scholarly journals Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

2015 ◽  
Vol 112 (29) ◽  
pp. E3806-E3815 ◽  
Author(s):  
Keenan C. Taylor ◽  
Massimo Buvoli ◽  
Elif Nihal Korkmaz ◽  
Ada Buvoli ◽  
Yuqing Zheng ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Structural Similarity ◽  
Thick Filament ◽  
Biological Properties ◽  
Stable States ◽  
Filament Assembly ◽  
High Structural Similarity ◽  
Heptad Repeats ◽  
Local Relaxation ◽  
Molecular Hinge

The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

scholarly journals Hydrophobicity variations along the surface of the coiled-coil rod may mediate striated muscle myosin assembly in Caenorhabditis elegans.

1996 ◽  
Vol 135 (2) ◽  
pp. 371-382 ◽  
Author(s):  
P E Hoppe ◽  
R H Waterston
Keyword(s):  
Caenorhabditis Elegans ◽  
Striated Muscle ◽  
Coiled Coil ◽  
Thick Filament ◽  
Surface Hydrophobicity ◽  
Filament Assembly ◽  
Thick Filaments ◽  
Characteristic Variation ◽  
Muscle Myosin

Caenorhabditis elegans body wall muscle contains two isoforms of myosin heavy chain, MHC A and MHC B, that differ in their ability to initiate thick filament assembly. Whereas mutant animals that lack the major isoform, MHC B, have fewer thick filaments, mutant animals that lack the minor isoform, MHC A, contain no normal thick filaments. MHC A, but not MHC B, is present at the center of the bipolar thick filament where initiation of assembly is thought to occur (Miller, D.M.,I. Ortiz, G.C. Berliner, and H.F. Epstein. 1983. Cell. 34:477-490). We mapped the sequences that confer A-specific function by constructing chimeric myosins and testing them in vivo. We have identified two distinct regions of the MHC A rod that are sufficient in chimeric myosins for filament initiation function. Within these regions, MHC A displays a more hydrophobic rod surface, making it more similar to paramyosin, which forms the thick filament core. We propose that these regions play an important role in filament initiation, perhaps mediating close contacts between MHC A and paramyosin in an antiparallel arrangement at the filament center. Furthermore, our analysis revealed that all striated muscle myosins show a characteristic variation in surface hydrophobicity along the length of the rod that may play an important role in driving assembly and determining the stagger at which dimers associate.

scholarly journals A Structural Model for Phosphorylation Control of Dictyostelium Myosin II Thick Filament Assembly

1999 ◽  
Vol 147 (5) ◽  
pp. 1039-1048 ◽  
Author(s):  
Wenchuan Liang ◽  
Hans M. Warrick ◽  
James A. Spudich
Keyword(s):  
Structural Model ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Thick Filament ◽  
Tail Region ◽  
Filament Assembly ◽  
Dictyostelium Myosin ◽  
Thick Filaments ◽  
Coil Structure

Myosin II thick filament assembly in Dictyostelium is regulated by phosphorylation at three threonines in the tail region of the molecule. Converting these three threonines to aspartates (3×Asp myosin II), which mimics the phosphorylated state, inhibits filament assembly in vitro, and 3×Asp myosin II fails to rescue myosin II–null phenotypes. Here we report a suppressor screen of Dictyostelium myosin II–null cells containing 3×Asp myosin II, which reveals a 21-kD region in the tail that is critical for the phosphorylation control. These data, combined with new structural evidence from electron microscopy and sequence analyses, provide evidence that thick filament assembly control involves the folding of myosin II into a bent monomer, which is unable to incorporate into thick filaments. The data are consistent with a structural model for the bent monomer in which two specific regions of the tail interact to form an antiparallel tetrameric coiled–coil structure.

scholarly journals Microwave Imaging of Breast Skin Utilizing Elliptical UWB Antenna and Reverse Problems Algorithm

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 647
Author(s):  
Sameer Alani ◽  
Zahriladha Zakaria ◽  
Tale Saeidi ◽  
Asmala Ahmad ◽  
Muhammad Ali Imran ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Imaging System ◽  
Signal Transmission ◽  
Similarity Index ◽  
Structural Similarity ◽  
Microwave Imaging ◽  
Ultra Wideband ◽  
Uwb Antenna ◽  
System A ◽  
High Structural Similarity

Skin cancer is one of the most widespread and fast growing of all kinds of cancer since it affects the human body easily due to exposure to the Sun’s rays. Microwave imaging has shown better outcomes with higher resolution, faster processing time, mobility, and less cutter and artifact effects. A miniaturized elliptical ultra-wideband (UWB) antenna and its semi-spherical array arrangement were used for signal transmission and reception from the defected locations in the breast skin. Several conditions such as various arrays of three, six, and nine antenna elements, smaller tumor, multi-tumors, and skin on a larger breast sample of 30 cm were considered. To assess the ability of the system, a breast shape container with a diameter of 130 mm and height of 60 mm was 3D printed and then filled with fabricated skin and breast fat to perform the experimental investigation. An improved modified time-reversal algorithm (IMTR) was used to recreate 2D images of tumors with the smallest radius of 1.75 mm in any location within the breast skin. The reconstructed images using both simulated and experimental data verified that the system can be a reliable imaging system for skin cancer diagnosis having a high structural similarity index and resolution.

