http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
Validation on the molecular docking efficiency of lipocalin family of proteins
Sriram Sokalingam,Ganapathiraman Munussami,김중래,이선구 한국공업화학회 2018 Journal of Industrial and Engineering Chemistry Vol.67 No.-
Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin–ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.
Sriram Sokalingam,Bharat Madan,Govindan Raghunathan,이선구 한국생물공학회 2013 Biotechnology and Bioprocess Engineering Vol.18 No.5
Charged amino acids having ionizable side chains play crucial roles in maintaining the solubility and stability of a protein. These charged amino acids are mostly exposed on protein surface and participate in electrostatic interactions with neighboring charged amino acids as well as with solvent. Therefore, the change in the solvent pH affects the protein stability in most cases. Previously, we reported a GFP variant, GFP14R having 14 surface lysines replaced with arginines, that showed enhanced stability under alkaline pH. Here, we analyzed the factors that contribute to the stability of the GFP14R under alkaline pH quantitatively using molecular dynamics simulations. Protonation state of the charged amino acids of GFP14R and control GFP under neutral pH and alkaline pH were modeled,and molecular dynamics simulations were performed. This comparative analysis revealed that the GFP14R with more arginine frequency on the surface maintained the stability under both pH conditions without much change in their salt-bridge interactions as well as the hydrogen bond interactions with solvent. On the other hand, these interactions were significantly reduced for the control GFP under alkaline pH due to the deprotonated lysine side chains. These results suggest that the advantageous property of arginine over lysine can be considered one of the parameter for the protein stability engineering under alkaline pH conditions.
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.
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.
Modulation of protein stability and aggregation properties by surface charge engineering
Raghunathan, Govindan,Sokalingam, Sriram,Soundrarajan, Nagasundarapandian,Madan, Bharat,Munussami, Ganapathiraman,Lee, Sun-Gu The Royal Society of Chemistry 2013 Molecular bioSystems Vol.9 No.9
<P>An attempt to alter protein surface charges through traditional protein engineering approaches often affects the native protein structure significantly and induces misfolding. This limitation is a major hindrance in modulating protein properties through surface charge variations. In this study, as a strategy to overcome such a limitation, we attempted to co-introduce stabilizing mutations that can neutralize the destabilizing effect of protein surface charge variation. Two sets of rational mutations were designed; one to increase the number of surface charged amino acids and the other to decrease the number of surface charged amino acids by mutating surface polar uncharged amino acids and charged amino acids, respectively. These two sets of mutations were introduced into Green Fluorescent Protein (GFP) together with or without stabilizing mutations. The co-introduction of stabilizing mutations along with mutations for surface charge modification allowed us to obtain functionally active protein variants (s-GFP(+15–17) and s-GFP(+5–6)). When the protein properties such as fluorescent activity, folding rate and kinetic stability were assessed, we found the possibility that the protein stability can be modulated independently of activity and folding by engineering protein surface charges. The aggregation properties of GFP could also be altered through the surface charge engineering.</P> <P>Graphic Abstract</P><P>Engineering surface charge of proteins to modulate the properties of proteins by introducing surface charge mutations with and without stabilizing mutations. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3mb70068b'> </P>
Assessment of Computational Modeling of Fc-Fc Receptor Binding Through Protein-protein Docking Tool
Jebamani Petrina,SOKALINGAM SRIRAM,SRIRAMULU DINESH KUMAR,정상택,이선구 한국생물공학회 2020 Biotechnology and Bioprocess Engineering Vol.25 No.5
Structural information of Fc-Fc receptor interaction may contribute to the design of drugs or therapeutic antibodies associated with the interaction. Computational protein-protein docking can be employed in structural study of protein-protein interaction, but its efficiency and reliability are still unstable and need to be validated and optimized for respective target protein complexes. In this study, we investigated and assessed the computational modeling efficiency of Fc-FcγR complex through HADDOCK by defining five different sets of active residues, a major parameter to determine the prediction efficiency of HADDOCK. The binding residues identified experimentally or the residues in the binding pocket were confirmed to be efficient active residues to achieve a high prediction efficiency, and too narrower or wider specification of active residues led to poor prediction efficiency. Most binding residues and crucial molecular interactions such as conserved interactions and hydrogen bonds in the crystal structure were reproduced in the best model. The HADDOCK docking condition determined in this study is expected to be applied to the computational characterization of various Fc-Fc receptor complexes and mutants.