Wookyung Yu

Daegu Gyeongbuk Institute of Science and Technology | DGIST · Department of Brain Science

Prostate cancer (PC) is the second leading cause of cancer-related death among men. Treatment of PC becomes difficult after progression because PC that used to be androgen-dependent becomes androgen-independent prostate cancer (AIPC). Veratramine, an alkaloid extracted from the root of the Veratrum genus, has recently been reported to have anticanc...

The growing use of plastic materials has resulted in a constant increase in the risk associated with microplastics (MPs). Ultra-violet (UV) light and wind break down modify MPs in the environment into smaller particles known as weathered MPs (WMPs) and these processes increase the risk of MP toxicity. The neurotoxicity of weathered polystyrene-MPs...

Glucagon is a peptide hormone which posits a significant potential as a therapeutic molecule for various human diseases. One of the major challenges hampering medicinal application of glucagon, however, is its insoluble and aggregation-prone property. Although glucagon is dissolvable, it aggregates easily and forms amyloid fibrils. To date, despite...

High-voltage-activated Ca ²⁺ (Ca V ) channels that adjust Ca ²⁺ influx upon membrane depolarization are differentially regulated by phosphatidylinositol 4,5-bisphosphate (PIP 2 ) in an auxiliary Ca V β subunit-dependent manner. However, the molecular mechanism by which the β subunits control the PIP 2 sensitivity of Ca V channels remains unclear. B...

Although several studies have focused on cancer diagnosis and therapy, prostate cancer (PC) remains an intractable disease. Androgen deprivation therapy (ADT), which is used to treat early stage PC can lead to the development of castration-resistant prostate cancer (CRPC), which is highly associated with androgen receptor (AR) mutations. Nucleolar...

Aggregation of intrinsically disordered α-synuclein (αSN) under various conditions is closely related to synucleinopathies. Although various biological membranes have shown to alter the structure and aggregation propensity of αSN, a thorough understanding of the molecular and mechanical mechanism of amyloidogenesis in membranes remains unanswered....

Repeated cocaine use poses many serious health risks to users. One of the risks is hypoxia and ischemia (HI). To restore the biological system against HI, complex biological mechanisms operate at the gene level. Despite the complexity of biological mechanisms, there are common denominator genes that play pivotal roles in various defense systems. Am...

Polymerase chain reaction (PCR) is a powerful tool to diagnose infectious diseases. Uracil DNA Glycosylase (UDG) has been broadly used to remove carryover contamination in PCR. However, UDG can contribute to false negative results due to UDG not being inactivated completely, leading to DNA degradation during the amplification step. In this study, w...

Background The progression of prostate cancer (PC) to the highly aggressive metastatic castration-resistant prostate cancer (mCRPC) or neuroendocrine prostate cancer (NEPC) is a fatal condition and the underlying molecular mechanisms are poorly understood. Here, we identified the novel transcriptional factor ZNF507 as a key mediator in the progress...

The cannabinoid receptor 1 (CB1) is a class A G-protein coupled receptor (GPCR) that can exert various effects on the human body through the endocannabinoid system. Understanding CB1 activation has many benefits for the medical use of cannabinoids. A previous study reported that CB1 has two notable residues referred to as the toggle switch, F3.36 a...

Hsp33, a prokaryotic redox-regulated holding chaperone, has been recently identified to be able to exhibit an unfoldase and aggregase activity against elongation factor Tu (EF-Tu) in its reduced state. In this study, we investigated the effect of elongation factor Ts (EF-Ts) and trigger factor (TF) on Hsp33-mediated EF-Tu unfolding and aggregation...

Site-specific ubiquitination can regulate the functions of Rab proteins in membrane trafficking. Previously we showed that site-specific monoubiquitination on Rab5 downregulates its function. Rab7 acts in the downstream of Rab5. Although site-specific ubiquitination of Rab7 can affect its function, it remains elusive how the ubiquitination is invol...

Monomer dissociation and subsequent misfolding of the transthyretin (TTR) is one of the most critical causative factors of TTR amyloidosis. TTR amyloidosis causes several human diseases, such as senile systemic amyloidosis and familial amyloid cardiomyopathy/polyneuropathy; therefore, it is important to understand the molecular details of the struc...

Aggregation of intrinsically disordered amyloid β (Aβ) is a hallmark of Alzheimer’s disease. Although complex aggregation mechanisms have been increasingly revealed, structural ensembles of Aβ monomers with heterogeneous and transient properties still hamper detailed experimental accesses to early events of amyloidogenesis. We herein developed a ne...