scholarly journals Different modes of internalization of apoptotic alkyl-lysophospholipid and cell-rescuing lysophosphatidylcholine

2003 ◽  
Vol 374 (3) ◽  
pp. 747-753 ◽  
Author(s):  
Arnold H. van der LUIT ◽  
Marianne BUDDE ◽  
Marcel VERHEIJ ◽  
Wim J. van BLITTERSWIJK
Keyword(s):  
Lipid Rafts ◽  
De Novo ◽  
Structural Similarity ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Chemotherapeutic Drugs ◽  
Alternative Substrate ◽  
High Structural Similarity ◽  
Additional Cell ◽  
Cell Membrane Level

The synthetic alkyl-lysophospholipid (ALP), Et-18-OCH3 (1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine), can induce apoptosis in tumour cells. Unlike conventional chemotherapeutic drugs, ALP acts at the cell-membrane level. We have reported previously that ALP is internalized, and interferes with phosphatidylcholine (PC) biosynthesis de novo, which appeared to be essential for survival in lymphoma cells [Van der Luit, Budde, Ruurs, Verheij and Van Blitterswijk (2002) J. Biol. Chem. 277, 39541–39547]. Here, we report that, in HeLa cells, ALP accumulates in lipid rafts, and that internalization is inhibited by low temperature, monensin, disruption of lipid rafts and expression of a dominant-negative mutant of dynamin bearing a replacement of Lys44 with alanine (K44A). Thus ALP is internalized via raft- and dynamin-mediated endocytosis. Dynamin-K44A alleviated the ALP-induced inhibition of PC synthesis and rescued the cells from apoptosis induction. Additional cell rescue was attained by exogenous lysoPC, which after internalization serves as an alternative substrate for PC synthesis (through acylation). Unlike ALP, and despite the high structural similarity to ALP, lysoPC uptake did not occur via lipid rafts and did not depend on functional dynamin, indicating no involvement of endocytosis. Albumin back-extraction experiments suggested that (radiolabelled) lysoPC undergoes transbilayer movement (flipping). We conclude that ALP is internalized by endocytosis via lipid rafts to cause apoptosis, while exogenous cell-rescuing lysoPC traverses the plasma membrane outside rafts by flipping. Additionally, our data imply the importance of ether bonds in lyso-phospholipids, such as in ALP, for partitioning in lipid rafts.

A Hybrid Approach Based on Self-Organizing Neural Networks and the K-Nearest Neighbors Method to Study Molecular Similarity

2011 ◽  
Vol 1 (1) ◽  
pp. 75-95 ◽  
Author(s):  
Abdelmalek Amine ◽  
Zakaria Elberrichi ◽  
Michel Simonet ◽  
Ali Rahmouni
Keyword(s):  
Neural Networks ◽  
Molecular Similarity ◽  
Learning Algorithm ◽  
Hybrid Approach ◽  
Structural Similarity ◽  
Biological Properties ◽  
Learning Tools ◽  
K Nearest Neighbors ◽  
Virtual Chemical Libraries ◽  
Self Organizing

The “Molecular Similarity Principle” states that structurally similar molecules tend to have similar properties—physicochemical and biological. The question then is how to define “structural similarity” algorithmically and confirm its usefulness. Within this framework, research by similarity is registered, which is a practical approach to identify molecule candidates (to become drugs or medicines) from databases or virtual chemical libraries by comparing the compounds two by two. Many statistical models and learning tools have been developed to correlate the molecules’ structure with their chemical, physical or biological properties. The role of data mining in chemistry is to evaluate “hidden” information in a set of chemical data. Each molecule is represented by a vector of great dimension (using molecular descriptors), the applying a learning algorithm on these vectors. In this paper, the authors study the molecular similarity using a hybrid approach based on Self-Organizing Neural Networks and Knn Method.

scholarly journals Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1633 ◽  
Author(s):  
Giel Stalmans ◽  
Anastasia V. Lilina ◽  
Pieter-Jan Vermeire ◽  
Jan Fiala ◽  
Petr Novák ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Molecular Model ◽  
Coiled Coil ◽  
Cross Linking ◽  
Specific Interactions ◽  
Molecular Architecture ◽  
Filament Assembly ◽  
Assembly Mechanism ◽  
Recombinant Fragments ◽  
Chemical Cross Linking

The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal ‘head-to-tail’ interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.

scholarly journals Screening of Heteroaromatic Scaffolds against Cystathionine Beta-Synthase Enables Identification of Substituted Pyrazolo[3,4-c]Pyridines as Potent and Selective Orthosteric Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3739
Author(s):  
Anna-Maria Fantel ◽  
Vassilios Myrianthopoulos ◽  
Anastasios Georgoulis ◽  
Nikolaos Lougiakis ◽  
Iliana Zantza ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Structural Similarity ◽  
Binding Mode ◽  
Aminoacetic Acid ◽  
Heteroaromatic Compounds ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
High Structural Similarity ◽  
Key Enzyme ◽  
Inhibitory Potential

