scholarly journals Protein Conformational Dynamics of Homodimeric Hemoglobin Revealed by Combined Time-Resolved Spectroscopic Probes

ChemPhysChem ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 109-114 ◽  
Author(s):  
Jungkweon Choi ◽  
Srinivasan Muniyappan ◽  
John T. Wallis ◽  
William E. Royer ◽  
Hyotcherl Ihee
Keyword(s):  
Conformational Dynamics ◽  
Time Resolved ◽  
Protein Conformational Dynamics ◽  
Spectroscopic Probes

scholarly journals An interdomain bridge influences RNA binding of the human La protein

2018 ◽  
Vol 294 (5) ◽  
pp. 1529-1540 ◽  
Author(s):  
Stefano A. Marrella ◽  
Kerene A. Brown ◽  
Farnaz Mansouri-Noori ◽  
Jennifer Porat ◽  
Derek J. Wilson ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Polymerase Iii ◽  
Conformational Dynamics ◽  
Direct Interaction ◽  
Rna Recognition Motif ◽  
Binding Modes ◽  
Nuclear Retention ◽  
Time Resolved ◽  
La Protein ◽  
C Terminus

La proteins are RNA chaperones that perform various functions depending on distinct RNA-binding modes and their subcellular localization. In the nucleus, they help process UUU-3′OH–tailed nascent RNA polymerase III transcripts, such as pre-tRNAs, whereas in the cytoplasm they contribute to translation of poly(A)-tailed mRNAs. La accumulation in the nucleus and cytoplasm is controlled by several trafficking elements, including a canonical nuclear localization signal in the extreme C terminus and a nuclear retention element (NRE) in the RNA recognition motif 2 (RRM2) domain. Previous findings indicate that cytoplasmic export of La due to mutation of the NRE can be suppressed by mutations in RRM1, but the mechanism by which the RRM1 and RRM2 domains functionally cooperate is poorly understood. In this work, we use electromobility shift assays (EMSA) to show that mutations in the NRE and RRM1 affect binding of human La to pre-tRNAs but not UUU-3′OH or poly(A) sequences, and we present compensatory mutagenesis data supporting a direct interaction between the RRM1 and RRM2 domains. Moreover, we use collision-induced unfolding and time-resolved hydrogen–deuterium exchange MS analyses to study the conformational dynamics that occur when this interaction is intact or disrupted. Our results suggest that the intracellular distribution of La may be linked to its RNA-binding modes and provide the first evidence for a direct protein–protein interdomain interaction in La proteins.

scholarly journals Examining the conformational dynamics of macromolecules with time-resolved synchrotron X-ray ‘footprinting’

Structure ◽  
1997 ◽  
Vol 5 (7) ◽  
pp. 865-869 ◽  
Author(s):  
Mark R Chance ◽  
Bianca Sclavi ◽  
Sarah A Woodson ◽  
Michael Brenowitz
Keyword(s):  
Conformational Dynamics ◽  
Time Resolved ◽  
X Ray

scholarly journals A Complex Interplay of Anionic Phospholipid Binding Regulates 3′-Phosphoinositide-Dependent-Kinase-1 Homodimer Activation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Gloria de las Heras-Martínez ◽  
Véronique Calleja ◽  
Remy Bailly ◽  
Jean Dessolin ◽  
Banafshé Larijani ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Pi3k Pathway ◽  
Correlation Spectroscopy ◽  
Fluorescence Lifetime Imaging ◽  
Anionic Phospholipid ◽  
Direct Role ◽  
Time Resolved ◽  
Anionic Phospholipids ◽  
Spatio Temporal ◽  
Phosphoinositide Dependent Kinase

Abstract 3′-Phosphoinositide-dependent-Kinase-1 (PDK1) is a master regulator whereby its PI3-kinase-dependent dysregulation in human pathologies is well documented. Understanding the direct role for PtdIns(3,4,5)P3 and other anionic phospholipids in the regulation of PDK1 conformational dynamics and its downstream activation remains incomplete. Using advanced quantitative-time-resolved imaging (Fluorescence Lifetime Imaging and Fluorescence Correlation Spectroscopy) and molecular modelling, we show an interplay of antagonistic binding effects of PtdIns(3,4,5)P3 and other anionic phospholipids, regulating activated PDK1 homodimers. We demonstrate that phosphatidylserine maintains PDK1 in an inactive conformation. The dysregulation of the PI3K pathway affects the spatio-temporal and conformational dynamics of PDK1 and the activation of its downstream substrates. We have established a new anionic-phospholipid-dependent model for PDK1 regulation, depicting the conformational dynamics of multiple homodimer states. We show that the dysregulation of the PI3K pathway perturbs equilibrium between the PDK1 homodimer conformations. Our findings provide a role for the PtdSer binding site and its previously unrewarding role in PDK1 downregulation, suggesting a possible therapeutic strategy where the constitutively active dimer conformer of PDK1 may be rendered inactive by small molecules that drive it to its PtdSer-bound conformer.

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