A5090370706- Protein Structure and Dynamics
- Monoclonal and Polyclonal Antibodies Research
- Bacteriophages and microbial interactions
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- SARS-CoV-2 and COVID-19 Research
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Viral gastroenteritis research and epidemiology
- Cellular transport and secretion
- Neuropeptides and Animal Physiology
- Receptor Mechanisms and Signaling
- Protein purification and stability
- Bioinformatics and Genomic Networks
- Solar and Space Plasma Dynamics
- Solar Radiation and Photovoltaics
- RNA and protein synthesis mechanisms
- Transgenic Plants and Applications
- Toxin Mechanisms and Immunotoxins
- Cancer, Stress, Anesthesia, and Immune Response
- Ubiquitin and proteasome pathways
- Machine Learning in Materials Science
- Mass Spectrometry Techniques and Applications
- Regulation of Appetite and Obesity
- Lipid Membrane Structure and Behavior
Seoul National University
2019-2024
This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in viral membrane. First, starting from PDB: 6VSB 6VXX, S structures were modeled using template-based modeling, de-novo structure prediction, loop techniques GALAXY suite. Then, the recently determined most occupied glycoforms, 22 N-glycans 1 O-glycan each monomer Glycan Reader & Modeler CHARMM-GUI. These model assessed further refined against low-resolution data...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme (ACE2) and is considered the major target for drug vaccine development. We previously built fully glycosylated full-length SARS-CoV-2 S models in a viral membrane including both open closed conformations receptor-binding domain (RBD) different templates stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations...
Neuropeptide Y (NPY) is highly abundant in the brain and involved various physiological processes related to food intake anxiety, as well human diseases such obesity cancer. However, molecular details of interactions between NPY its receptors are poorly understood. Here, we report a cryo-electron microscopy structure NPY-bound neuropeptide Y1 receptor (Y1R) complex with Gi1 protein. The C-terminal segment forming extended conformation binds deep into Y1R transmembrane core, where amidated...
While deep learning (DL) has brought a revolution in the protein structure prediction field, still an important question remains how can be transferred to advances structure-based drug discovery. Because lessons from recent GPCR dock challenge were inconclusive primarily due size of dataset, this work we further elaborated on 70 diverse complexes bound either small molecules or peptides investigate best-practice modeling and docking strategies for From our quantitative analysis, it is shown...
The precision design of antibodies, which naturally recognize diverse molecules through six variable loops, remains a critical challenge in therapeutic molecule discovery. In this study, we demonstrate that precise, sensitive, and specific antibody can be achieved without prior information across distinct target proteins. For each target, binders were identified from yeast display scFv library approximately 10 6 sequences, constructed by combining 2 designed light chain sequences with 4...
Somatostatin is a peptide hormone that regulates endocrine systems by binding to G-protein-coupled somatostatin receptors. receptor 2 (SSTR2) human and highly implicated in disorders, cancers, neurological diseases. Here, we report the high-resolution cryo-EM structure of full-length SSTR2 bound agonist (SST-14) complex with inhibitory G (G i ) proteins. Our structural mutagenesis analyses show seven transmembrane helices form deep pocket for ligand recognizes conserved Trp-Lys motif SST-14...
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending pandemic. spike (S) protein on viral envelope mediates human angiotensin-converting enzyme binding thus is target variety antibodies. In this work, we built various S trimer–antibody complex structures basis fully glycosylated models described in our previous work performed all-atom...
Many proteins need to form oligomers be functional, so oligomer structures provide important clues biological roles of proteins. Prediction therefore can a useful tool in the absence experimentally resolved structures. In this article, we describe server and human methods that used predict CASP13 experiment. Performances on 42 targets consisting 30 homo-oligomers 12 hetero-oligomers are discussed. Our method, Seok-assembly, generated models with interface contact similarity measure greater...
We participated in CARPI rounds 38-45 both as a server predictor and human predictor. These CAPRI provided excellent opportunities for testing prediction methods three classes of protein interactions, that is, protein-protein, protein-peptide, protein-oligosaccharide interactions. Both template-based (GalaxyTBM monomer protein, GalaxyHomomer homo-oligomer GalaxyPepDock protein-peptide complex) ab initio docking (GalaxyTongDock GalaxyPPDock oligomer, GalaxyPepDock-ab-initio complex,...
ABSTRACT This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in viral membrane. First, starting from PDB:6VSB 6VXX, S structures were modeled using template-based modeling, de-novo structure prediction, loop techniques GALAXY suite. Then, the recently-determined most occupied glycoforms, 22 N-glycans 1 O-glycan each monomer Glycan Reader & Modeler CHARMM-GUI. These model assessed further refined against...
Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction may be a useful tool in absence experimentally resolved structures. Here, we describe our server and human-expert methods used to predict CASP14 experiment. Examples are provided for cases which manual...
As of now, more than 60 years have passed since the first determination protein structures through crystallography, and a significant portion can be predicted by computers. This is due to groundbreaking enhancement in structure prediction achieved neural network training utilizing extensive sequence data. However, substantial challenges persist limited data availability, with antibody standing as one such challenge. In this paper, we propose novel architecture that effectively enables...
Abstract Protein loops, characterized by their versatile structures with varying sizes and shapes, can recognize a wide range of targets high specificity affinity. The variable loops the antibody complementarity-determining region (CDR) are particularly crucial for immune responses therapeutic applications due to effective target recognition capabilities. Accurate structure prediction these is essential efficient in silico design target-binding antibodies or industrial use. However,...
ABSTRACT The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme (ACE2), and is considered the major target for drug vaccine development. We previously built fully-glycosylated full-length SARS-CoV-2 S models in a viral membrane including both open closed conformations receptor domain (RBD) different templates stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations...
We have analyzed 210 data of daily sunspot observations made during the period January 3 to December 31 in 2000 and presented relative numbers. For this work we estimated conversion factors derive numbers: k=0.72 for 20 cm refractor k=0.56 Solar Flare Telescope KAO. During year 2000, our annual average numbers is found be 99.4. This number obtained from averaged 8.9 spot groups, which there are about 62.5 distinct spots observed. According appearance 423 analysis shows that mean life time...
Abstract Somatostatin is a peptide hormone regulating endocrine systems through binding to G-protein-coupled somatostatin receptors. receptor 2 (SSTR2) one of the human receptors and highly implicated in cancers neurological disorders. Here, we report high resolution cryo-EM structure full-length SSTR2 bound agonist (SST-14) complex with inhibitory G (G i ) proteins. Our shows that seven transmembrane helices form deep pocket for ligand conserved Trp-Lys motif SST-14 positions at bottom...
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending pandemic. spike (S) protein on viral envelope mediates human angiotensin-converting enzyme (ACE2) binding thus is target variety antibodies. In this work, we built various S trimer-antibody complex structures basis fully glycosylated models described in our previous performed all-atom...