Reversal in solvatochromism in some novel styrylpyridinium dyes having a hydrophobic cleft

2007 ◽  
Vol 68 (3) ◽  
pp. 757-762 ◽  
Author(s):  
Mallika Panigrahi ◽  
Sukalyan Dash ◽  
Sabita Patel ◽  
P.K. Behera ◽  
B.K. Mishra
Keyword(s):  
Hydrophobic Cleft ◽  
Styrylpyridinium Dyes

Bischromophoric styrylpyridinium dyes

2007 ◽  
Vol 67 (2) ◽  
pp. 306-315 ◽  
Author(s):  
Beata Jędrzejewska ◽  
Janina Kabatc ◽  
Borys Ośmiałowski ◽  
Jerzy Pączkowski
Keyword(s):  
Styrylpyridinium Dyes

Solvatochromic behavior of some α-styrylpyridinium dyes

2014 ◽  
Vol 125 ◽  
pp. 422-430 ◽  
Author(s):  
Sarita Tripathy ◽  
Partha Sarathi Guru ◽  
Sukalyan Dash
Keyword(s):  
Styrylpyridinium Dyes

scholarly journals Identification of a Hydrophobic Cleft in the LytTR Domain of AgrA as a Locus for Small Molecule Interactions That Inhibit DNA Binding

Biochemistry ◽  
2012 ◽  
Vol 51 (50) ◽  
pp. 10035-10043 ◽  
Author(s):  
Paul G. Leonard ◽  
Ian F. Bezar ◽  
David J. Sidote ◽  
Ann M. Stock
Keyword(s):  
Dna Binding ◽  
Small Molecule ◽  
Molecule Interactions ◽  
Hydrophobic Cleft

scholarly journals Cryo-EM structure of alpha-synuclein fibrils

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Ricardo Guerrero-Ferreira ◽  
Nicholas MI Taylor ◽  
Daniel Mona ◽  
Philippe Ringler ◽  
Matthias E Lauer ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Lewy Bodies ◽  
Alpha Synuclein ◽  
Diagnosis And Treatment ◽  
Lewy Neurites ◽  
Cryo Electron Microscopy ◽  
High Concentrations ◽  
Hydrophobic Cleft

Parkinson’s disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in affected neurons. Its hallmark are intracellular inclusions called Lewy bodies and Lewy neurites. We here report the structure of cytotoxic alpha-synuclein fibrils (residues 1–121), determined by cryo-electron microscopy at a resolution of 3.4 Å. Two protofilaments form a polar fibril composed of staggered β-strands. The backbone of residues 38 to 95, including the fibril core and the non-amyloid component region, are well resolved in the EM map. Residues 50–57, containing three of the mutation sites associated with familial synucleinopathies, form the interface between the two protofilaments and contribute to fibril stability. A hydrophobic cleft at one end of the fibril may have implications for fibril elongation, and invites for the design of molecules for diagnosis and treatment of synucleinopathies.

Dynamics of Zika Virus Capsid Protein in Solution: The Properties and Exposure of the Hydrophobic Cleft Are Controlled by the α-Helix 1 Sequence

Biochemistry ◽  
2019 ◽  
Author(s):  
Maria A. Morando ◽  
Glauce M. Barbosa ◽  
Christine Cruz-Oliveira ◽  
Andrea T. Da Poian ◽  
Fabio C. L. Almeida
Keyword(s):  
Capsid Protein ◽  
Zika Virus ◽  
Virus Capsid ◽  
Α Helix ◽  
Hydrophobic Cleft ◽  
Virus Capsid Protein

Oxidation of Styrylpyridinium Dyes by Permanganate Ion

1994 ◽  
Vol 67 (12) ◽  
pp. 3289-3296 ◽  
Author(s):  
Sukalyan Dash ◽  
Bijay K. Mishra
Keyword(s):  
Styrylpyridinium Dyes ◽  
Permanganate Ion

scholarly journals Fluorescence Response Mechanism of D-Glucose Selectivity for Supramolecular Probes Composed of Phenylboronic-acid-modified β-Cyclodextrin and Styrylpyridinium Dyes

