Improvement of GFP stability by mutagenesis of surface lysines to arginines

( Sriram Sokalingam ),허미애,이선구 한국공업화학회 2022 한국공업화학회 연구논문 초록집 Vol.2022 No.1

2P-365 Blind/Focussed Docking Studies on Ligand Binding Mode to Lipocalin Proteins

( Sriram Sokalingam ),이선구 한국공업화학회 2017 한국공업화학회 연구논문 초록집 Vol.2017 No.1

Lipocalins are diverse group of proteins with varied functions, such as transport, pheromone activity, camouflage, immunomodulation, olfaction, enzymatic synthesis and regulation of cell homeostasis. Therefore, understanding the ligand binding modes of these distinctive functional lipocalins will render a clear understanding about the dynamicity of lipocalins for scaffold protein engineering. In this study, we characterized the binding modes of various ligands to lipocalin protein by performing docking studies. Specifically, blind dockings were attempted to understand the specific and nonspecific bindings of ligands, and focussed docking study was carried out to characterize the specific binding of ligands.

The N-end rule pathway: emerging functions and molecular principles of substrate recognition

Sriram, Shashikanth M.,Kim, Bo Yeon,Kwon, Yong Tae Nature Publishing Group, a division of Macmillan P 2011 Nature reviews. Molecular cell biology Vol.12 No.11

The N-end rule defines the protein-destabilizing activity of a given amino-terminal residue and its post-translational modification. Since its discovery 25 years ago, the pathway involved in the N-end rule has been thought to target only a limited set of specific substrates of the ubiquitin??proteasome system. Recent studies have provided insights into the components, substrates, functions and structural basis of substrate recognition. The N-end rule pathway is now emerging as a major cellular proteolytic system, in which the majority of proteins are born with or acquire specific N-terminal degradation determinants through protein-specific or global post-translational modifications.

A Study of the<i>Kepler K2</i>Variable EPIC 211957146 Exhibiting a Variable O’ Connell Effect

Sriram, K.,Malu, S.,Choi, C. S.,Rao, P. Vivekananda American Astronomical Society 2017 The Astronomical journal Vol.153 No.5

<P>We present the multi-band photometric and spectroscopic study of an over-contact binary system, EPIC 211957146. The light curves exhibit a variable O' Connell effect, confirmed from our observational data and the Kepler K2 data. The best photometric solution incorporating a dark spot over the primary component unveils that the system has a low-mass ratio (q similar to 0.17) and a high inclination (i similar to 85 degrees). To confirm the solution and constrain the uncertainty, Monte-Carlo simulations are performed and the results are reported. Based on the O-C diagram analysis, we see that the variable shows a period increase at the rate of dP/dt similar to 1.06. x. 10(-6) days yr(-1), which is higher than the theoretically predicted value. Presence of a third body having a period of similar to 16.23 years is evident from the O-C diagram. No filled-in effect is observed in the Ha line, while the effect is vividly present in the Na line. From the Kepler K2 data, we found that the primary and secondary minima exhibit an anti-correlated O-C variation followed by an erratic behavior. This is possibly caused by the longitudinal motion of the spot, and hence, we set a lower limit of similar to 40 days for the spot modulation. We also observe a possibly associated photometric difference in the primary depth by comparing our light curves with Kepler K2 normalized light curves. This system has a low-mass ratio and a high fill-out factor, and, theoretically, such a physical configuration would lead to a merger.</P>

A SPECTRAL STUDY OF THE RAPID TRANSITIONS OF TYPE-B QUASI-PERIODIC OSCILLATIONS IN THE BLACK HOLE TRANSIENT XTE J1859+226

Sriram, K.,Rao, A. R.,Choi, C. S. IOP Publishing 2013 The Astrophysical journal Vol.775 No.1

<P>The fast transitions of type-B and type-A quasi-periodic oscillations (QPOs) are rarely found, and they are observed at the peak of the outburst in black hole transient (BHT) sources. The associated spectral variations during such events are crucial to understand the origin and location of such QPOs in the accretion disk. During the 1999 outburst of XTE J1859+226, on four occasions a rapid transition of type-B/A QPOs was noted. We performed broadband spectral analysis on these four observations to unveil the responsible spectral parameter causing the rapid transitions. After invoking simple spectral models, it was observed that disk parameters were consistently varying along with disk and power-law fluxes, and almost no change was noted in the power-law index parameter. Though using a complex physical model showed consistent results, the spectral parameter variations across the transitions were not significant. It was observed that the type-B QPO was always associated with an inner disk front which is closer to the BH. In one observation, a type-A QPO appeared as the source count rate suddenly dropped, and the power-law index as well as disk normalization parameter considerably changed during this transition. The spectral changes in this particular observation were similar to the changes observed in XTE J1817-330, indicating a common underlying mechanism. We have also examined a similar observation of BHT source GX 339-4, where a sudden transition of a type-A/B QPO was noted. Similar spectral study again revealed that the disk parameters were changing. We discuss the results in the framework of a truncated disk model and conclude that the movement of the coupled inner disk-corona region is responsible for such rapid transitions of type-B QPOs.</P>

