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Littérature scientifique sur le sujet « Rhodopsin proteins »

Auteur : Grafiati

Publié le 14 mars 2023

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Articles de revues sur le sujet "Rhodopsin proteins"

Meng, Chao Luo, Gang Dai et Tatsuo Iwasa. « Identification of Microbial Rhodopsin Genes from Salt Lake in Inner Mongolia ». Advanced Materials Research 518-523 (mai 2012) : 380–83. http://dx.doi.org/10.4028/www.scientific.net/amr.518-523.380.

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Microbial rhodopsins are photoactive proteins that use retinal molecule as the photoactive center. Because of the structural simplicity and functional diversity, microbial rhodopsins have been an excellent model system for structural biology. In the past decades microbial rhodopisns were identified from diverse environments including salt lakes, fresh water, sea water, human and plant tissues as fungal pathogens. In the present work, we tried to identify microbial rhodopsin genes from salt lake in Inner Mongolia, China. Two bacteriorhodopsin-like genes were identified. The retrieved sequences were analyzed by comparing with four most widely studied haloarchaeal rhodopsins.

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Shen, Libing, Chao Chen, Hongxiang Zheng et Li Jin. « The Evolutionary Relationship between Microbial Rhodopsins and Metazoan Rhodopsins ». Scientific World Journal 2013 (2013) : 1–10. http://dx.doi.org/10.1155/2013/435651.

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Rhodopsins are photoreceptive proteins with seven-transmembrane alpha-helices and a covalently bound retinal. Based on their protein sequences, rhodopsins can be classified into microbial rhodopsins and metazoan rhodopsins. Because there is no clearly detectable sequence identity between these two groups, their evolutionary relationship was difficult to decide. Through ancestral state inference, we found that microbial rhodopsins and metazoan rhodopsins are divergently related in their seven-transmembrane domains. Our result proposes that they are homologous proteins and metazoan rhodopsins originated from microbial rhodopsins. Structure alignment shows that microbial rhodopsins and metazoan rhodopsins share a remarkable structural homology while the position of retinal-binding lysine is different between them. It suggests that the function of photoreception was once lost during the evolution of rhodopsin genes. This result explains why there is no clearly detectable sequence similarity between the two rhodopsin groups: after losing the photoreception function, rhodopsin gene was freed from the functional constraint and the process of divergence could quickly change its original sequence beyond recognition.

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Tam, Beatrice M., Orson L. Moritz, Lawrence B. Hurd et David S. Papermaster. « Identification of an Outer Segment Targeting Signal in the Cooh Terminus of Rhodopsin Using Transgenic Xenopus laevis ». Journal of Cell Biology 151, n^o 7 (25 décembre 2000) : 1369–80. http://dx.doi.org/10.1083/jcb.151.7.1369.

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Mislocalization of the photopigment rhodopsin may be involved in the pathology of certain inherited retinal degenerative diseases. Here, we have elucidated rhodopsin's targeting signal which is responsible for its polarized distribution to the rod outer segment (ROS). Various green fluorescent protein (GFP)/rhodopsin COOH-terminal fusion proteins were expressed specifically in the major red rod photoreceptors of transgenic Xenopus laevis under the control of the Xenopus opsin promoter. The fusion proteins were targeted to membranes via lipid modifications (palmitoylation and myristoylation) as opposed to membrane spanning domains. Membrane association was found to be necessary but not sufficient for efficient ROS localization. A GFP fusion protein containing only the cytoplasmic COOH-terminal 44 amino acids of Xenopus rhodopsin localized exclusively to ROS membranes. Chimeras between rhodopsin and α adrenergic receptor COOH-terminal sequences further refined rhodopsin's ROS localization signal to its distal eight amino acids. Mutations/deletions of this region resulted in partial delocalization of the fusion proteins to rod inner segment (RIS) membranes. The targeting and transport of endogenous wild-type rhodopsin was unaffected by the presence of mislocalized GFP fusion proteins.

