Filters








45 Hits in 11.8 sec

RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils

A. Rose, S. Lorenzen, A. Goede, B. Gruening, P. W. Hildebrand
2009 Nucleic Acids Research  
RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins.  ...  The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters ('channels') or other membrane proteins ('membrane-coils').  ...  ACKNOWLEDGEMENTS We thank Dr Cornelius Fro¨mmel and Dr Robert Preissner for helpful discussions and Simon Ward for reading the manuscript.  ... 
doi:10.1093/nar/gkp418 pmid:19465378 pmcid:PMC2703963 fatcat:nkd4oxkenbfjboed33jdbefhia

Structural introspection of a putative fluoride transporter in plants

Aditya Banerjee, Aryadeep Roychoudhury
2019 3 Biotech  
The xenobiotic fluoride is a detrimental toxin which is exported by a double-barrelled fluoride channel (Fluc) in prokaryotes and a single-barrelled fluoride exporter (FEX) in lower eukaryotes.  ...  FEXs were predicted to contain lipid moieties which anchor the transporters to the plasma membrane.  ...  Compliance with ethical standards Conflict of interest The authors declare that there is no conflict of interest in publishing the manuscript.  ... 
doi:10.1007/s13205-019-1629-4 pmid:30800614 pmcid:PMC6386761 fatcat:2qosjvpngfae7lwqlthhxmsqdu

Characterization of the Connexin45 Carboxyl-Terminal Domain Structure and Interactions with Molecular Partners

Jennifer L. Kopanic, Mona H. Al-mugotir, Fabien Kieken, Sydney Zach, Andrew J. Trease, Paul L. Sorgen
2014 Biophysical Journal  
Mechanisms underlying the initiation and persistence of lethal cardiac rhythms are of significant clinical and scientific interests.  ...  Cx45CT resonance assignments were also used to identify the binding sites and affinities of molecular partners involved in the Cx45 regulation; although none disrupted dimerization, many of these proteins  ...  The authors thank Ed Ezell for his assistance with NMR. We also thank the UNMC Structural Biology Facility for technical help and useful discussion regarding dynamic light scattering.  ... 
doi:10.1016/j.bpj.2014.03.045 pmid:24853747 pmcid:PMC4052358 fatcat:dyqkghti5nf6pnfeu5uwek3ux4

Large conformational changes in FtsH create an opening for substrate entry [article]

Vanessa Carvalho, Roland Kieffer, Nick de Lange, Andreas Engel, Marie-Eve Aubin-Tam
2017 bioRxiv   pre-print
FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control.  ...  A flexible linker of ~20 residues between the second transmembrane helix and the cytosolic domain permits the observed large tilting movements, thereby facilitating the entry of substrate proteins towards  ...  Acknowledgements 417 The authors thank Dr. Simon Lindhoud for useful initial discussions; Prof. Dr. Ulrich Baumann for the 418 plasmids; and Dr. Carlos Oscar Sorzano, Prof.  ... 
doi:10.1101/209445 fatcat:j44l3wiicrgyhfe2i632bubhci

Membrane Topology Mapping of the O-Antigen Flippase (Wzx), Polymerase (Wzy), and Ligase (WaaL) from Pseudomonas aeruginosa PAO1 Reveals Novel Domain Architectures

S. T. Islam, V. L. Taylor, M. Qi, J. S. Lam
2010 mBio  
Protein orientation in the inner membrane was confirmed via C-terminal fusion to green fluorescent protein.  ...  For an important first step in deciphering the mechanisms of LPS assembly, we set out to map the membrane topology of these proteins.  ...  ACKNOWLEDGMENTS We are thankful for the kind gifts of plasmid pMA632 from Herbert H.  ... 
doi:10.1128/mbio.00189-10 pmid:20824106 pmcid:PMC2932511 fatcat:ffxtzhorzfg3dnq7szneo66og4

In silico characteration of GmSOS1 provides a comprehensive understaning for its role in soybean salt tolerance [article]

Ling-Yan Yang, Zhi-Chao Mei, Zhi-Min Liu, Xin-Zhao Hou, Li-Jun Xie
2020 bioRxiv   pre-print
Plant SOS1 gene encodes plasma membrane Na+/H+ antiporter, which helps in the exclusion of Na+ and improves plant salt tolerance.  ...  In the present study, we carried out a comprehensive bioinformatics analysis of SOS1 gene in soybean.  ...  Typical domains were indentified by PfamScan [25] and CDD [26] , the specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane was predicted by TOPCONS  ... 
doi:10.1101/2020.02.21.951061 fatcat:5tjciyfjhzfvfjjvrw2fm5zqw4

A Mechanism of Calmodulin Modulation of the Human Cardiac Sodium Channel

Christopher N. Johnson, Franck Potet, Matthew K. Thompson, Brett M. Kroncke, Andrew M. Glazer, Markus W. Voehler, Bjorn C. Knollmann, Alfred L. George, Walter J. Chazin
2018 Structure  
CaM has been reported to bind in a Ca 2+ -dependent manner to two sites in the intracellular-loop that is critical for inactivation of Na V 1.5 (inactivation gate; IG).  ...  Patch clamp recordings for wild-type and mutant channels with an impaired CaM-IG interaction revealed CaM binding to the IG promotes recovery from inactivation while impeding the kinetics of inactivation  ...  Research on Ca 2+ binding proteins in the Chazin laboratory is supported by an endowed chair from Vanderbilt University and in part by NIH grant R35 GM118089.  ... 
doi:10.1016/j.str.2018.03.005 pmid:29606593 pmcid:PMC5932218 fatcat:a67572p46neepillmsaydcpkqe

