Search results for "protein complexes"
showing 10 items of 113 documents
Usher syndrome: molecular links of pathogenesis, proteins and pathways.
2006
Contains fulltext : 50437.pdf (Publisher’s version ) (Closed access) Usher syndrome is the most common form of deaf-blindness. The syndrome is both clinically and genetically heterogeneous, and to date, eight causative genes have been identified. The proteins encoded by these genes are part of a dynamic protein complex that is present in hair cells of the inner ear and in photoreceptor cells of the retina. The localization of the Usher proteins and the phenotype in animal models indicate that the Usher protein complex is essential in the morphogenesis of the stereocilia bundle in hair cells and in the calycal processes of photoreceptor cells. In addition, the Usher proteins are important in…
Structural and Functional Analysis of the Antiparallel Strands in the Lumenal Loop of the Major Light-harvesting Chlorophyll a/b Complex of Photosyst…
2007
The light-harvesting chlorophyll a/b-binding protein of photosystem II (LHCIIb) fulfills multiple functions, such as light harvesting and energy dissipation under different illuminations. The crystal structure of LHCIIb at the near atomic resolution reveals an antiparallel strands structure in the lumenal loop between the transmembrane helices B/C. To study the structural and functional significances of this structure, three amino acids (Val-119, His-120, and Ser-123) in this region have been exchanged to Phe, Leu, and Gly, respectively, and the influence of the mutagenesis on the structure and function of LHCIIb has been investigated. The results are as follows. 1) Circular dichroism spect…
"DEVELOPMENT OF A DECISION SUPPORT SYSTEM FOR BIOINFORMATICS. EXTRACTION OF PROTEIN COMPLEXES FROM A PROTEIN-PROTEIN INTERACTION NETWORK: A CASE STUD…
2011
Decision Support Systems and Workflow Management Systems have become essential tools for some business and scientific field. This thesis propose a new hybrid architecture for problem solving expertise and decision-making process, that aims to support high-quality research in the field of bioinformatics and system biology. The first part of the dissertation introduces the project to which belong this thesis work, i.e. the “Bioinformatics Organized Resources - an Intelligent System” (BORIS) project of the ICAR-CNR; the main goal of BORIS is to provide an helpful and effective support to researchers or experimentalist, that have no familiarity with tools and techniques to solve computational p…
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression
2008
Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Δ cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice an…
Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors
2019
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus.…
Amino acids in the second transmembrane helix of the Lhca4 subunit are important for formation of stable heterodimeric light-harvesting complex LHCI-…
2007
Photosynthetic light-harvesting complexes (LHCs) are assembled from apoproteins (Lhc proteins) and non-covalently attached pigments. Despite a considerable amino acid sequence identity, these proteins differ in their oligomerization behavior. To identify the amino acid residues determining the heterodimerization of Lhca1 and Lhca4 to form LHCI-730, we mutated the poorly conserved second transmembrane helix of the two subunits. Mutated genes were expressed in Escherichia coli and the resultant proteins were refolded in vitro and subsequently analyzed by gel electrophoresis. Replacement of the entire second helix in Lhca4 by the one of Lhca3 abolished heterodimerization, whereas it had no eff…
Modular organization in the reductive evolution of protein-protein interaction networks
2006
Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.
Insertion of light-harvesting chlorophyll a/b protein into the thylakoid
2000
The major light-harvesting chlorophyll a/b-binding protein (Lhcb1,2) of photosystem II is inserted into the thylakoid via the signal recognition particle dependent pathway. However, the mechanism by which the protein enters the membrane is at this time unknown. In order to define some topographical restrictions for this process, we constructed several recombinant derivatives of Lhcb1 carrying hexahistidine tags at either protein terminus or in the stromal loop domain. Additionally, green fluorescent protein (GFP) was fused to either terminus. None of the modifications significantly impair the pigment-binding properties of the protein in the in vitro reconstitution of LHCII. With the excepti…
Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences
2020
Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocell…
Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density
2018
Dynamics-function correlations are usually inferred when molecular mobility and protein function are simultaneously impaired at characteristic temperatures or hydration levels. In this sense, excitation energy transfer in the photosynthetic light-harvesting complex II (LHC II) is an untypical example because it remains fully functional even at cryogenic temperatures relying mainly on interactions of electronic states with protein vibrations. Here, we study the vibrational and conformational protein dynamics of monomeric and trimeric LHC II from spinach using inelastic neutron scattering (INS) in the temperature range of 20-305 K. INS spectra of trimeric LHC II reveal a distinct vibrational …