scholarly journals Observation of unphosphorylated STAT3 core protein binding to targetdsDNA by PEMSA and X-ray crystallography

FEBS Letters ◽  
2013 ◽  
Vol 587 (7) ◽  
pp. 833-839 ◽  
Author(s):  
Edwin Nkansah ◽  
Rahi Shah ◽  
Gavin W. Collie ◽  
Gary N. Parkinson ◽  
Jonathan Palmer ◽  
...  
Keyword(s):  
Protein Binding ◽  
Core Protein ◽  
X Ray ◽  
X Ray Crystallography

Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules

2016 ◽  
Vol 45 (30) ◽  
pp. 12206-12214 ◽  
Author(s):  
Marco Caterino ◽  
Ariel A. Petruk ◽  
Alessandro Vergara ◽  
Giarita Ferraro ◽  
Daniela Marasco ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Binding ◽  
Binding Sites ◽  
Raman Microspectroscopy ◽  
Rnase A ◽  
Protein Binding Sites ◽  
X Ray ◽  
X Ray Crystallography ◽  
Model Protein ◽  
Circular Dichroïsm

Mass spectrometry, Raman microspectroscopy, circular dichroism and X-ray crystallography have been used to investigate the reaction of CO-releasing molecule Cs2IrCl5CO with the model protein RNase A.

scholarly journals 2.7 Å cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity

2020 ◽  
Vol 6 (16) ◽  
pp. eaay6410 ◽  
Author(s):  
Dilip Kumar ◽  
Xinzhe Yu ◽  
Sue E. Crawford ◽  
Rodolfo Moreno ◽  
Joanita Jakana ◽  
...  
Keyword(s):  
Core Protein ◽  
Messenger Rnas ◽  
Helicase Activity ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Rna Triphosphatase ◽  
Modular Domain ◽  
Biochemical Analyses ◽  
Nascent Transcripts

In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo–electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.

scholarly journals Small Molecules Bound to Unique Sites in the Target Protein Binding Cleft of Calcium-Bound S100B As Characterized by Nuclear Magnetic Resonance and X-ray Crystallography

Biochemistry ◽  
2009 ◽  
Vol 48 (26) ◽  
pp. 6202-6212 ◽  
Author(s):  
Thomas H. Charpentier ◽  
Paul T. Wilder ◽  
Melissa A. Liriano ◽  
Kristen M. Varney ◽  
Shijun Zhong ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Protein Binding ◽  
Small Molecules ◽  
Target Protein ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Cleft ◽  
Nuclear Magnetic

β2 integrin phosphorylation on Thr758 acts as a molecular switch to regulate 14-3-3 and filamin binding

Blood ◽  
2008 ◽  
Vol 112 (5) ◽  
pp. 1853-1862 ◽  
Author(s):  
Heikki Takala ◽  
Elisa Nurminen ◽  
Susanna M. Nurmi ◽  
Maria Aatonen ◽  
Tomas Strandin ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Protein Binding ◽  
Immune Cell ◽  
Phosphorylation Site ◽  
Molecular Switch ◽  
X Ray ◽  
X Ray Crystallography ◽  
Β2 Integrin ◽  
Coated Surfaces ◽  
Β2 Integrins

Abstract Leukocyte integrins of the β2 family are essential for immune cell-cell adhesion. In activated cells, β2 integrins are phosphorylated on the cytoplasmic Thr758, leading to 14-3-3 protein recruitment to the β2 integrin. The mutation of this phosphorylation site impairs cell adhesion, actin reorganization, and cell spreading. Thr758 is contained in a Thr triplet of β2 that also mediates binding to filamin. Here, we investigated the binding of filamin, talin, and 14-3-3 proteins to phosphorylated and unphosphorylated β2 integrins by biochemical methods and x-ray crystallography. 14-3-3 proteins bound only to the phosphorylated integrin cytoplasmic peptide, with a high affinity (Kd, 261 nM), whereas filamin bound only the unphosphorylated integrin cytoplasmic peptide (Kd, 0.5 mM). Phosphorylation did not regulate talin binding to β2 directly, but 14-3-3 was able to outcompete talin for the binding to phosphorylated β2 integrin. X-ray crystallographic data clearly explained how phosphorylation eliminated filamin binding and induced 14-3-3 protein binding. Filamin knockdown in T cells led to an increase in stimulated cell adhesion to ICAM-1–coated surfaces. Our results suggest that the phosphorylation of β2 integrins on Thr758 acts as a molecular switch to inhibit filamin binding and allow 14-3-3 protein binding to the integrin cytoplasmic domain, thereby modulating T-cell adhesion.

scholarly journals Perturbation of ACE2 structural ensembles by SARS-CoV-2 spike protein binding

2021 ◽  
Author(s):  
Arzu Uyar ◽  
Alex Dickson
Keyword(s):  
Protein Binding ◽  
Machine Learning Method ◽  
Learning Method ◽  
Protein Interface ◽  
Linear Discriminant ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Ensembles ◽  
Dynamics Simulations ◽  
Tailspike Protein

AbstractThe human ACE2 enzyme serves as a critical first recognition point of coronaviruses, including SARS-CoV-2. In particular, the extracellular domain of ACE2 interacts directly with the S1 tailspike protein of the SARS-CoV-2 virion through a broad protein-protein interface. Although this interaction has been characterized by X-ray crystallography and Cryo-EM, these structures do not reveal significant differences in ACE2 structure upon S1 protein binding. In this work, using several all-atom molecular dynamics simulations, we show persistent differences in ACE2 structure upon binding. These differences are determined with the Linear Discriminant Analysis (LDA) machine learning method and validated using independent training and testing datasets, including long trajectories generated by D. E. Shaw Research on the Anton 2 supercomputer. In addition, long trajectories for 78 potent ACE2-binding compounds, also generated by D. E. Shaw Research, were projected onto the LDA classification vector in order to determine whether the ligand-bound ACE2 structures were compatible with S1 protein binding. This allows us to predict which compounds are “apo-like” vs “complex-like”, as well as to pinpoint long-range ligand-induced allosteric changes of ACE2 structure.

New palladium(II) complexes of 3-methoxysalicylaldehyde-4(N)-substituted thiosemicarbazones: Synthesis, spectroscopy, X-ray crystallography and DNA/protein binding study

Polyhedron ◽  
2014 ◽  
Vol 80 ◽  
pp. 97-105 ◽  
Author(s):  
P. Kalaivani ◽  
C. Umadevi ◽  
R. Prabhakaran ◽  
F. Dallemer ◽  
P.S. Mohan ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Study ◽  
X Ray ◽  
X Ray Crystallography

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

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