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Fu, Hsu-Yuan, Yu-Cheng Lin, Yung-Ning Chang, Hsiaochu Tseng, Ching-Che Huang, Kang-Cheng Liu, Ching-Shin Huang et al. « A Novel Six-Rhodopsin System in a Single Archaeon ». Journal of Bacteriology 192, n^o 22 (27 août 2010) : 5866–73. http://dx.doi.org/10.1128/jb.00642-10.

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ABSTRACT Microbial rhodopsins, a diverse group of photoactive proteins found in Archaea, Bacteria, and Eukarya, function in photosensing and photoenergy harvesting and may have been present in the resource-limited early global environment. Four different physiological functions have been identified and characterized for nearly 5,000 retinal-binding photoreceptors, these being ion transporters that transport proton or chloride and sensory rhodopsins that mediate light-attractant and/or -repellent responses. The greatest number of rhodopsins previously observed in a single archaeon had been four. Here, we report a newly discovered six-rhodopsin system in a single archaeon, Haloarcula marismortui, which shows a more diverse absorbance spectral distribution than any previously known rhodopsin system, and, for the first time, two light-driven proton transporters that respond to the same wavelength. All six rhodopsins, the greatest number ever identified in a single archaeon, were first shown to be expressed in H. marismortui, and these were then overexpressed in Escherichia coli. The proteins were purified for absorption spectra and photocycle determination, followed by measurement of ion transportation and phototaxis. The results clearly indicate the existence of a proton transporter system with two isochromatic rhodopsins and a new type of sensory rhodopsin-like transducer in H. marismortui.

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Poupault, Clara, Diane Choi, Khanh Lam-Kamath, Deepshe Dewett, Ansa Razzaq, Joseph Bunker, Alexis Perry, Irene Cho et Jens Rister. « A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila ». PLOS Genetics 17, n^o 6 (23 juin 2021) : e1009613. http://dx.doi.org/10.1371/journal.pgen.1009613.

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Color vision in Drosophila melanogaster is based on the expression of five different color-sensing Rhodopsin proteins in distinct subtypes of photoreceptor neurons. Promoter regions of less than 300 base pairs are sufficient to reproduce the unique, photoreceptor subtype-specific rhodopsin expression patterns. The underlying cis-regulatory logic remains poorly understood, but it has been proposed that the rhodopsin promoters have a bipartite structure: the distal promoter region directs the highly restricted expression in a specific photoreceptor subtype, while the proximal core promoter region provides general activation in all photoreceptors. Here, we investigate whether the rhodopsin promoters exhibit a strict specialization of their distal (subtype specificity) and proximal (general activation) promoter regions, or if both promoter regions contribute to generating the photoreceptor subtype-specific expression pattern. To distinguish between these two models, we analyze the expression patterns of a set of hybrid promoters that combine the distal promoter region of one rhodopsin with the proximal core promoter region of another rhodopsin. We find that the function of the proximal core promoter regions extends beyond providing general activation: these regions play a previously underappreciated role in generating the non-overlapping expression patterns of the different rhodopsins. Therefore, cis-regulatory motifs in both the distal and the proximal core promoter regions recruit transcription factors that generate the unique rhodopsin patterns in a combinatorial manner. We compare this combinatorial regulatory logic to the regulatory logic of olfactory receptor genes and discuss potential implications for the evolution of rhodopsins.

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Chuang, Jen-Zen, et Ching-Hwa Sung. « The Cytoplasmic Tail of Rhodopsin Acts as a Novel Apical Sorting Signal in Polarized MDCK Cells ». Journal of Cell Biology 142, n^o 5 (7 septembre 1998) : 1245–56. http://dx.doi.org/10.1083/jcb.142.5.1245.

