• IMMUNE NETWORK
• /
• v.13 no.2
• /
• pp.55-62
• /
• 2013

Swiprosin-1 exhibits the highest expression in $CD8^+$ T cells and immature B cells and has been proposed to play a role in lymphocyte biology through actin remodeling. However, regulation of swiprosin-1 gene expression is poorly understood. Here we report that swiprosin-1 is up-regulated in T cells by PKC pathway. Targeted inhibition of the specific protein kinase C (PKC) isotypes by siRNA revealed that $PKC-{\theta}$ is involved in the expression of swiprosin-1 in the human T cells. In contrast, down-regulation of swiprosin-1 by A23187 or ionomycin suggests that calcium-signaling plays a negative role. Interestingly, swiprosin-1 expression is only reduced by treatment with $NF-{\kappa}B$ inhibitors but not by NF-AT inhibitor, suggesting that the $NF-{\kappa}B$ pathway is critical for regulation of swiprosin-1 expression. Collectively, these results suggest that swiprosin-1 is a $PKC-{\theta}$-inducible gene and that it may modulate the late phase of T cell activation after antigen challenge.

• Proceedings of the Korean Biophysical Society Conference
• /
• 1996.07a
• /
• pp.21-21
• /
• 1996

The hyperthermostable protein, rubredoxin from Pyrococcus furiosus is 53-residue protein with a three-stranded anti-parallel $\beta$-sheet and several loops. To investigate the effect of changes of electrostatic and hydrophobic interactions on the structure and dynamic property of P. furiosus rubredoxin, molecular dynamics simulations in water were performed on three mesophilic rubredoxins, P, furiosus rubresoxin, and 5 mutants of P. furiosus rubredoxin. (omitted)

• International Journal of Industrial Entomology and Biomaterials
• /
• v.14 no.1
• /
• pp.37-44
• /
• 2007

A study was made of the haemolymph protein spectrum of mulberry silkworm (Bomhyx mori L.) from the first larval instar to imago. Horizontal starch gel electrophoresis was used. Sixteen races and eight F1 interracial hybrids, raised in Bulgaria, were analyzed. During the ontogenesis, a total of 17 protein bands (15 cathodic and 2 anodic) were detected. Distinct dynamics in the haemolymph protein spectrum was observed, in result of different expression during the individual development associated with the processes of growth, histolysis and histogenesis. Based on the ontogenetic dynamics found, a correspondence was assumed between some proteins detected by us using the starch gel electrophoresis and major haemolymph proteins (SP1, SP2, MHPs and Vg) detected by other authors using the polyacrilamide gel electrophoresis. Intraracial and interracial polymorphism was observed in four protein zones. The effect of four polymorphic loci with codominant and null alleles was suggested.

• International Journal of Control, Automation, and Systems
• /
• v.4 no.3
• /
• pp.382-393
• /
• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Proceeding of EDISON Challenge
• /
• 2016.03a
• /
• pp.62-66
• /
• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.122-125
• /
• 2002

Coherent oscillations in is fluorescence dynamics of W.-t. PYP and its site-directed mutants have been observed. Two oscillatory modes coupled with the ultrafast fluorescence due to the twisting of the excited chromophore were identified, a high ftequency mode (∼135 cm$\^$-1/) with ∼550 is damping time and a low frequency overdamped mode (-45 cm$\^$-1/) with ∼250 is damping time, respectively. Both modes disappear in the fluorescence dynamics of denatured PYP emphasizing the important role of the protein nanospace as the environment for photoreaction. The qualitative picture of fluorescence dynamics in site-directed mutants was rather similar to that in W.-t. PYP, i.e., similar oscillatory modes (∼130-140 cm$\^$-1/ and ∼40-70 cm$\^$-1/) have been observed. This indicates that the vibrational modes and electron-vibration couplings do not change dramatically due to the mutation though the damping time of low frequency mode a little decreases as the protein nanospace structure becomes looser and more disordered by mutation. On the other hand, in the case of some PYP analogues, the qualitative picture of fluorescence dynamics changes, showing the familiar picture of solvation effect whereas the oscillations are almost damped. Comparative analyses of these observations are presented.

• BMB Reports
• /
• v.48 no.7
• /
• pp.369-370
• /
• 2015

Actin dynamics is critical for the formation and sustainment of the immunological synapse (IS) during T cell interaction with antigen-presenting cells (APC). Thus, many actin regulating proteins are involved in spatial and temporal actin remodeling at the IS. However, little is known whether or how actin stabilizing protein controls IS and the consequent T cell functions. TAGLN2 − an actin-binding protein predominantly expressed in T cells − displays a novel function to stabilize cortical F-actin, thereby augmenting F-actin contents at the IS, and acquiring leukocyte function-associated antigen-1 activation following T cell activation. TAGLN2 also competes with cofilin to protect F-actin in vitro and in vivo. During cytotoxic T cell interaction with cancer cells, the expression level of TAGLN2 at the IS correlates with the T cell adhesion to target cancer cells and production of lytic granules such as granzyme B and perforin, thus expressing cytotoxic T cell function. These findings identify a novel function for TAGLN2 as an actin stabilizing protein that is essential for stable immunological synapse formation, thereby regulating T cell immunity. [BMB Reports 2015; 48(7): 369-370]

• Bulletin of the Korean Chemical Society
• /
• v.27 no.12
• /
• pp.1940-1960
• /
• 2006

Theoretical descriptions of two-dimensional (2D) vibrational and electronic spectroscopy are presented. By using a coupled multi-chromophore model, some examples of 2D spectroscopic studies of peptide solution structure determination and excitation transfer process in electronically coupled multi-chromophore system are discussed. A few remarks on perspectives of this research area are given.

• Journal of the Korean Magnetic Resonance Society
• /
• v.16 no.2
• /
• pp.103-110
• /
• 2012

Membrane proteins play a essential role in the biological systems and it is not easy to handle a membrane protein for its structural study. Solid-state NMR (ssNMR) can be a good tool to investigate the structures and dynamics of membrane proteins. In ssNMR, Magic Angle Spinning (MAS) and Cross Polarization (CP) can be utilized to reduce the line-broadening, leading to high resolution and sensitivity in the spectrum. ssNMR, if combined with other spectroscopic methods, can provide us a enough knowledge on structures and dynamics of membrane proteins in biological condition.

• Journal of the Korean Magnetic Resonance Society
• /
• v.23 no.2
• /
• pp.56-60
• /
• 2019

Study on the structure and dynamics of molecules at the atomic level is of great significance for understanding their function and stability as well as roles for various chemico-physical and biological processes. $^{17}O$ NMR spectroscopy has appeared as an elegant technique for investigating of the physicochemical and structural properties of oxygen-containing compounds such as metal organic frameworks and nanosized oxides. This method has drawn much attention as it provides unique insights into the properties of targets based on atomistic information of local oxygen environments which is otherwise difficult to obtain using other methods. In this mini review, we introduce and discuss the recent study and developments of $^{17}O$ NMR techniques which are tailored for the investigation on the structure and dynamics of water and inorganic materials.