Publications by authors named "Yuan-Yu Chang"

Variants in the gap junction beta-2 () gene are the most common cause of hereditary hearing impairment. However, how variants lead to local physicochemical and structural changes in the hexameric ion channels of connexin 26 (Cx26), resulting in hearing impairment, remains elusive. In this study, using molecular dynamics (MD) simulations, we showed that detached inner-wall N-terminal "plugs" aggregated to reduce the channel ion flow in a highly prevalent V37I variant in humans.

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Since the 90s, keyword-based search engines have been the only option for people to locate relevant web content through a simple query comprising one to a few keywords. These engines, whether free or paid, retained users' search queries and preferences, often to deliver targeted ads. Additionally, user-uploaded articles for plagiarism detection can further be stored as part of service providers' expanding databases for profit.

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A novel fluorescence resonance energy transfer (FRET)-based ratiometric emission fluorescent probe AT was designed and developed in which the imidazo[1,5-α]pyridine was served as a FRET donor and tricyanofuran (TCF) as the FRET acceptor to detect SO/HSO based on the Michael addition reaction. Probe AT had a high energy transfer efficiency (95%) and a large pseudo-Stokes shift (259 nm) in EtOH/PBS buffer (5/5, v/v). It also possessed good selectivity and quick response to SO/HSO.

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The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided.

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A mild and high efficient method to prepare indolizines by two-component reaction with the acid as the catalyst was developed. In this reaction, a new ring efficiently formed in one-step reaction. A wide range of substrates could be applied and the desired products were obtained in 8-95% yields under metal-free conditions.

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Opioids account for 69,000 overdose deaths per annum worldwide and cause serious side effects. Safer analgesics are urgently needed. The endogenous opioid peptide Leu-Enkephalin (Leu-ENK) is ineffective when introduced peripherally due to poor stability and limited membrane permeability.

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Life ticks as fast as how proteins move. Computationally expensive molecular dynamics simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely to their slowest ends. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of structured biomolecules.

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Motivation: Programmed ribosomal frameshifting (PRF) is widely used by viruses and bacteria to produce different proteins from a single mRNA template. How steric hindrance of a PRF-stimulatory mRNA structure transiently modifies the conformational dynamics of the ribosome, and thereby allows tRNA slippage, remains elusive.

Results: Here, we leverage linear response theories and resolution-exchanged simulations to construct a structural/dynamics model that connects and rationalizes existing structural, single-molecule and mutagenesis data by resolution-exchanged structural modelling and simulations.

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DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment.

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Article Synopsis
  • Sortases are enzymes in Gram-positive bacteria that attach surface proteins to the cell wall, using a specific signal at the protein's C-terminus.
  • The study investigates how sortase B (Cd-SrtB) specifically recognizes and binds to the peptide substrate PPKTG, utilizing structural studies and computational modeling.
  • Key findings indicate that the fourth amino acid from the cleavage site of PPKTG is crucial for effective recognition and cleavage by sortase B, enhancing our understanding of substrate specificity in these enzymes.
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Receptor-binding and subsequent signal-activation of interleukin-1 beta (IL-1β) are essential to immune and proinflammatory responses. We mutated 12 residues to identify sites important for biological activity and/or receptor binding. Four of these mutants with mutations in loop 9 (T117A, E118K, E118A, E118R) displayed significantly reduced biological activity.

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Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.

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Objective: To determine the patterns of urinary proteins in bladder cancer subjects using pooled urine from 27 bladder cancer patients.

Methods: The urine matrix was removed by acetonitrile precipitation followed by molecular weight cutoff. High performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) was used to analyze the urinary proteome.

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