Fast transition of type-B quasi-periodic oscillation in the black hole transient XTE J1817-330

Sriram, K.,Rao, A. R.,Choi, C. S. EDP Sciences 2012 Astronomy and astrophysics Vol.541 No.-

COUPLED HBO AND NBO VARIATIONS IN THE Z SOURCE GX 5-1: INNER ACCRETION DISK AS THE LOCATION OF QPOs

Sriram, K.,Rao, A. R.,Choi, C. S. IOP Publishing 2011 ASTROPHYSICAL JOURNAL LETTERS - Vol.743 No.2

<P>The simultaneous and coupled evolution of horizontal branch oscillation (HBO) and normal branch oscillation (NBO) in Z-type sources suggests that the production of HBO is connected to NBO and is caused by changes in the physical/radiative properties of the inner accretion disk, although there is a lack of substantial spectral evidence to support this. In this Letter, we present the results of an analysis of an RXTE observation of the Z source GX 5-1, where the 6 Hz NBO is simultaneously detected along with an HBO at 51 Hz. The variations in the intensity and the associated power density spectrum indicate that the HBO and NBO are strongly coupled, originating from the same location in the inner accretion disk. The absence of HBO and NBO in the lower energy bands, an increase in the rms amplitude with energy, and a smooth transition among them suggest that they are produced in the hot inner regions of the accretion disk. Based on a spectral analysis, we found a signature of changing or physically modified inner disk front during the coupled HBO and NBO evolution. We explore the various models to explain the observed phenomenon and propose that the NBO is affiliated to the oscillations in the thick/puffed-up inner region of the accretion disk.</P>

Development and Characterization of Monomeric N-End Rule Inhibitors through <i>In Vitro</i> Model Substrates

Sriram, Shashi,Lee, Jung Hoon,Mai, Binh Khanh,Jiang, Yanxialei,Kim, Yongho,Yoo, Young Dong,Banerjee, Rajkumar,Lee, Seung-Han,Lee, Min Jae American Chemical Society 2013 Journal of medicinal chemistry Vol.56 No.6

<P>In the N-end rule pathway, a set of N-terminal amino acids, called N-degrons, are recognized and ubiquitinated by the UBR proteins. Here we examined various N-end rule inhibitors to identify essential structural components of the system. Our study using <I>in vitro</I> biochemical assay indicated that the <SMALL>l</SMALL>-conformation and protonated α-amino group of the first residue were critical for N-degrons to properly interact with the UBR proteins. The monomeric molecules with minimum interacting motifs showed endopeptidase resistance and better inhibitory activities than traditional dipeptide inhibitors. Collectively, our study identifies a pharmacophore of N-end rule inhibitors, which provides a structural platform to improve the efficiency and druggable properties of inhibitors. Considering that the N-end rule has been implicated in many pathophysiological processes in cells, inhibitors of this pathway, such as <I>p</I>-chloroamphetamine, are potentially of clinical interest in a novel aspect of action mechanisms.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jmcmar/2013/jmcmar.2013.56.issue-6/jm400046q/production/images/medium/jm-2013-00046q_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jm400046q'>ACS Electronic Supporting Info</A></P>

In silico Study on the Effect of Surface Lysines and Arginines on the Electrostatic Interactions and Protein Stability

Sriram Sokalingam,Bharat Madan,Govindan Raghunathan,이선구 한국생물공학회 2013 Biotechnology and Bioprocess Engineering Vol.18 No.1

Charged amino acids are mostly exposed on a protein surface, thereby forming a network of interactions with the surrounding amino acids as well as with water. In particular, positively charged arginine and lysine have different side chain geometries and provide a different number of potential electrostatic interactions. This study reports a comparative analysis of the difference in the number of two representative electrostatic interactions,such as salt-bridges and hydrogen bonds, contributed by surface arginine and lysine, as well as their effect on protein stability using molecular modeling and dynamics simulation techniques. Two in silico variants, the R variant with all arginines and the K variant with all lysines on the protein surface, were modeled by mutating all the surface lysines to arginines and the surface arginines to lysines,respectively, for each of the 10 model proteins. A structural comparison of the respective two variants showed that the majority of R variants possessed more salt-bridges and hydrogen bond interactions than the K variants, indicating that arginine provides a higher probability of electrostatic interactions than lysine owing to its side chain geometry. Molecular dynamics simulations of these variants revealed the R variants to be more stable than the K variants at room temperature but this effect was not prominent under protein denaturating conditions, such as 353 and 333 K with 8 M urea. These results suggest that the arginine residues on a protein surface contribute to the protein stability slightly more than lysine by enhancing the electrostatic interactions.

A detection of an anti-correlated hard X-ray lag in AM Herculis

Sriram, K.,Choi, C. S.,Rao, A. R. EDP Sciences 2011 Astronomy and astrophysics Vol.525 No.-