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All basolateral sorting signals described to date reside in the cytoplasmic domain of proteins, whereas apical targeting motifs have been found to be lumenal. In this report, we demonstrate that wild-type rhodopsin is targeted to the apical plasma membrane via the TGN upon expression in polarized epithelial MDCK cells. Truncated rhodopsin with a deletion of 32 COOH-terminal residues shows a nonpolar steady-state distribution. Addition of the COOH-terminal 39 residues of rhodopsin redirects the basolateral membrane protein CD7 to the apical membrane. Fusion of rhodopsin's cytoplasmic tail to a cytosolic protein glutathione S-transferase (GST) also targets this fusion protein (GST–Rho39Tr) to the apical membrane. The targeting of GST–Rho39Tr requires both the terminal 39 amino acids and the palmitoylation membrane anchor signal provided by the rhodopsin sequence. The apical transport of GST–Rho39Tr can be reversibly blocked at the Golgi complex by low temperature and can be altered by brefeldin A treatment. This indicates that the membrane-associated GST–Rho39Tr protein may be sorted along a yet unidentified pathway that is similar to the secretory pathway in polarized MDCK cells. We conclude that the COOH-terminal tail of rhodopsin contains a novel cytoplasmic apical sorting determinant. This finding further indicates that cytoplasmic sorting machinery may exist in MDCK cells for some apically targeted proteins, analogous to that described for basolaterally targeted proteins.

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Tarlachkov, Sergey V., Taras V. Shevchuk, Maria del Carmen Montero-Calasanz et Irina P. Starodumova. « Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments ». Bioinformatics 36, n^o 6 (11 novembre 2019) : 1668–72. http://dx.doi.org/10.1093/bioinformatics/btz840.

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Abstract Motivation A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions. Results This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family. Supplementary information Supplementary data are available at Bioinformatics online.

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Ahrendt, Steven R., Edgar Mauricio Medina, Chia-en A. Chang et Jason E. Stajich. « Exploring the binding properties and structural stability of an opsin in the chytridSpizellomyces punctatususing comparative and molecular modeling ». PeerJ 5 (27 avril 2017) : e3206. http://dx.doi.org/10.7717/peerj.3206.

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BackgroundOpsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores.MethodsWe used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found inSpizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squidTodarodes pacificus.ResultsOur results indicate that theSpizellomycesopsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology ofSpizellomycesopsins to animal type 2 rhodopsins.DiscussionThis represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

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Shtyrov, Andrey A., Dmitrii M. Nikolaev, Vladimir N. Mironov, Andrey V. Vasin, Maxim S. Panov, Yuri S. Tveryanovich et Mikhail N. Ryazantsev. « Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins : Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima ». International Journal of Molecular Sciences 22, n^o 6 (16 mars 2021) : 3029. http://dx.doi.org/10.3390/ijms22063029.

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A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties.

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Konno, Masae, Yumeka Yamauchi, Keiichi Inoue et Hideki Kandori. « Expression analysis of microbial rhodopsin-like genes in Guillardia theta ». PLOS ONE 15, n^o 12 (3 décembre 2020) : e0243387. http://dx.doi.org/10.1371/journal.pone.0243387.

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The Cryptomonad Guillardia theta has 42 genes encoding microbial rhodopsin-like proteins in their genomes. Light-driven ion-pump activity has been reported for some rhodopsins based on heterologous E. coli or mammalian cell expression systems. However, neither their physiological roles nor the expression of those genes in native cells are known. To reveal their physiological roles, we investigated the expression patterns of these genes under various growth conditions. Nitrogen (N) deficiency induced color change in exponentially growing G. theta cells from brown to green. The 29 rhodopsin-like genes were expressed in native cells. We found that the expression of 6 genes was induced under N depletion, while that of another 6 genes was reduced under N depletion.

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Thèses sur le sujet "Rhodopsin proteins"

Perera, Mahakumarage Suchithranga, et Mahakumarage Suchithranga Perera. « Investigation of Rhodopsin Activation Using Spectroscopic and Scattering Techniques ». Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/622975.

