wu, Chu-Ya
A new water-soluble pi-conjugated main-chain polymer P1 bearing a beta-cyclodextrin (beta-CD) pendant was designed and synthesized. The aggregation and disaggregation of P1 generated faded yellow-greenish and bright-yellow emissions, respectively. The inclusion complexation capability of P1 through beta-CD pendant with a cationic surfactant cetyltrimethylammonium bromide (CTAB) guest and associative interactions of P1 with Fe3+ through triazole spacers resulted in significantly enhanced and completely diminished emission profiles of P1 in pure water, respectively. Interestingly, ADRhB as another rhodamine B (RhB) tagged adamantyl guest was transformed into ADRhB(0), i.e., the open form of ADRhB, to generate RhB emission in the presence of Fe3+ ion selectively for the pendent host beta-CD of PI, and the further interaction of.ADRhB(0)/Fe3+ with P1 prevailed a completely quenched RhB emission via the inclusion complexation of adamantyl terminal of ADRhB (0) in beta-CD. Moreover, stronger interactions of CTAB with beta-CD further generated RhB emission of ADRhB(0) even in the presence of acceptor Pl. Finally, a novel beta-CD bearing water-soluble P1 with selective and strong interactions of CTAB toward disaggregation events in pure water, and further electrostatic repulsion and utilization of RhB via RhB-tagged adamantyl guest ADRhB(0) as a donor revealed the reverse fluorescence resonance energy transfer (FRET) process of P1.
Structural Basis for the Improved Potency of Peroxisome Proliferator-Activated Receptor (PPAR) Agonists
(2010-10-04)
Peng, Yi-Hui
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Coumar, Mohane Selvaraj
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Leou, Jiun-Shyang
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Wu, Jian-Sung
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Shiao, Hui-Yi
The need to develop safer and more effective antidiabetic drugs is essential owing to the growth worldwide of the diabetic population. Targeting the PPAR receptor is one strategy for the treatment of diabetes; the PPAR agonists rosiglitazone and pioglitazone are already on the market. Here we report the identification of a potent PPAR agonist, 15, whose PPAR gamma activation was more than 20 times better than that of rosiglitazone. Compound 15 was designed to incorporate an indole head with a carboxylic acid group, and 4-phenylbenzophenone tail to achieve a PPAR gamma EC(50) of 10 nm. Compound 15 showed the most potent PPAR gamma agonist activity among the compounds we investigated. To gain molecular insight into the improved potency of 15, a structural biology study and binding energy calculations were carried out. Superimposition of the X-ray structures of 15 and agonist 10 revealed that, even though they have the same indole head part, they adopt different conformations. The head part of 15 showed stronger interactions toward PPAR gamma; this could be due to the presence of the novel tail part 4-phenylbenzophenone, which could enhance the binding efficiency of 15 to PPAR gamma.
Structural Basis for the Improved Potency of Peroxisome Proliferator-Activated Receptor (PPAR) Agonists
(2010-10-04)
Peng, Yi-Hui
;
Coumar, Mohane Selvaraj
;
Leou, Jiun-Shyang
;
Wu, Jian-Sung
;
Shiao, Hui-Yi
The need to develop safer and more effective antidiabetic drugs is essential owing to the growth worldwide of the diabetic population. Targeting the PPAR receptor is one strategy for the treatment of diabetes; the PPAR agonists rosiglitazone and pioglitazone are already on the market. Here we report the identification of a potent PPAR agonist, 15, whose PPAR gamma activation was more than 20 times better than that of rosiglitazone. Compound 15 was designed to incorporate an indole head with a carboxylic acid group, and 4-phenylbenzophenone tail to achieve a PPAR gamma EC(50) of 10 nm. Compound 15 showed the most potent PPAR gamma agonist activity among the compounds we investigated. To gain molecular insight into the improved potency of 15, a structural biology study and binding energy calculations were carried out. Superimposition of the X-ray structures of 15 and agonist 10 revealed that, even though they have the same indole head part, they adopt different conformations. The head part of 15 showed stronger interactions toward PPAR gamma; this could be due to the presence of the novel tail part 4-phenylbenzophenone, which could enhance the binding efficiency of 15 to PPAR gamma.