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New methods for structural investigations of nanocrystalline and amorphous organic compounds

Martin U. Schmidt
2016 Acta Crystallographica Section A: Foundations and Advances  
Developments aiming at disentangling conformational and species heterogeneity, which are very common in this family of biomolecular complexes, will be explained.  ...  The existence of proteins that despite not having permanent structural elements are fully functional have required the reformulation of the traditional structure/function paradigm, one of the historical  ... 
doi:10.1107/s2053273316099812 fatcat:gzjcwnxo5bgodmo5ar6hyjwpm4

A Friend in Common: A Small GTPase in Independent PTI and ETI Immune Receptor Complexes

Ryohei Thomas Nakano
2021 Plant and Cell Physiology  
On the other hand, cytoplasmic receptors called NLR proteins mediate ETI through the recognition of an effector, a microbial molecule directly injected into the host cells that interferes with the host  ...  The molecular mechanisms and outputs of PTI and ETI have been extensively studied during the last two decades.  ...  whether OsCERK1 and Pit form part of the same protein complex remained unclear.  ... 
doi:10.1093/pcp/pcab154 pmid:34698866 fatcat:mupoeiwdu5f5llx37efcjypv5i

Clarifying the Opaque: Identification of Direct Targets of Maize Opaque2:

Jennifer Mach
2015 The Plant Cell  
disentangle.  ...  These findings may also find applications in efforts to improve maize as an industrial or biofuels feedstock, which might require grain with low protein contents.  ...  The Plant Cell, Vol. 27: 484, March 2015, www.plantcell This information is current as of May 1, 2019  ... 
doi:10.1105/tpc.15.00156 pmid:25724643 pmcid:PMC4558677 fatcat:k45e3qdcdnapfcuzvpym2vxbpm

Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings [article]

Caitlyn L McCafferty, David W Taylor, Edward M. Marcotte
2021 bioRxiv   pre-print
Electron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes.  ...  Unfortunately, structures of some complexes are limited to low- to medium-resolution due to biochemical or conformational heterogeneity.  ...  Acknowledgments All code and sample files are available at https://github.com/marcottelab/CoEVxIMP , along with our final integrative model of the bacterial holo-translocon.  ... 
doi:10.1101/2021.01.14.426447 fatcat:3nezmse6ejgnnbpvjchvrsygju

Disentangling the Web of Life

Jordi Bascompte
2009 Science  
VanHookA small G protein may limit the toxicity of mutant huntingtin to the brain.  ...  at www.sciencemag.org/apollo11.Disentangling the Web of LifeTranscriptional Regulatory Circuits: Predicting Numbers from Alphabets H.  ... 
doi:10.1126/science.1170749 pmid:19628856 fatcat:p4kn6kh3ancibonfnf7fikvo6u

Page 1037 of Circulation Vol. 21, Issue 5 [page]

1960 Circulation  
” is, in its greatest part, only the chemistry of globular proteins—A.  ...  If we extract cells or tissues with water, a considerable part, the smaller half of the protein will be dissolved, but it will be globular proteins only which pass into solution while the basic structure  ... 

Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction

Andrew K. C. Wong, Ho Yin Sze-To, Gary L. Johanning
2018 Scientific Reports  
One recent attempt 17 using different R2R-I predictors for different types of PPI requiring prior knowledge of the type of PPI of the input protein sequences from users.  ...  In Protein-Protein interaction (PPI), residue-residue interaction (R2R-I) prediction refers to the identification of pairs of interacting residues, usually under close contact, residing on separate interacting  ...  Availability of data, materials and methods. The PPI structure data is publicly available, where the data accessible method is described in the data availability statements.  ... 
doi:10.1038/s41598-018-32834-z fatcat:3nffe3nt25b7piy5tf7ggb4pxe

The Slx4-Dpb11 scaffold complex: coordinating the response to replication fork stalling in S-phase and the subsequent mitosis

Lissa N Princz, Dalia Gritenaite, Boris Pfander
2014 Cell Cycle  
Acknowledgments We are grateful to Dana Branzei, Stefan Jentsch, Michael Lisby, Joao Matos and members of the Pfander and Jentsch labs for helpful discussion and critical reading of the manuscript.  ...  Funding Work in the Pfander lab is supported by the Max-Planck Society and the German Research Council (DFG). The authors declare that they have no competing financial interest.  ...  Given that Dpb11 expression levels are low, it is therefore possible that by competing with checkpoint proteins Slx4 may be limiting the amounts of how much Dpb11 checkpoint complex can form.  ... 
doi:10.4161/15384101.2014.989126 pmid:25496009 pmcid:PMC4612105 fatcat:g7hgf7oyibbu5otpdyws3fxfma

Disentangling protein and lipid interactions that control a molecular switch in photosynthetic light harvesting