2007 ◽  
Vol 23 (10) ◽  
pp. 1167-1171 ◽  
Author(s):  
Iwao SUZUKI ◽  
Akiyo YAMAUCHI ◽  
Yoshiko SAKASHITA ◽  
Kazuaki HIROSE ◽  
Takashi MIURA ◽  
...  
Keyword(s):  
Phenylboronic Acid ◽  
Response Mechanism ◽  
Fluorescence Response ◽  
Styrylpyridinium Dyes

scholarly journals Structural Insight into the Binding of TGIF1 to SIN3A PAH2 Domain through a C-Terminal Amphipathic Helix

2021 ◽  
Vol 22 (23) ◽  
pp. 12631
Author(s):  
Xiaoling He ◽  
Yao Nie ◽  
Heng Zhou ◽  
Rui Hu ◽  
Ying Li ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Structural Basis ◽  
Hydrophobic Core ◽  
Amphipathic Helix ◽  
Structural Insight ◽  
Function Relationship ◽  
And Function ◽  
Key Residues ◽  
Hydrophobic Cleft ◽  
Insight Into

TGIF1 is a transcriptional repressor playing crucial roles in human development and function and is associated with holoprosencephaly and various cancers. TGIF1-directed transcriptional repression of specific genes depends on the recruitment of corepressor SIN3A. However, to date, the exact region of TGIF1 binding to SIN3A was not clear, and the structural basis for the binding was unknown. Here, we demonstrate that TGIF1 utilizes a C-terminal domain (termed as SIN3A-interacting domain, SID) to bind with SIN3A PAH2. The TGIF1 SID adopts a disordered structure at the apo state but forms an amphipathic helix binding into the hydrophobic cleft of SIN3A PAH2 through the nonpolar side at the holo state. Residues F379, L382 and V383 of TGIF1 buried in the hydrophobic core of the complex are critical for the binding. Moreover, homodimerization of TGIF1 through the SID and key residues of F379, L382 and V383 was evidenced, which suggests a dual role of TGIF1 SID and a correlation between dimerization and SIN3A-PAH2 binding. This study provides a structural insight into the binding of TGIF1 with SIN3A, improves the knowledge of the structure–function relationship of TGIF1 and its homologs and will help in recognizing an undiscovered SIN3A-PAH2 binder and developing a peptide inhibitor for cancer treatment.

scholarly journals Electrostatic Forces Mediate the Specificity of RHO GTPase-GDI Interactions

2021 ◽  
Vol 22 (22) ◽  
pp. 12493
Author(s):  
Niloufar Mosaddeghzadeh ◽  
Neda S. Kazemein Jasemi ◽  
Jisca Majolée ◽  
Si-Cai Zhang ◽  
Peter L. Hordijk ◽  
...  
Keyword(s):  
Rho Gtpases ◽  
Rho Gtpase ◽  
Kinetic Mechanism ◽  
Membrane Extraction ◽  
Rho Protein ◽  
Switch Regions ◽  
Charged Clusters ◽  
Rho Family ◽  
Hydrophobic Cleft

Three decades of research have documented the spatiotemporal dynamics of RHO family GTPase membrane extraction regulated by guanine nucleotide dissociation inhibitors (GDIs), but the interplay of the kinetic mechanism and structural specificity of these interactions is as yet unresolved. To address this, we reconstituted the GDI-controlled spatial segregation of geranylgeranylated RHO protein RAC1 in vitro. Various biochemical and biophysical measurements provided unprecedented mechanistic details for GDI function with respect to RHO protein dynamics. We determined that membrane extraction of RHO GTPases by GDI occurs via a 3-step mechanism: (1) GDI non-specifically associates with the switch regions of the RHO GTPases; (2) an electrostatic switch determines the interaction specificity between the C-terminal polybasic region of RHO GTPases and two distinct negatively-charged clusters of GDI1; (3) a non-specific displacement of geranylgeranyl moiety from the membrane sequesters it into a hydrophobic cleft, effectively shielding it from the aqueous milieu. This study substantially extends the model for the mechanism of GDI-regulated RHO GTPase extraction from the membrane, and could have implications for clinical studies and drug development.

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