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Crystal structure of a snake venom cardiotoxin

B. Rees, J. P. Samama, J. C. Thierry, M. Gilibert, J. Fischer, H. Schweitz, M. Lazdunski, D. Moras
1987 Proceedings of the National Academy of Sciences of the United States of America  
Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules.  ...  Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the moleculq. Hydrophobic residues are clustered in two distinct areas.  ...  In conclusion, the 3D structures of neurotoxin and cardiotoxin are similar but not identical, and the observed differences may provide a clue to understanding the variation in the physiological effects  ... 
doi:10.1073/pnas.84.10.3132 pmid:3472200 pmcid:PMC304822 fatcat:rdved42uhnczzncjxshtohphou

Architecture and self-assembly of the jumbo bacteriophage nuclear shell [article]

Thomas G Laughlin, Amar Deep, Amy M Prichard, Christian Seitz, Yajie Gu, Eray Enustun, Sergey Suslov, Kanika Khanna, Erica A Birkholz, Emily Armbruster, J. Andrew McCammon, Rommie E Amaro (+3 others)
2022 bioRxiv   pre-print
However, the principle composition and structure of this compartment remain unknown. Here, we find that the bacteriophage nuclear shell assembles primarily from one protein, termed chimallin.  ...  The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport,  ...  Molecular graphics and analyses was performed in part with UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization, and Informatics at the UCSF with support from National Institutes of  ... 
doi:10.1101/2022.02.14.480162 fatcat:tpyy5uivfbebpffaazqvbges6q

The Structure of the Lingo-1 Ectodomain, a Module Implicated in Central Nervous System Repair Inhibition

Lidia Mosyak, Andrew Wood, Brian Dwyer, Madhavan Buddha, Mark Johnson, Ann Aulabaugh, Xiaotian Zhong, Eleonora Presman, Susan Benard, Kerry Kelleher, James Wilhelm, Mark L. Stahl (+7 others)
2006 Journal of Biological Chemistry  
The structure, together with biophysical analysis of its solution properties, reveals that in the crystals and in solution Lingo-1 persistently associates with itself to form a stable tetramer and that  ...  Specifically, in the crystal structure protomers of Lingo-1 associate in a ring-shaped tetramer, with each LRR domain filling an open cleft in an adjacent protomer.  ...  Acknowledgements-We gratefully acknowledge x-ray resources provided by the Southeast Regional Collaborative Access Team 22-ID beamline at the Advanced Photon Source, Argonne National Laboratory.  ... 
doi:10.1074/jbc.m607314200 pmid:17005555 fatcat:o45rapzvzza73p7lb4i5ae5bqi

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus

Cedric Leyrat, Max Renner, Karl Harlos, Juha T. Huiskonen, Jonathan M. Grimes
2014 Structure  
The conservation of the Ca 2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses.  ...  Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca 2+ binding site.  ...  Helical, three-dimensional reconstruction of this tubule revealed an arrangement of subunits with a rise of 5.16 Å and a turn of À56.6 degrees ( Figure 4G ).  ... 
doi:10.1016/j.str.2013.10.013 pmid:24316400 pmcid:PMC3887258 fatcat:h4lk3wnhojbkliw6aaiff3bqsq

Quaternary organization of GPIb-IX complex and insights into Bernard-Soulier syndrome revealed by the structures of GPIb and a GPIb /GPIX chimera

P. A. McEwan, W. Yang, K. H. Carr, X. Mo, X. Zheng, R. Li, J. Emsley
2011 Blood  
The chimera (GPIbβ Eabc ), but not GPIbβ E , forms a tetramer in the crystal, revealing a quaternary interface between GPIbβ and GPIX.  ...  The structure of a chimera of GPIbβ E and three loops (a,b,c) taken from the GPIX ectodomain sequence was also determined.  ...  Rather than utilizing the LRR concave face this structure reveals interactions occur through the C-terminal cap of GPIbβ E and convex face loops of GPIX E .  ... 
doi:10.1182/blood-2011-05-356253 pmid:21908432 pmcid:PMC3217411 fatcat:obvz7e6pxrgmzky5ftqpi3kllu

Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems [chapter]

Didier Barradas-Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández-Recio
2018 Advances in Protein Chemistry and Structural Biology  
Indeed, structural characterization of protein-protein interactions at atomic resolution has many applications in biomedicine, from diagnosis and vaccine design, to drug discovery.  ...  the interacting molecules, and ii) scoring for the identification of the correct orientations.  ...  Still, many of the structures determined by this method are low-resolution and do not reveal the atomic details needed for most biological applications.  ... 
doi:10.1016/bs.apcsb.2017.06.003 pmid:29412997 fatcat:6dsojxsybrfrthdz3yhlqmplxu

Crystal Structure of ATVORF273, a New Fold for a Thermo- and Acido-Stable Protein from the Acidianus Two-Tailed Virus

Catarina Felisberto-Rodrigues, Stéphanie Blangy, Adeline Goulet, Gisle Vestergaard, Christian Cambillau, Roger A. Garrett, Miguel Ortiz-Lombardía, Narayanaswamy Srinivasan
2012 PLoS ONE  
To understand this intriguing phenomenon, we have undertaken structural studies of ATV virion proteins and here we present the crystal structure of one of these proteins, ATV ORF 273 .  ...  The crystal structure has properties typical of hyperthermostable proteins, including a relatively high number of salt bridges. However, the protein also exhibits flexible loops and surface pockets.  ...  We are also grateful to the staff of the ID14eh4 and ID29 beamlines for their support.  ... 
doi:10.1371/journal.pone.0045847 pmid:23056221 pmcid:PMC3466262 fatcat:6yzaydoyzjdxpknpefiq3wuylq

