@article {50,
	title = {Molecular models of the interface between anterior pharynx-defective protein 1 (APH-1) and presenilin involving GxxxG motifs.},
	journal = {ChemMedChem},
	volume = {3},
	year = {2008},
	month = {2008 Apr},
	pages = {627-34},
	abstract = {Gamma-secretase is an integral membrane protease, which is a complex of four membrane proteins. Improper functioning of gamma-secretase was found to be critical in the pathogenesis of Alzheimer{\textquoteright}s disease. Despite numerous efforts, the structure of the protease as well as its proteolytic mechanism remains poorly understood. In this work we constructed a model of interactions between two proteins forming gamma-secretase: APH-1 and presenilin. This interface is based on a highly conserved GxxxGxxxG motif in the APH-1 protein. It can form a tight contact with a small-residue AxxxAxxxG motif in presenilin. Here, four binding modes based on similar structures involving GxxxG motifs in glycophorin and aquaporin were proposed and verified. The resulting best model employs antiparallel orientations of interacting helices and is in agreement with the currently accepted topology of both proteins. This model can be used for further structural characterization of gamma-secretase and its components.},
	keywords = {Alzheimer Disease, Amyloid Precursor Protein Secretases, Genotype, Humans, Membrane Proteins, Models, Molecular, Peptide Hydrolases, Presenilin-1},
	issn = {1860-7187},
	doi = {10.1002/cmdc.200700189},
	author = {Jozwiak, Krzysztof and Krzy{\'s}ko, Krystiana A and Bojarski, Lukasz and Gacia, Magdalena and Filipek, S{\l}awomir}
}
@article {51,
	title = {Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment.},
	journal = {Biochimica et biophysica acta},
	volume = {1758},
	year = {2006},
	month = {2006 Apr},
	pages = {537-44},
	abstract = {Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard-Jones contact interactions is applied to model the protein-membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.},
	keywords = {Bacterial Proteins, Bacteriorhodopsins, Cell Membrane, Computer Simulation, Halobacterium salinarum, Lipid Bilayers, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Structure, Secondary},
	issn = {0006-3002},
	doi = {10.1016/j.bbamem.2006.03.028},
	author = {Cieplak, Marek and Filipek, S{\l}awomir and Janovjak, Harald and Krzy{\'s}ko, Krystiana A}
}
@article {52,
	title = {Two novel presenilin 1 gene mutations connected with frontotemporal dementia-like clinical phenotype: genetic and bioinformatic assessment.},
	journal = {Experimental neurology},
	volume = {200},
	year = {2006},
	month = {2006 Jul},
	pages = {82-8},
	abstract = {Mutations in the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) genes are associated with early-onset familial Alzheimer{\textquoteright}s disease (EOAD). There are several reports describing mutations in PSEN1 in cases with frontotemporal dementia (FTD). We identified two novel mutations in the PSEN1 gene: L226F and L424H. The first mutation was detected in a patient with a clinical diagnosis of FTD and a post-mortem diagnosis of AD. The second mutation is connected with a clinical phenotype of variant AD with strong FTD signs. In silico modeling revealed that the mutations, as well as mutations used for comparison (F177L and L424R), change the local structure, stability and/or properties of the transmembrane regions of the presenilin 1 protein (PS1). In contrast, a silent non-synonymous substitution F175S is eclipsed by external residues and has no influence on PS1 interfacial surface. We suggest that in silico analysis of PS1 substitutions can be used to characterize novel PSEN1 mutations, to discriminate between silent polymorphisms and a potential disease-causing mutation. We also propose that PSEN1 mutations should be considered in FTD patients with no MAPT mutations.},
	keywords = {Adult, Computational Biology, Dementia, Diagnosis, Differential, Female, Genetic Testing, Humans, Male, Membrane Proteins, Models, Molecular, Mutation, Phenotype, Presenilin-1},
	issn = {0014-4886},
	doi = {10.1016/j.expneurol.2006.01.022},
	author = {Zekanowski, Cezary and Golan, Maciej P and Krzy{\'s}ko, Krystiana A and Lipczy{\'n}ska-{\L}ojkowska, Wanda and Filipek, S{\l}awomir and Kowalska, Anna and Rossa, Grzegorz and Pep{\l}o{\'n}ska, Beata and Styczy{\'n}ska, Maria and Maruszak, Aleksandra and Religa, Dorota and Wender, Mieczys{\l}aw and Kulczycki, Jerzy and Barcikowska, Maria and Ku{\'z}nicki, Jacek}
}
@article {53,
	title = {A concept for G protein activation by G protein-coupled receptor dimers: the transducin/rhodopsin interface.},
	journal = {Photochemical \& photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology},
	volume = {3},
	year = {2004},
	month = {2004 Jun},
	pages = {628-38},
	abstract = {G protein-coupled receptors (GPCRs) are ubiquitous and essential in modulating virtually all physiological processes. These receptors share a similar structural design consisting of the seven-transmembrane alpha-helical segments. The active conformations of the receptors are stabilized by an agonist and couple to structurally highly conserved heterotrimeric G proteins. One of the most important unanswered questions is how GPCRs couple to their cognate G proteins. Phototransduction represents an excellent model system for understanding G protein signaling, owing to the high expression of rhodopsin in rod photoreceptors and the multidisciplinary experimental approaches used to study this GPCR. Here, we describe how a G protein (transducin) docks on to an oligomeric GPCR (rhodopsin), revealing structural details of this critical interface in the signal transduction process. This conceptual model takes into account recent structural information on the receptor and G protein, as well as oligomeric states of GPCRs.},
	keywords = {Animals, Dimerization, Models, Molecular, Protein Conformation, Protein Structure, Secondary, Receptors, G-Protein-Coupled, Rhodopsin},
	issn = {1474-905X},
	doi = {10.1039/b315661c},
	author = {Filipek, S{\l}awomir and Krzy{\'s}ko, Krystiana A and Fotiadis, Dimitrios and Liang, Yan and Saperstein, David A and Engel, Andreas and Palczewski, Krzysztof}
}
