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1.
Predicting the burial status (the residue exposure to the lipid bilayer or buried within the protein core) of transmembrane
(TM) residues of α-helix membrane protein (αHMP) is of great importance for genome-wide annotation and for experimental researchers
to elucidate diverse physiological processes. In this work, we developed a new computational model that can be used for predicting
the burial status of TM residues of αHMP. By incorporating physicochemical scales and conservation index, an efficient prediction
model using least squares support vector machine (LS-SVM) was developed. The model was developed from 43 protein chains and
its prediction ability was evaluated by an independent test set of other non-redundant ten protein chains. The prediction
accuracy of our method was much better than the results of the reported works. Our results demonstrate that the LS-SVM prediction
model incorporating structural and physicochemical features derived from sequence information could greatly improve the prediction
accuracy. 相似文献
2.
The mode of α-synuclein binding to membranes depends on lipid composition and lipid to protein ratio
Interactions of the presynaptic protein α-synuclein with membranes are involved in its physiological action as well as in the pathological misfolding and aggregation related to Parkinsons's disease. We studied the conformation and orientation of α-synuclein bound to model vesicular membranes using multiparametric response polarity-sensitive fluorescent probes together with CD and EPR measurements. At low lipid to α-synuclein ratio the protein binds membranes through its N-terminal domain. When lipids are in excess, the α-helical content and the role of the C-terminus in binding increase. Highly rigid membranes also induce a greater α-helical content and a lower polarity of the protein microenvironment. 相似文献
3.
Jeyachandran Sivakamavalli Chandrabose Selvaraj Sanjeev Kumar Singh 《Journal of biomolecular structure & dynamics》2013,31(11):1841-1854
In Prophenoloxidase (ProPO) cascade, two targets namely serine protease and α-2-macroglobulin are key regulators involved in the defense system of crustaceans. In biological systems, routine role of cell systems requires the understanding in protein–protein interactions through experimental and theoretical concepts, which might yield useful insights into the cellular responses. Response of cells to regulating the immune system is governed by the interactions-involved biomolecular simulations. Unfortunately, studies on the inhibitors (SP and α-2M) that negatively regulate the proPO system or melanization in penaeid shrimp are not yet available. In order to understand how these interactions change the proPO mechanism in Indian white shrimp Fenneropenaeus indicus was determined. In F. indicus, innate immune system is in a sensitive balance of intricate interactions; elucidating these interactions by the integration of in silico and in vitro has great potential. We have determined the expression of both the SP and α-2M enzymes in regulatory mechanism, which are analyzed through qRT-PCR, protein–protein docking, and simulation studies. From this work, we propose a novel approach for studying an organism at the systems level by integrating genome-wide computational analysis and the gene expression data. 相似文献