G protein-coupled receptors (GPCRs) regulate diverse physiological events, which makes them as the major targets for many approved drugs. G proteins are downstream molecules that receive signals from GPCRs and trigger cell responses. The GPCR-G protein selectivity mechanism on how they properly and timely interact is still unclear. Here, we analyze...

Serum amyloid A (SAA) is an acute phase protein produced primarily in the liver that plays a key role in both the initiation and maintenance of inflammation. Rapidly secreted SAA induces neutrophilia at inflammatory sites, initiating inflammation and inducing the secretion of various cytokines, including TNF-α, IL-6, and IL-17. IL-17 is expressed i...

Heterotrimeric guanine nucleotide-binding proteins (G proteins) are composed of α, β, and γ subunits. Gα switches between guanosine diphosphate (GDP)-bound inactive and guanosine triphosphate (GTP)-bound active states, and Gβγ interacts with the GDP-bound state. The GDP-binding regions are composed of two sites: the phosphate-binding and guanine-bi...

Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). Hydrophobic interaction is the main driving force for protein folding, and critically affects the stability and solvability. To examine the importance of the hydrophobic core in the PrP, we chose six amino acids (V176...

Background: Evolutionary information contained in the amino acid sequences of proteins specifies the biological function and fold, but exactly what information contained in the protein sequence drives both of these processes? Considerable progress has been made to answer this fundamental question, but it remains challenging to explore the potentia...

Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a syste...

Cannabinoid receptor 1 (CB1) is a promising therapeutic target for a variety of disorders. Distinct efficacy profiles showed different therapeutic effects on CB1 dependent on three classes of ligands: agonists, antagonists, and inverse agonists. To discriminate the distinct efficacy profiles of the ligands, we carried out molecular dynamics (MD) si...

Statistical analysis plays a significant role in both protein sequences and structures, expanding in recent years from the studies of co-evolution guided single-site mutations to protein folding in silico . Here we describe a computational tool, termed Sibe, with a particular focus on protein sequence analysis, folding and design. Since Sibe has va...

Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a syste...

Significance The basis of protein-folding cooperativity and stability elicits a variety of opinions, as does the existence and importance of possible residual structure in the denatured state. We examine these issues in a protein that is striking in its dearth of hydrophobic burial and its lack of canonical α and β structures, while having a low se...

Significance Fast-folding proteins provide a testing ground for theories and simulations of folding at the extreme limit, in particular when it occurs on the timescale of chain diffusion and potentially in the elusive barrier-free limit. Whereas most fast-folding studies probe the reaction near the transition point with limited resolution, we apply...

Significance An outstanding issue in protein science is identifying the relationship between sequence and folding, e.g., do sequences having similar structures have similar folding pathways? The homologs Proteins G & L have been cited as a primary example where sequence variations dramatically affect folding dynamics. However, our new results indic...

Significance Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to a...

Protein conformation change depending not only on the values of temperature, denaturant concentration but also on the values of solvent pH. The difference of the pH-denaturation from the thermal or urea denaturation is that hydrogen atoms (un)bind exclusively to R, K, Y, C, H, D, E amino acids. Thus the pH effect on the protein conformation is sele...

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with der...

Unravelling the complex correlation between chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H (α), (15) N, (1) H ( N ) atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the thr...

Macrolide-specific efflux pump MacAB-TolC has been identified in diverse Gram-negative bacteria including Escherichia coli. The inner membrane transporter MacB requires the outer membrane factor TolC and the periplasmic adaptor protein MacA to form a functional tripartite complex. In this study, we used a chimeric protein containing the tip region...

Macrolide-specific efflux pump MacAB-TolC has been identified in diverse Gram-negative bacteria including Escherichia coli. The inner membrane transporter MacB requires the outer membrane factor TolC and the periplasmic adaptor protein MacA to form a functional tripartite complex. In this study, we used a chimeric protein containing the tip region...

Recent experiments claiming that Naf-BBL protein follows a global downhill folding raised an important controversy as to the folding mechanism of fast-folding proteins. Under the global downhill folding scenario, not only do proteins undergo a gradual folding, but folding events along the continuous folding pathway also could be mapped out from the...

Recent experiments claiming that Naf-BBL protein follows a global downhill folding raised an important controversy as to the folding mechanism of fast-folding proteins. Under the global downhill folding scenario, not only do proteins undergo a gradual folding, but folding events along the continuous folding pathway also could be mapped out from the...