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
In the present study, we aimed to improve the ExM method for imaging of proteins in human clinical tissue samples, for diagnostic pathology and research.  ...  limited to a 250nm resolution).  ...  In this intent, a new family of synthetic ion channels was developed in our laboratory using a transmembrane helical peptide as framework bearing six crown ethers to create a transmembrane channel for  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

Structure-function relationships of helical membrane proteins [article]

Peter Hildebrand, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
2011
In contrast, only a minor fraction (September 2010: 1.8%) of the protein structures deposited in the protein data bank (PDB) belongs to this structural class.  ...  of helical membrane proteins such as the type of helix pairing or the occurrence of hydrogen bonds.  ...  RHYTHM, a prediction tool that will be described in detail in this work, is the first server that predicts the exposure or burial of transmembrane residues taking into account the structural specificities  ... 
doi:10.17169/refubium-6251 fatcat:zlf33djd3raufbvrbpbibag2dy

Flagella-mediated secretion of a novel Vibrio cholerae cytotoxin affecting both vertebrate and invertebrate hosts

Mitesh Dongre, Bhupender Singh, Kyaw Min Aung, Per Larsson, Regina Miftakhova, Karina Persson, Fatemeh Askarian, Mona Johannessen, Jonas von Hofsten, Jenny L. Persson, Marc Erhardt, Simon Tuck (+2 others)
2018 Communications Biology  
the flagellum channel in a proton motive force-dependent manner.  ...  Our findings reveal an unrecognized role for V. cholerae flagella in cytotoxin export that may contribute both to environmental spread of the bacteria by promoting survival and proliferation in encounters  ...  Acknowledgements This work was performed within the Umeå Centre for Microbial Research (UCMR) Linnaeus Programme and was supported by grants to SNW and BEU from the Swedish Research Council (521-2013-  ... 
doi:10.1038/s42003-018-0065-z fatcat:vzqi5pcvdbgvrgb2nayimkihci

第54回年会予稿集

2016 Seibutsu Butsuri  
To dissociate Abs at more neutral pH, we designed a novel affinity ligand, FPA, which is a fusion of the B domain of PA and the coiled-coil region of c-Fos.  ...  We will introduce a server to predict functional regions by using the index, and the extension of the index to another bioinformatics problem, homology modeling. [ We have developed the Sugorok method,  ...  3Pos313 Ohashi, Kaoru (大橋 郁) 3Pos279 3Pos284 Ohba, Yasunori (大庭 裕範) 3Pos065 Ohba, Yusuke (大場 雄介) 3SAA-03 Ohgita, Takashi (扇田 隆司) 3Pos072 Ohira, Ayaka (大平 彩花) 1Pos257 Ohki, Mio (大木 規央) 3Pos076 Ohkoshi, A.  ... 
doi:10.2142/biophys.56.s1 fatcat:jxxuc3tfpbhc5isjcmprzec2gi

The 28th Annual Symposium of The Protein Society: Program & Abstracts

2014 Protein Science  
A recent crystal structure of a pentameric arrangement of the cytosolic part of TmCorA suggests counterbalancing forces located in the trans-membrane part of the channel helices and the binding sites of  ...  helices in the inner membrane.  ...  In order to further understand this shift in the observed "equilibrium" transitions of 1O6D, a combination of in silico, experimental folding and Nuclear Magnetic Resonance experiments will be discussed  ... 
doi:10.1002/pro.2504 pmid:25043257 pmcid:PMC4116645 fatcat:yjhug3aif5futn3icovvrkgebm

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Monika Schmoll, Christoph Dattenböck, Nohemí Carreras-Villaseñor, Artemio Mendoza-Mendoza, Doris Tisch, Mario Ivan Alemán, Scott E. Baker, Christopher Brown, Mayte Guadalupe Cervantes-Badillo, José Cetz-Chel, Gema Rosa Cristobal-Mondragon, Luis Delaye (+28 others)
2016 Microbiology and Molecular Biology Reviews  
In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content.  ...  Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes.  ...  ACKNOWLEDGMENTS We declare we have no conflicts of interest.  ... 
doi:10.1128/mmbr.00040-15 pmid:26864432 pmcid:PMC4771370 fatcat:h2ojkieysrboplnbqjfusygwsq

NRSF [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
The membranes are equipped with ion channels. Nerve Growth Factor (NGF, neurotrophin): A stimulatory factor of growth and differentiation of nerve cells.  ...  Electromagnetic radiation is pulsed at small 15-20-kDa proteins in a strong magnetic field. This results in a change in the orientation of the magnetic dipole of the atomic nuclei.  ...  In some organisms there are three or four layers of membranes indicating that they absorbed the nucleomorph(s) of the symbiont(s) and retained it as a plastid (s) Nucleosome: A histone octamer is wrapped  ... 
doi:10.1007/978-1-4020-6754-9_11585 fatcat:r5ybk4fgovebphvk7xkzgr5q34

Nitrogen Cycle [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
The membranes are equipped with ion channels. Nerve Growth Factor (NGF, neurotrophin): A stimulatory factor of growth and differentiation of nerve cells.  ...  Electromagnetic radiation is pulsed at small 15-20-kDa proteins in a strong magnetic field. This results in a change in the orientation of the magnetic dipole of the atomic nuclei.  ...  In some organisms there are three or four layers of membranes indicating that they absorbed the nucleomorph(s) of the symbiont(s) and retained it as a plastid (s) Nucleosome: A histone octamer is wrapped  ... 
doi:10.1007/978-1-4020-6754-9_11438 fatcat:l3g7v7z6zbeqbcnxd5bpkr5myy
« Previous Showing results 1 — 15 out of 45 results