A5041175392- Enzyme Structure and Function
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Biochemical and Molecular Research
- Mass Spectrometry Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Computational Drug Discovery Methods
- Streptococcal Infections and Treatments
- Infective Endocarditis Diagnosis and Management
- Enzyme function and inhibition
- Cancer Research and Treatments
- Bacterial Genetics and Biotechnology
- Neonatal and Maternal Infections
- Amino Acid Enzymes and Metabolism
- Cytomegalovirus and herpesvirus research
- Insect symbiosis and bacterial influences
- RNA Research and Splicing
- Enzyme Production and Characterization
- Photosynthetic Processes and Mechanisms
- Innovative Microfluidic and Catalytic Techniques Innovation
- Toxin Mechanisms and Immunotoxins
- Metal-Catalyzed Oxygenation Mechanisms
- Steroid Chemistry and Biochemistry
Seoul National University
2015-2024
Soonchunhyang University
2017
University of Wisconsin–Madison
2003-2015
The crystal structures of adenylate kinases from the psychrophile Bacillus globisporus and mesophile subtilis have been solved compared with that thermophile stearothermophilus. This is first example we know where a trio protein has same number amino acids high level identity (66-74%) yet come organisms different operating temperatures. enzymes were characterized for their own thermal denaturation inactivation, they exhibited temperature preferences as source organisms. three highly...
Ever since the first atomic structure of an enzyme was solved, discovery mechanism and dynamics reactions catalyzed by biomolecules has been key goal for understanding molecular processes that drive life on earth. Despite a large number successful methods trapping reaction intermediates, direct observation ongoing possible only in rare exceptional cases.
The intense arms race between bacteria and phages has led to the development of diverse antiphage defense systems in bacteria. Unlike well-known restriction-modification CRISPR-Cas systems, recently discovered are poorly characterized. One such system is Thoeris system, which consists two genes, thsA thsB. Here, we report structural functional analyses ThsA ThsB. exhibits robust NAD+ cleavage activity a two-domain architecture containing sirtuin-like SLOG-like domains. Mutation analysis...
Aging alters morphology and locomotor function in diverse organisms, yet standardized model systems for studying these changes remain limited to a relatively few species. Here, we present comprehensive analysis of age- sex-dependent morphological variations house crickets (Acheta domesticus), integrating refined husbandry protocols enhance reproducibility translational relevance. We observed progressive increases body weight, length, appendage dimensions with age, pronounced sexual...
Protein dynamics, including conformational switching, are recognized to be crucial for the function of many systems. These motions more challenging study than simple static structures. Here, we present evidence suggesting that in enzyme adenylate kinase large “hinge bending” closely related catalysis regulated by intrinsic properties moving domains and not their hinges, anchoring domains, or remote allosteric-like regions. From a pair highly homologous mesophilic thermophilic kinases,...
Abstract The bacterial CRISPR-Cas system provides adaptive immunity against invading phages. Cas9, an RNA-guided endonuclease, specifically cleaves target DNA substrates and constitutes a well-established platform for genome editing. Recently, anti-CRISPR (Acr) proteins that inhibit Cas9 have been discovered, promising useful off-switch to avoid undesirable off-target effects. Here, we report the solution structure dynamics of Listeria monocytogenes AcrIIA4 inhibits Streptococcus pyogenes (...
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide bacteria with RNA-based adaptive immunity against phage infection. To counteract this defense mechanism, phages evolved anti-CRISPR (Acr) that inactivate the CRISPR-Cas systems. AcrIIA1, encoded by Listeria monocytogenes prophages, is most prevalent among Acr targeting type II-A systems has been used as a marker to identify other proteins. Here, we report crystal structure of...
Molecular dynamics simulations were performed to study thermal stabilization of proteins via electrostatic interactions ion pairs. Dynamic motions four pairs previously proposed be important in stability adenylate kinase from the thermophile Bacillus stearothermophilus monitored during simulation. One identified crystal structure, Lys180-Asp114, was not maintained close contact suggesting that pair does contribute stability. Among other three pairs, Arg116-Glu198 most for To predict...
