scholarly journals NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain

2006 ◽  
Vol 15 (11) ◽  
pp. 2552-2557 ◽  
Author(s):  
Hee-Chul Ahn ◽  
Yen T.H. Le ◽  
Partha S. Nagchowdhuri ◽  
Eugene F. DeRose ◽  
Cindy Putnam-Evans ◽  
...  
Keyword(s):  
Sh3 Domain ◽  
Conformational Ensemble

The Native State Conformational Ensemble of the SH3 Domain from α-Spectrin†

Biochemistry ◽  
1999 ◽  
Vol 38 (28) ◽  
pp. 8899-8906 ◽  
Author(s):  
Mourad Sadqi ◽  
Salvador Casares ◽  
María A. Abril ◽  
Obdulio López-Mayorga ◽  
Francisco Conejero-Lara ◽  
...  
Keyword(s):  
Sh3 Domain ◽  
Conformational Ensemble ◽  
Native State

In vitro binding activity between HCK SH3 domain and HIV-1 Nef protein

2011 ◽  
Vol 31 (3) ◽  
pp. 262-265
Author(s):  
Xiao-lin QIN ◽  
Chao-qi LIU ◽  
Dong-ming REN ◽  
Yong-qin ZHOU
Keyword(s):  
Sh3 Domain ◽  
Binding Activity ◽  
Hiv 1

scholarly journals The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

2021 ◽  
Vol 7 (17) ◽  
pp. eabf6106
Author(s):  
Weiwei He ◽  
Yen-Lin Chen ◽  
Lois Pollack ◽  
Serdal Kirmizialtin
Keyword(s):  
Structural Diversity ◽  
Conformational Ensemble ◽  
Structural Variations ◽  
Dna And Rna ◽  
X Ray Scattering ◽  
Double Stranded Dna ◽  
Binding Partners ◽  
Rna Duplexes ◽  
Dynamics Simulations ◽  
Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

scholarly journals Basic Residue Clusters in Intrinsically Disordered Regions of Peripheral Membrane Proteins: Modulating 2D Diffusion on Cell Membranes

Physchem ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 152-162
Author(s):  
Miquel Pons
Keyword(s):  
Membrane Proteins ◽  
Electrostatic Interactions ◽  
Lipid Membrane ◽  
Conformational Ensemble ◽  
Basic Residue ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Peripheral Membrane Proteins ◽  
Charged Residues ◽  
Disordered Regions

A large number of peripheral membrane proteins transiently interact with lipids through a combination of weak interactions. Among them, electrostatic interactions of clusters of positively charged amino acid residues with negatively charged lipids play an important role. Clusters of charged residues are often found in intrinsically disordered protein regions, which are highly abundant in the vicinity of the membrane forming what has been called the disordered boundary of the cell. Beyond contributing to the stability of the lipid-bound state, the pattern of charged residues may encode specific interactions or properties that form the basis of cell signaling. The element of this code may include, among others, the recognition, clustering, and selective release of phosphatidyl inositides, lipid-mediated protein-protein interactions changing the residence time of the peripheral membrane proteins or driving their approximation to integral membrane proteins. Boundary effects include reduction of dimensionality, protein reorientation, biassing of the conformational ensemble of disordered regions or enhanced 2D diffusion in the peri-membrane region enabled by the fuzzy character of the electrostatic interactions with an extended lipid membrane.

scholarly journals On the use of 3J-coupling NMR data to derive structural information on proteins

2021 ◽  
Vol 75 (1) ◽  
pp. 39-70
Author(s):  
Lorna J. Smith ◽  
Wilfred F. van Gunsteren ◽  
Bartosz Stankiewicz ◽  
Niels Hansen
Keyword(s):  
Protein Structure ◽  
Structural Information ◽  
Protein Structure Determination ◽  
High Sensitivity ◽  
Time Averaging ◽  
Conformational Ensemble ◽  
Torsional Angle ◽  
Conformational Variability ◽  
Egg White Lysozyme ◽  
Coupling Time

AbstractValues of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.

scholarly journals The temperature dependence of the hydrogen exchange in the SH3 domain of α-spectrin

FEBS Letters ◽  
2002 ◽  
Vol 527 (1-3) ◽  
pp. 86-90 ◽  
Author(s):  
M. Sadqi ◽  
S. Casares ◽  
O. López-Mayorga ◽  
F. Conejero-Lara
Keyword(s):  
Temperature Dependence ◽  
Hydrogen Exchange ◽  
Sh3 Domain

scholarly journals ANKRD54 preferentially selects Bruton’s Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library

PLoS ONE ◽  
2017 ◽  
Vol 12 (4) ◽  
pp. e0174909 ◽  
Author(s):  
Manuela O. Gustafsson ◽  
Dara K. Mohammad ◽  
Erkko Ylösmäki ◽  
Hyunseok Choi ◽  
Subhash Shrestha ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Sh3 Domain ◽  
Bruton’S Tyrosine Kinase ◽  
Bruton's Tyrosine Kinase ◽  
Src Homology 3 ◽  
Src Homology
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