Viral tolerance in Aedes aegypti relies on the negative cooperativity between Toll5A and the cytokine ligand Spz1C [article]

Yoann Saucereau, Thomas H Wilson, Martin C. Moncrieffe, Steven W Hardwick, Dimitri Y Chirgadze, Maria Jose Marcaida, Nicholas J Gay, Monique Gangloff
2021 bioRxiv   pre-print
Binding of the first ligand alters receptor-receptor interactions and promotes asymmetric contacts in the vicinity of the Z-loop in Toll5A.  ...  Given the remarkable DENV-induced expression patterns of these proteins, our data rationalises how Spz1C upregulation might promote innate immunity in the midgut, and Toll5A upregulation, viral tolerance  ...  We also thank Joe for training in SEC-MALS and Dr Nathan Cowieson, for supporting the SEC-SAXS at B21 Diamond Light Source.  ... 
doi:10.1101/2021.09.06.459066 fatcat:rphxnjk3izbbhonmj32ohm4ypm

Visualizing large RNA molecules in solution

A. Gopal, Z. H. Zhou, C. M. Knobler, W. M. Gelbart
2011 RNA: A publication of the RNA Society  
Their equilibrium properties therefore reflect the average of an ensemble of structures.  ...  The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size.  ...  ACKNOWLEDGMENTS The measurements and analyses reported would not have been possible without extensive discussions with and timely support from the following people: Dr.  ... 
doi:10.1261/rna.027557.111 pmid:22190747 pmcid:PMC3264915 fatcat:ngcnol4tc5ewlc5xg6g2jvbqja

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment

Peter J. Munson, Raj K. Singh
1997 Protein Science  
Three lines of evidence support the significance and utility of the four-body potential for sequence-structure matching.  ...  Delaunay tessellation of the C"-atom representation of protein structure has been suggested as a means of defining multi-body interactions.  ...  DiFrancesco for a critical reading of our manuscript, and Dr. D. Carr who suggested appropriate references for the four-dimensional co-plots.  ... 
doi:10.1002/pro.5560060711 pmid:9232648 pmcid:PMC2143734 fatcat:2zgpwhoksnawphtmdzz7qtwklq

IntegratingIn SilicoPrediction Methods, Molecular Docking, and Molecular Dynamics Simulation to Predict the Impact of ALK Missense Mutations in Structural Perspective

C. George Priya Doss, Chiranjib Chakraborty, Luonan Chen, Hailong Zhu
2014 BioMed Research International  
Understanding the likelihood of disease causing mutations in complex diseases as pathogenic or neutral remains as a major task and even impossible in the structural context because of its time consuming  ...  Combination of computational methods provides a way in understanding the impact of deleterious mutations in altering the protein drug targets and eventually leading to variable patient's drug response.  ...  The authors take this opportunity to thank the management of VIT and Galgotias University for providing the facilities and encouragement to carry out this work.  ... 
doi:10.1155/2014/895831 pmid:25054154 pmcid:PMC4098886 fatcat:je2xxldub5a7lm3pnnurdeplca

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes [article]

Dapeng Sun, Zhe Sang, Jeff Kim, Yufei Xiang, Tomer Cohen, Anna K Belford, Alexis Huet, James F Conway, Ji Sun, Derek Taylor, Cheng Zhang, Wei Huang (+1 others)
2021 biorxiv/medrxiv  
Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs.  ...  There is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2.  ...  This work was performed in part at the National Center for cryo-EM Access and Training (NCCAT) and the Simons Electron Microscopy Center located at the New York Structural Biology Center, supported in  ... 
doi:10.1101/2021.03.09.434592 pmid:33758850 pmcid:PMC7987009 fatcat:lcdecdjwxjbmvkrc7kzyszzupm

Three-dimensional femtosecond laser processing for lab-on-a-chip applications

Felix Sima, Koji Sugioka, Rebeca Martínez Vázquez, Roberto Osellame, Lóránd Kelemen, Pal Ormos
2018 Nanophotonics  
This review paper describes the principles and applications of femtosecond laser 3D micro- and nanofabrication for lab-on-a-chip applications.  ...  Subtractive processing can realize the direct fabrication of 3D microfluidics, micromechanics, microelectronics, and photonic microcomponents in glass.  ...  Simple spherical lenses [127] and concave-convex lenses with improved imaging and focusing performance [128] were already developed.  ... 
doi:10.1515/nanoph-2017-0097 fatcat:hhyatg6d4rdp7hewribjaicehy

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap

Roger Abseher, Lennard Horstink, Cornelis W. Hilbers, Michael Nilges
1998 Proteins: Structure, Function, and Bioinformatics  
We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility.  ...  Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics.  ...  ACKNOWLEDGMENTS The authors thank Daan van Aalten for stimulating discussions about the essential dynamics analysis and Rob Hooft and Gert Vriend for the excellent support with the WHATIF package.  ... 
doi:10.1002/(sici)1097-0134(19980601)31:4<370::aid-prot4>3.3.co;2-x pmid:9626697 fatcat:4ca4o6ogczegvhussxo5r4y624

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap

Roger Abseher, Lennard Horstink, Cornelis W. Hilbers, Michael Nilges
1998 Proteins: Structure, Function, and Bioinformatics  
We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility.  ...  Large concerted motions of proteins which span its "essential space," are an important component of protein dynamics.  ...  ACKNOWLEDGMENTS The authors thank Daan van Aalten for stimulating discussions about the essential dynamics analysis and Rob Hooft and Gert Vriend for the excellent support with the WHATIF package.  ... 
doi:10.1002/(sici)1097-0134(19980601)31:4<370::aid-prot4>3.0.co;2-m pmid:9626697 fatcat:mihfkqyl2fgp5l4acyooyrpwx4
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