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G-protein–coupled receptors are the largest superfamily in the human genome, and involved in critical cellular signaling processes in living cells. Protein structural fluctuations are the key for GPCR function that is driven and modulated by a variety of factors that are not well understood. This dissertation focusses on understanding the activation of GPCRs using the visual receptor, rhodopsin as the prototype. Rhodopsin is an ideal candidate for this study, as it represents the largest class of GPCRs, and is known to demonstrate more noticeable structural changes upon activation compared to the other GPCRs. What structural fluctuations occur, the role of water, and how the retinal cofactor regulates the protein dynamics during rhodopsin activation are specific research problems addressed in this work. Hypothesizing an ensemble activation mechanism, experiments were conducted using a variety of techniques to probe structural and dynamical fluctuations of rhodopsin in native membranes, as well as in membrane mimetics such as detergent micelles. Time-resolved wide-angle X-ray scattering (TR-WAXS), small-angle neutron scattering (SANS), quasielastic neutron scattering (QENS), and electronic spectroscopy are among the prominent techniques used to gain insights into the photo-intermediates that are key to understanding the rhodopsin activation process. The small-angle neutron scattering (SANS) experiments revealed a volumetric expansion of the protein molecule upon photoactivation of rhodopsin. Electronic spectroscopy together with the differential hydration study revealed the crucial role of water in rhodopsin signaling process and signal amplification by water. The quasielastic neutron scattering study conducted on powdered rhodopsin probed the changes in the local dynamics that are regulated by the retinal cofactor of the rhodopsin molecule. The increased local steric crowding in the ligand-free opsin is consistent with collapsing of the apoprotein structure in the absence of the retinal chromophore leading to inactive opsin conformation. Finally, a time-resolved wide-angle X-ray scattering study was conducted using the X-ray free electron laser at the SLAC national laboratory to probe the early structural fluctuations in rhodopsin photoactivation. The preliminary pump-probe experiments conducted on rhodopsin in CHAPS detergent micelles revealed a light-triggered protein quake that occurs during the early activation stages of rhodopsin photoactivation. Thus the protein fluctuations underlying the GPCR function are revealed by neutrons, X-rays, and other photons in a combined implementation of both spectroscopic and scattering techniques as applied to the investigation of rhodopsin activation.

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Birkholz, Denise A. « Photoreceptor cell fate determination and rhodopsin expression in the developing eye of Drosophila / ». Connect to full text via ProQuest. IP filtered, 2005.

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Farmer, Nicola Ann. « Folding and assembly of two alpha helical membrane proteins, rhodopsin and bacteriorhodopsin ». Thesis, University of Bristol, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402351.

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Murray, Anne Riché. « The functional significance of rhodopsin's N-linked glycosylation ». Oklahoma City : [s.n.], 2009.

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Zhao, Xinyu. « Characterization of molecular forms of G protein-coupled receptor kinase 1 (rhodopsin kinase) in vertebrate retina and pineal gland / ». Thesis, Connect to this title online ; UW restricted, 1997. http://hdl.handle.net/1773/6259.

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Sapra, K. Tanuj. « Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy ». Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1175696409847-74867.