Emanuela Crisafi, Anjali Pandit
2017 Biochimica et Biophysica Acta - Biomembranes  
To disentangle the effects of protein-protein and protein-lipid interactions on the LHCII photoprotective switch, we compared the structural and fluorescent properties of LHCII lipid nanodiscs and proteoliposomes  ...  with very low protein -to-lipid ratios.  ...  Acknowledgements This work was supported by a VIDI grant (project number 723.012.103) of the Chemical Sciences division, Netherlands Organization of Scientific Research awarded to A. Pandit. M. C. A.  ... 
doi:10.1016/j.bbamem.2016.10.010 pmid:27793630 fatcat:2vbqwgyks5hyfe6yl4zxr2klgm

Disentangling DNA during replication: a tale of two strands

C. D. Hardy, N. J. Crisona, M. D. Stone, N. R. Cozzarelli
2004 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Rather, it is the combined effects of topoisomerase action, chromosome organization and DNA-condensing proteins that allow the successful partitioning of chromosomes into dividing cells.  ...  The seminal papers by Watson and Crick in 1953 on the structure and function of DNA clearly enunciated the challenge their model presented of how the intertwined strands of DNA are unwound and separated  ...  A portion of the helical MukBEF filament is shown in red, with each protein complex binding a loop of ca. 20 kb of DNA (black line).  ... 
doi:10.1098/rstb.2003.1363 pmid:15065655 pmcid:PMC1693293 fatcat:3y2uyzsshncvdceyuxtz65jer4

Disentangling Dynamical Quantum Coherences in the Fenna-Matthews-Olson Complex [article]

Hong-Guang Duan, Ajay Jha, Lipeng Chen, Vandana Tiwari, Richard J. Cogdell, Khuram Ashraf, Valentyn I. Prokhorenko, Michael Thorwart, R. J. Dwayne Miller
2021 arXiv   pre-print
of the fluctuations and reorganization dynamics of the protein matrix, or bath.  ...  In this work, we reaffirm this from a different point of view by finding that the true onset of electronic quantum coherence only occurs at extremely low temperatures of ~20 K.  ...  protein complexes.  ... 
arXiv:2104.01462v1 fatcat:cwqcewxab5b23exe3r6tbjc47m

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Célia M. Silveira, Lidia Zuccarello, Catarina Barbosa, Giorgio Caserta, Ingo Zebger, Peter Hildebrandt, Smilja Todorovic
2021 Molecules  
, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.  ...  This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules26164852 pmid:34443440 pmcid:PMC8398457 fatcat:egqiszutwvdoxmahhfblbhwsni

The mutational landscape of a prion-like domain

Benedetta Bolognesi, Andre J. Faure, Mireia Seuma, Jörn M. Schmiedel, Gian Gaetano Tartaglia, Ben Lehner
2019 Nature Communications  
Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS).  ...  We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity.  ...  While allowing us to understand the impact of mutations within low-complexity regions, these data provide the basis to understand by which mechanism protein inclusions drive pathogenesis.  ... 
doi:10.1038/s41467-019-12101-z pmid:31519910 pmcid:PMC6744496 fatcat:v4xku3rpxbfo3jgz5k3p2nmlky

Disentangling the low-energy states of the major light-harvesting complex of plants and their role in photoprotection

Tjaart P.J. Krüger, Cristian Ilioaia, Matthew P. Johnson, Alexander V. Ruban, Rienk van Grondelle
2014 Biochimica et Biophysica Acta - Bioenergetics  
The ability to dissipate large fractions of their absorbed light energy as heat is a vital photoprotective function of the peripheral light-harvesting pigment-protein complexes in photosystem II of plants  ...  The major component of this process, known as qE, is characterised by the appearance of low-energy (red-shifted) absorption and fluorescence bands.  ...  Krüger, et al., Disentangling the low-energy states of the major light-harvesting complex of plants and their role in photoprotection, Biochim. Biophys.  ... 
doi:10.1016/j.bbabio.2014.02.014 pmid:24560812 fatcat:knl6g222nraspcueooszs6cjd4

Exploring particle dynamics during self-organization processes via rotationally invariant latent representations [article]

Sergei V. Kalinin, Shuai Zhang, Mani Valleti, Harley Pyles, David Baker, James J. De Yoreo, Maxim Ziatdinov
2020 arXiv   pre-print
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic  ...  The latter allows for disentanglement of the particle orientation from other degrees of freedom and compensates for shifts.  ...  This methodology particularly relies on the recognized capability of the VAEs to reduce high-dimensional data sets to the low-dimensional continuous latent variables, and disentangle the representations  ... 
arXiv:2009.00783v1 fatcat:fgdbshantrgddbudsdwso67i3i
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