Engineering proteins for higher thermal stability is an important and difficult challenge. We describe a bioinformatic method incorporating sequence alignments to redesign be more stable through optimization of local structural entropy. Using this method, improved configurational entropy (ICE), we were able design variants mesophilic adenylate kinase with only the information one psychrophilic homologue. The redesigned display considerable increases in their stabilities while still retaining...
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute a microbial immune system against invading genetic elements, such as plasmids phages. Csn2 is an Nmeni subtype-specific Cas protein, was suggested to function in the adaptation process, during which parts of foreign nucleic acids are integrated into host genome enable immunity future invasion. Here, we report 2.2 Å crystal structure Streptococcus pyogenes Csn2. The revealed...
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR-Cas systems, the Cas1-Cas2 integrase complex subtype-specific Csn2 comprise CRISPR adaptation module, which cooperates with Cas9 nuclease effector for spacer selection. Here, we report molecular organization of Streptococcus pyogenes module its interaction via Csn2. We determined crystal...
Protein thermal stability is an important field since thermally stable proteins are desirable in many academic and industrial settings. Information on protein stabilization can be obtained by comparing homologous from organisms living at distinct temperatures. Here, we report structural mutational analyses of adenylate kinases (AKs) psychrophilic Bacillus globisporus (AKp) mesophilic subtilis (AKm). Sequence comparison showed suboptimal hydrophobic packing around Thr26 the CORE domain AKp,...
Adenylate kinases (AKs, ATP:AMP phosphotransferase, EC 2.7.4.3) are a family of enzymes which catalyze the following reaction: Mg2+ATP + AMP ↔ Mg2+ADP ADP. Several structural works have revealed that AKs two highly flexible domains close over bound substrates.1 The LID domain covers ATP and site phosphoryl transfer AMP-binding closes on when it is bound. Key residues to closure substrate binding conserved five arginines in active site. In Escherichia coli AK, they Arg36, Arg88, Arg123,...
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one most abundant prokaryotic antiviral systems consists two proteins, GajA GajB. has been characterized experimentally as sequence-specific DNA endonuclease. Although GajB was previously predicted to be UvrD-like helicase, its function unclear. Here, we report results structural functional analyses The crystal...
Psychrophiles are extremophilic organisms capable of thriving in cold environments. Proteins from these cold-adapted can remain physiologically functional at low temperatures, but structurally unstable even moderate temperatures. Here, we report the crystal structure adenylate kinase (AK) Antarctic fish Notothenia coriiceps, and identify structural basis adaptation by comparison with homologues tropical fishes including Danio rerio. The N. coriiceps AK (AKNc) revealed suboptimal hydrophobic...
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide adaptive immunity to prokaryotes against invading phages plasmids. As a countermeasure, have evolved anti-CRISPR (Acr) that neutralize the CRISPR immunity. AcrIIA5, isolated from virulent phage of Streptococcus thermophilus, strongly inhibits diverse Cas9 homologs, but molecular mechanism underlying inhibition remains unknown. Here, we report solution structure which features...
Cytokinins are a class of plant hormones regulating cell division and variety developmental events.1 Cytokinin homeostasis is important in many aspects growth, their control has economic significance agriculture.2 These chemically adenine derivatives with variable N6 substituent. Most catabolism regulated by cytokinin dehydrogenase (CKX, EC 1.5.99.12),3 which involved oxidative cleavage cytokinins to the CKX originally been thought be an oxidase transferring electrons molecular oxygen.4...
Thermally stable proteins are desirable for research and industrial purposes, but redesigning higher thermal stability can be challenging. A number of different techniques have been used to improve the proteins, extents enhancement were sometimes unpredictable not significant. Here, we systematically tested effects multiple stabilization including a bioinformatic method structure-guided mutagenesis on single protein, thereby providing an integrated approach protein stabilization. Using...