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Single-molecule force spectroscopy (SMFS) with atomic force microscope (AFM) has advanced our knowledge of the mechanical aspects of biological processes, and helped us take big strides in the hitherto unexplored areas of protein (un)folding. One such virgin land is that of membrane proteins, where the advent of AFM has not only helped to visualize the difficult to crystallize membrane proteins at the single-molecule level, but also given a new perspective in the understanding of the interplay of molecular interactions involved in the construction of these molecules. My PhD work was tightly focused on exploiting this sensitive technique to decipher the intra- and intermolecular interactions in membrane proteins, using bacteriorhodopsin and bovine rhodopsin as model systems. Using single-molecule unfolding measurements on different bacteriorhodopsin oligomeric assemblies - trimeric, dimeric and monomeric - it was possible to elucidate the contribution of intra- and interhelical interactions in single bacteriorhodopsin molecules. Besides, intriguing insights were obtained into the organization of bacteriorhodopsin as trimers, as deduced from the unfolding pathways of the proteins from different assemblies. Though the unfolding pathways of bacteriorhodopsin from all the assemblies remained the same, the different occurrence probability of these pathways suggested a kinetic stabilization of bacteriorhodopsin from a trimer compared to that existing as a monomer. Unraveling the knot of a complex G-protein coupled receptor, rhodopsin, showed the existence of two structural states, a native, functional state, and a non-native, non-functional state, corresponding to the presence or absence of a highly conserved disulfide bridge, respectively. The molecular interactions in absence of the native disulfide bridge mapped onto the three-dimensional structure of native rhodopsin gave insights into the molecular origin of the neurodegenerative disease retinitis pigmentosa. This presents a novel technique to decipher molecular interactions of a different conformational state of the same molecule in the absence of a high-resolution X-ray crystal structure. Interestingly, the presence of ZnCl2 maintained the integrity of the disulfide bridge and the nature of unfolding intermediates. Moreover, the increased mechanical and thermodynamic stability of rhodopsin with bound zinc ions suggested a plausible role for the bivalent ion in rhodopsin dimerization and consequently signal transduction. Last but not the least, I decided to dig into the mysteries of the real mechanisms of mechanical unfolding with the help of well-chosen single point mutations in bacteriorhodopsin. The monumental work has helped me to solve some key questions regarding the nature of mechanical barriers that constitute the intermediates in the unfolding process. Of particular interest is the determination of altered occurrence probabilities of unfolding pathways in an energy landscape and their correlation to the intramolecular interactions with the help of bioinformatics tools. The kind of work presented here, in my opinion, will not only help us to understand the basic principles of membrane protein (un)folding, but also to manipulate and tune energy landscapes with the help of small molecules, proteins, or mutations, thus opening up new vistas in medicine and pharmacology. It is just a matter of a lot of hard work, some time, and a little bit of luck till we understand the key elements of membrane protein (un)folding and use it to our advantage.

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Tomasello, Gaia <1981&gt. « Theoretical insight into the properties of light induced events of photochromic systems and rhodopsin proteins ». Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1726/1/Tomasello_Gaia_Tesi.pdf.

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Sapra, K. Tanuj. « Single-Molecule Measurements of Complex Molecular Interactions in Membrane Proteins using Atomic Force Microscopy ». Doctoral thesis, Technische Universität Dresden, 2006. https://tud.qucosa.de/id/qucosa%3A24922.

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Behnke, Craig A. « X-ray crystallographic analysis of three proteins : the novel structures of the corn Hageman factor inhibitor, the G-protein coupled receptor rhodopsin, and the ultra-high resolution structure of carbonic anhydrase / ». Thesis, Connect to this title online ; UW restricted, 2000. http://hdl.handle.net/1773/9206.

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Livres sur le sujet "Rhodopsin proteins"

Symposium on Rhodopsins and Phototransduction (1998 : Kyoto, Japan), dir. Rhodopsins and phototransduction. Chichester : John Wiley, 1999.

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Biomolecular electronics : An introduction via photosensitive proteins. Boston, Mass : Birkhäuser, 1998.

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Jean-Louis, Rigaud, et Institut national de la santé et de la recherche médicale (France), dir. Structures and functions of retinal proteins : Proceedings of the Vth International Conference on Retinal Proteins held in Dourdan (France) June 28-July 3, 1992. Paris, France : INSERM, 1992.

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1942-1985, Eisenstein Laura, Ebrey Thomas G et University of Illinois at Urbana-Champaign. Dept. of Physics., dir. Biophysical studies of retinal proteins : Proceedings of a conference in memory of Laura Eisenstein, held at Allerton Park Conference Center of the University of Illinois at Urbana-Champaign. Champaign, IL : Dept. of Physics, University of Illinois at Urbana-Champaign, 1987.

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L, Caron Marc, National Heart, Lung, and Blood Institute et American Heart Association, dir. Receptors and cell activation : A summary of the Frontiers in Basic Sciences That Relate to Heart, Lung, and Blood Diseases Symposium : National Heart, Lung, and Blood Institute : administrative report. Bethesda, Md : The Institute, 1987.

