• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• The Korean Journal of Petroleum Geology
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• v.5 no.1_2 s.6
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• pp.36-47
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• 1997

This study presents multi-variable sequence model for a broader application of sequence concept proposed by Exxon group. The concept of the multi-variable model is based on the fact that internal organization and boundary type of the sequences are determined by three varying factors including 3rd-order cycles of eustasy, and tectonic movement and sediment influx with 2nd-order changes. Instead of Exxon group's systems tracts, this model adopts parasequence sets as the fundamental building blocks of the sequence, because they are descriptive stratigraphic units simply defined by internal stacking pattern, reflecting interactions of accommodation and sediment influx. Seven sequence types which vary in number and type of internal parasequence sets are formulated as associations of four types of accommodation development and three grades of sediment influx. In the southwestern margin of Ulleung Basin, the multi-variable sequence analysis of shelf-slope sequence shows systematic changes in stratal patterns and the numbs, of constituent parasequence sets (i.e. sequence type). These changes are interpreted to reflect temporal and spatial changes in type and rate of tectonic movement and sediment influx, as a result of back-arc opening and closing. During the back-arc opening, rapid subsidence, continuous rise of relative sea level, and high sediment influx gave rise to sequences dominantly of single progradational parasequence set. In the early stage of back-arc closing accompanied by local contractional deformation, different types of sequences contemporaneously formed depending on the spatial changes in tectonically-controlled accommodation and influx rates. During the subsequent slow back-arc subsidence, rise-dominated relative sea-level cycle was coupled with moderate to high sedimentation rate to have resulted in sequences consisting of $2~3$ parasequence sets.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.