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• W2803237209 abstract "Membrane-active proteins are a class of proteins that interact with lipid membranesin the body. I study two kinds of membrane-active proteins, antimicrobialpeptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhDproject I did computer simulation studies with two AMPs, Gaduscidin-1 and -2(GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibitpH-dependent activity. In this work I have performed molecular dynamics (MD)simulations with the peptides in both histidine-charged and histidine-neutral forms,along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules,employing GROMACS software and an OPLS-AA force field. My results show a hightendency for pairs of histidines to interact with pore regions in both histidine-chargedand histidine-neutral simulations. This work is published in Biophysica et BiochimicaActa (BBA)-Biomembranes (2014).In the second part of my PhD research I performed computational simulations onlung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobicprotein with 79 residues, from the saposin superfamily. Because of the extremehydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus,I combined the Mini-B (a fragment of SP-B) experimental structure and homologymodelling based on proteins in saposin family to construct my initial model of SP-B.I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (usingPACE force field) simulations with GROMACS software. I modelled SP-B in openand bent (V-shaped) structures, placed within or near a POPC lipid bilayer. Myresults demonstrate energetically feasible structures for SP-B, in which salt bridges Membrane-active proteins are a class of proteins that interact with lipid membranesin the body. I study two kinds of membrane-active proteins, antimicrobialpeptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhDproject I did computer simulation studies with two AMPs, Gaduscidin-1 and -2(GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibitpH-dependent activity. In this work I have performed molecular dynamics (MD)simulations with the peptides in both histidine-charged and histidine-neutral forms,along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules,employing GROMACS software and an OPLS-AA force field. My results show a hightendency for pairs of histidines to interact with pore regions in both histidine-chargedand histidine-neutral simulations. This work is published in Biophysica et BiochimicaActa (BBA)-Biomembranes (2014).In the second part of my PhD research I performed computational simulations onlung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobicprotein with 79 residues, from the saposin superfamily. Because of the extremehydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus,I combined the Mini-B (a fragment of SP-B) experimental structure and homologymodelling based on proteins in saposin family to construct my initial model of SP-B.I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (usingPACE force field) simulations with GROMACS software. I modelled SP-B in openand bent (V-shaped) structures, placed within or near a POPC lipid bilayer. Myresults demonstrate energetically feasible structures for SP-B, in which salt bridges Membrane-active proteins are a class of proteins that interact with lipid membranesin the body. I study two kinds of membrane-active proteins, antimicrobialpeptides (AMPs) and lung surfactant (LS) proteins. In the first part of my PhDproject I did computer simulation studies with two AMPs, Gaduscidin-1 and -2(GAD-1 and GAD-2). These peptides are histidine rich and thus expected to exhibitpH-dependent activity. In this work I have performed molecular dynamics (MD)simulations with the peptides in both histidine-charged and histidine-neutral forms,along with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid molecules,employing GROMACS software and an OPLS-AA force field. My results show a hightendency for pairs of histidines to interact with pore regions in both histidine-chargedand histidine-neutral simulations. This work is published in Biophysica et BiochimicaActa (BBA)-Biomembranes (2014).In the second part of my PhD research I performed computational simulations onlung surfactant protein B (SP-B) interacting with lipid bilayer. SP-B is a hydrophobicprotein with 79 residues, from the saposin superfamily. Because of the extremehydrophobicity of SP-B, the experimental structure of the protein is unknown. Thus,I combined the Mini-B (a fragment of SP-B) experimental structure and homologymodelling based on proteins in saposin family to construct my initial model of SP-B.I run MD (using OPLS-AA and PACE force fields) and replica-exchange MD (usingPACE force field) simulations with GROMACS software. I modelled SP-B in openand bent (V-shaped) structures, placed within or near a POPC lipid bilayer. Myresults demonstrate energetically feasible structures for SP-B, in which salt bridges play a significant role. My simulations provide hypotheses for how SP-B promotesthe rearrangement of planar lipid bilayers. Part of this work has been accepted forpublication in Biophysica et Biochimica Acta (BBA)-Biomembranes (2016).In the third part of my project I employed solid state nuclear magnetic resonance(NMR) using ²H, ³¹P and ¹⁵N experiments, to study SP-B interacting with mechanicallyoriented lipid bilayer. Here, I used full-length ¹⁵N-labelled SP-B, which wasrecombinantly expressed in our lab, to find the orientation of protein with respect tothe bilayer. In this part of my thesis, the final goal was to compare the experimental¹⁵N spectra with the spectra, predicted from the structures we got from computationalsimulations to help define the protein’s structure. Since, I was not able to gain¹⁵N NMR signals in my SP-B in lipid bilayer experiments, I did not fulfill the finalgoal of this part of my project. However, I was able to predict ¹⁵N NMR spectra ofmy computational SP-B structures. My NMR results indicate that more optimizationneeds to be done to modify our SP-B preparation protocol to 1) increase the yieldsof isotope-labelled protein and 2) increase the protein:lipid ratio when refolding intolipids. My simulated ¹⁵N spectra indicate that uniform ¹⁵N-labelling is unlikely toconstrain SP-B’s structure and topology very much and it will likely be necessary touse a more specifically labelled sample for these experiments." @default.
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• W2803237209 date "2016-09-01" @default.
• W2803237209 modified "2023-09-27" @default.
• W2803237209 title "Membrane-active protein interactions with phospholipid bilayers" @default.
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