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Rees, Douglas C. Membrane Proteins (Advances in Protein Chemistry, Volume 63) (Advances in Protein Chemistry). Academic Press, 2003.

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Rees, Douglas C. Membrane Proteins. Elsevier Science & Technology Books, 2003.

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Membrane proteins. Amsterdam : Academic Press, 2003.

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Rhodopsins and Phototransduction. John Wiley & Sons, 2000.

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Ovchinnikov, Yu A. Retinal Proteins : Proceedings of the International Conference, Ussr, 1986. Brill Academic Publishers, 1987.

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Chapitres de livres sur le sujet "Rhodopsin proteins"

González, Laura Pedraza, Leonardo Barneschi, Daniele Padula, Luca De Vico et Massimo Olivucci. « Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol ». Dans Topics in Current Chemistry Collections, 105–52. Cham : Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-07658-9_5.

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AbstractIn recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.

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Fujita, Jun, Norika Sakurai et Takao Shinozawa. « Presence of rhodopsin-like proteins in the planarian head ». Dans Turbellarian Biology, 93–94. Dordrecht : Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-2775-2_14.

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Chabre, M., et M. L. Applebury. « Interaction of Photoactivated Rhodopsin with Photoreceptor Proteins : The cGMP Cascade ». Dans The Molecular Mechanism of Photoreception, 51–66. Berlin, Heidelberg : Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-70444-4_4.

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Durbeej, Bo. « A Computational Perspective on the Photochemistry of Photosensory Proteins : Phytochromes and Anabaena Sensory Rhodopsin ». Dans Quantum Simulations of Materials and Biological Systems, 169–94. Dordrecht : Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4948-1_10.

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Ryba, Nicholas J. P., Matthew D. Hall et John B. C. Findlay. « Rhodopsin ». Dans Molecular Biology of G-Protein-Coupled Receptors, 1–30. Boston, MA : Birkhäuser Boston, 1992. http://dx.doi.org/10.1007/978-1-4684-6772-7_1.

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Deretic, Dusanka, et David S. Papermaster. « Low Molecular Weight GTP-binding Proteins Associated with the Membranes Involved in Post-Golgi Transport of Rhodopsin ». Dans Molecular Mechanisms of Membrane Traffic, 408. Berlin, Heidelberg : Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-662-02928-2_86.

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Gautier, Antoine, et Daniel Nietlispach. « Solution NMR Studies of Integral Polytopic α-Helical Membrane Proteins : The Structure Determination of the Seven-Helix Transmembrane Receptor Sensory Rhodopsin II, pSRII ». Dans Membrane Protein Structure and Dynamics, 25–45. Totowa, NJ : Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-023-6_3.

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Hofmann, K. P. « Rhodopsin/G-Protein Interaction ». Dans GTPases in Biology II, 267–90. Berlin, Heidelberg : Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-78345-6_17.

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Findlay, J. B. C. « Rhodopsin and G-Protein Linked Receptors ». Dans Methods in Protein Sequence Analysis, 509–16. Berlin, Heidelberg : Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73834-0_67.

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Kandori, Hideki. « Protein-Controlled Isomerization in Rhodopsins ». Dans Chemical Science of π-Electron Systems, 695–713. Tokyo : Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55357-1_41.

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Actes de conférences sur le sujet "Rhodopsin proteins"

GUALTIERI, PAOLO. « RHODOPSIN-LIKE PROTEINS : THE UNIVERSAL AND PROBABLY UNIQUE PROTEINS FOR VISION ». Dans Proceedings of the International School of Biophysics. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799975_0002.

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Yu, Yunzhu, et Yuge Tong. « The evolutionary relationship of rhodopsin proteins across species ». Dans International Conference on Biomedical and Intelligent Systems (IC-BIS 2022), sous la direction de Ahmed El-Hashash. SPIE, 2022. http://dx.doi.org/10.1117/12.2660522.

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Hamm, P., M. Zurek et T. Röschinger. « Femtosecond VIS and mid-IR Spectroscopy of the Photoisomerisation of Retinal ». Dans International Conference on Ultrafast Phenomena. Washington, D.C. : Optica Publishing Group, 1996. http://dx.doi.org/10.1364/up.1996.tue.24.

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The light induced isomerisation of the retinal molecule (more exactly protonated Schiff base retinal, PSBR) plays an essential role in a number of important functional biomolecules like rhodopsin (responsible for vision), bacteriorhodopsin (BR, photosynthetic light induced proton pump) and halorhodopsin (HR, light induced chloride pump). These proteins were investigated in detail by femtosecond spectroscopy. In all cases, a fast S1 reaction occurs prior to the transition to the ground state. However, the details of the photoreaction critically depend on the specific surrounding of the chromophore in the protein: The 11-cis→all-trans isomerisation in rhodopsin and the all-trans→13-cis isomerisation in BR occur extremely fast with 200 fs [1] and 500 fs [2], respectively. A slower and biexponential process is observed for the all-trans→13-cis isomerisation of HR with 1.5 ps and 8.5 ps [3]. In order to separate the influence of the protein from the intrinsic properties of the retinal molecule, isolated all-trans-PSBR (in ethanol) was investigated in the present paper. In addition to standard VIS measurements, femtosecond IR experiments will be presented in order to reveal structural aspects of the photoreaction.

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Lutz, I. G., A. O. Sieg, J. Wachtveitl, W. Zinth, I. Boche, M. Otsuka et D. Oesterhelt. « Primary Reactions of Sensory Rhodopsin I and II : Two proteins with vastly different dynamics ». Dans International Conference on Ultrafast Phenomena. Washington, D.C. : OSA, 2000. http://dx.doi.org/10.1364/up.2000.wa6.

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Mukherjee, Rudranarayan M., Paul Crozier et Kurt S. Anderson. « Multibody Molecular Dynamics II : Applications and Results ». Dans ASME 2007 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/detc2007-35561.

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This is the second paper in a series of two papers on using multibody dynamics algorithms and methods for coarse grained molecular dynamics simulations. In the previous paper, the theoretical discussions on this topic have been presented. This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include water boxes, alkane chains, alanine dipeptide and carboxyl terminal fragments of Calmodulin, Ribosomal, and Rhodopsin proteins. The atomistic representations of these systems include several thousand degrees of freedom and results of several nano-second simulations of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

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Zhong, Q., S. Ruhman, M. Ottolenghi, M. Sheves, N. Friedman, G. H. Atkinson et J. K. Delaney. « A Comparative Study of the Initial Photoinduced Event in Bacteriorhodopsin : Can it be Isomerization ? » Dans International Conference on Ultrafast Phenomena. Washington, D.C. : Optica Publishing Group, 1996. http://dx.doi.org/10.1364/up.1996.pdp.5.

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Rhodopsins are a family of photoactivated 7 α-helix membrane proteins which play central roles in visual-transduction and bacterial photosynthesis. They share the same chromophore: A retinal polyene bound to the protein via a protonated Schiff base linkage. A comprehensive description of the molecular mechanism of light energy conversion in rhodopsins requires a detailed understanding of the primary photophysical events.

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Hofmann, Klaus P. « Visual process in retinal photoreceptors : analysis by intrinsic light scattering signals ». Dans OSA Annual Meeting. Washington, D.C. : Optica Publishing Group, 1989. http://dx.doi.org/10.1364/oam.1989.wd1.

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The rod photoreceptor of the retina is a quantum detector whose physiological function in physically unfavorable conditions (body temperature, salt solution) is made possible by specific protein interactions. Photon energy is stored by the receptor protein rhodopsin (R) in a structurally transformed state. Activated R interacts with transducin (a G-protein or guanine nucleotide binding protein). This catalyses binding to G of energy-rich nucleotide which in turn releases G in an activated form. Absorption of one photon leads to the activation of 1000 G in 1 s. Analogous relay systems are found from bacteria to man. Intrinsic physical properties of the rhodopsin G-protein system allow photometric studies in situ and in real time. Activation of R and interaction with G are measurable by absorption spectrophotometry. Activation of G is measurable by light scattering (LS) changes (signals) arising from the shift of the G-protein mass during activation. A continuous transretinal, near infrared LS probing beam affords direct monitoring of G-activation induced by visual stimuli. These optical techniques, combined with biochemical and physiological approaches, have been used to study the sites of R-G interaction and the thermodynamics of the G-relay in situ. G-activation is not modulated by previous illumination, indicating a remarkable constancy of the R-G amplification step in the visual transduction pathway.

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Altoè, Piero, Marco Stenta, Marco Garavelli, Theodore E. Simos et George Maroulis. « Rhodopsin and GFP Chromophores : QM∕MM Absorption Spectra in Solvent and Protein ». Dans COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING : Theory and Computation : Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007) : VOLUME 1. AIP, 2007. http://dx.doi.org/10.1063/1.2836178.

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Kholmurodov, Kholmirzo T., Yu E. Penionzhkevich et E. A. Cherepanov. « Computer Molecular Dynamics Studies on Protein Structures (Visual Pigment Rhodopsin and Cyclin-Dependent Kinases) ». Dans INTERNATIONAL SYMPOSIUM ON EXOTIC NUCLEI. AIP, 2007. http://dx.doi.org/10.1063/1.2746628.

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Rapports d'organisations sur le sujet "Rhodopsin proteins"

Rafaeli, Ada, Russell Jurenka et Chris Sander. Molecular characterisation of PBAN-receptors : a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, janvier 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are utilised by a variety of moth species to attract conspecific mates. In most of the moth species sex-pheromone biosynthesis is under circadian control by the neurohormone, PBAN (pheromone-biosynthesis-activating neuropeptide). In order to devise ideal strategies for mating disruption/prevention, we proposed to study the interactions between PBAN and its membrane-bound receptor in order to devise potential antagonists. Major conclusions: Within the framework of the planned objectives we have confirmed the similarities between the two Helicoverpa species: armigera and zea. Receptor sequences of the two Helicoverpa spp. are 98% identical with most changes taking place in the C-terminal. Our findings indicate that PBAN or PBAN-like receptors are also present in the neural tissues and may represent a neurotransmitter-like function for PBAN-like peptides. Surprisingly the gene encoding the PBAN-receptor was also present in the male homologous tissue, but it is absent at the protein level. The presence of the receptor (at the gene- and protein-levels), and the subsequent pheromonotropic activity are age-dependent and up-regulated by Juvenile Hormone in pharate females but down-regulated by Juvenile Hormone in adult females. Lower levels of pheromonotropic activity were observed when challenged with pyrokinin-like peptides than with HezPBAN as ligand. A model of the 3D structure of the receptor was created using the X-ray structure of rhodopsin as a template after sequence alignment of the HezPBAN-R with several other GPCRs and computer simulated docking with the model predicted putative binding sites. Using in silico mutagenesis the predicted docking model was validated with experimental data obtained from expressed chimera receptors in Sf9 cells created by exchanging between the three extracellular loops of the HezPBAN-R and the Drosophila Pyrokinin-R (CG9918). The chimera receptors also indicated that the 3ʳᵈ extracellular loop is important for recognition of PBAN or Diapause hormone ligands. Implications: The project has successfully completed all the objectives and we are now in a position to be able to design and screen potential antagonists for pheromone production. The successful docking simulation-experiments encourage the use of in silico experiments for initial (high-throughput) screening of potential antagonists. However, the differential responses between the expressed receptor (Sf9 cells) and the endogenous receptor (pheromone glands) emphasize the importance of assaying lead compounds using several alternative bioassays (at the cellular, tissue and organism levels). The surprising discovery of the presence of the gene encoding the PBAN-R in the male homologous tissue, but its absence at the protein level, launches opportunities for studying molecular regulation pathways and the evolution of these GPCRs. Overall this research will advance research towards the goal of finding antagonists for this important class of receptors that might encompass a variety of essential insect functions.

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