Cystathionine β-synthase (CBS) is a key enzyme in the production of the signaling molecule hydrogen sulfide, deregulation of which is known to contribute to a range of serious pathological states. Involvement of hydrogen sulfide in pathways of paramount importance for cellular homeostasis renders CBS a promising drug target. An in-house focused library of heteroaromatic compounds was screened for CBS modulators by the methylene blue assay and a pyrazolopyridine derivative with a promising CBS inhibitory potential was discovered. The compound activity was readily comparable to the most potent CBS inhibitor currently known, aminoacetic acid, while a promising specificity over the related cystathionine γ-lyase was identified. To rule out any possibility that the inhibitor may bind the enzyme regulatory domain due to its high structural similarity with cofactor s-adenosylmethionine, differential scanning fluorimetry was employed. A sub-scaffold search guided follow-up screening of related compounds, providing preliminary structure-activity relationships with respect to requisites for efficient CBS inhibition by this group of heterocycles. Subsequently, a hypothesis regarding the exact binding mode of the inhibitor was devised on the basis of the available structure-activity relationships (SAR) and a deep neural networks analysis and further supported by induced-fit docking calculations.

scholarly journals Crystal Structures of Putative Flavin Dependent Monooxygenase from Alicyclobacillus Acidocaldarius

Crystals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 548 ◽  
Author(s):  
Moon ◽  
Shin ◽  
Choe
Keyword(s):  
Crystal Structures ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Bound State ◽  
Flavin Mononucleotide ◽  
Biological Processes ◽  
Substrate Binding Pocket ◽  
High Structural Similarity ◽  
Alicyclobacillus Acidocaldarius ◽  
Group D

Flavin dependent monooxygenases catalyze various reactions to play a key role in biological processes, such as catabolism, detoxification, and biosynthesis. Group D flavin dependent monooxygenases are enzymes with an Acyl-CoA dehydrogenase (ACAD) fold and use Flavin adenine dinucleotide (FAD) or Flavin mononucleotide (FMN) as a cofactor. In this research, crystal structures of Alicyclobacillus acidocaldarius protein formerly annotated as an ACAD were determined in Apo and FAD bound state. Although our structure showed high structural similarity to other ACADs, close comparison of substrate binding pocket and phylogenetic analysis showed that this protein is more closely related to other bacterial group D flavin dependent monooxygenases, such as DszC (sulfoxidase) and DnmZ and Kijd3 (nitrososynthases).

scholarly journals Intramolecular Repression of Mouse Heat Shock Factor 1

1998 ◽  
Vol 18 (2) ◽  
pp. 906-918 ◽  
Author(s):  
Thomas Farkas ◽  
Yulia A. Kutskova ◽  
Vincenzo Zimarino
Keyword(s):  
Heat Shock ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Coiled Coil ◽  
Heat Shock Factor ◽  
Heat Shock Factor 1 ◽  
Reticulocyte Lysate ◽  
Heptad Repeats ◽  
Intramolecular Mechanism

ABSTRACT The pathway leading to transcriptional activation of heat shock genes involves a step of heat shock factor 1 (HSF1) trimerization required for high-affinity binding of this activator protein to heat shock elements (HSEs) in the promoters. Previous studies have shown that in vivo the trimerization is negatively regulated at physiological temperatures by a mechanism that requires multiple hydrophobic heptad repeats (HRs) which may form a coiled coil in the monomer. To investigate the minimal requirements for negative regulation, in this work we have examined mouse HSF1 translated in rabbit reticulocyte lysate or extracted from Escherichia coli after limited expression. We show that under these conditions HSF1 behaves as a monomer which can be induced by increases in temperature to form active HSE-binding trimers and that mutations of either HR region cause activation in both systems. Furthermore, temperature elevations and acidic buffers activate purified HSF1, and mild proteolysis excises fragments which form HSE-binding oligomers. These results suggest that oligomerization can be repressed in the monomer, as previously proposed, and that repression can be relieved in the apparent absence of regulatory proteins. An intramolecular mechanism may be central for the regulation of this transcription factor in mammalian cells, although not necessarily sufficient.

Exploring RNA-ligand interactions

2009 ◽  
Vol 81 (2) ◽  
pp. 263-272 ◽  
Author(s):  
Yitzhak Tor
Keyword(s):  
Therapeutic Potential ◽  
Protein Complexes ◽  
Nucleoside Analogs ◽  
Structural Similarity ◽  
Absorption Bands ◽  
Rna Molecules ◽  
Design And Synthesis ◽  
Cell Functions ◽  
High Structural Similarity ◽  
Ligand Interactions

RNA molecules play essential roles in biological processes and are evolving as important targets for therapeutic intervention. Small molecules that specifically bind unique RNA sites and prevent the formation of functional RNA folds or RNA-protein complexes can modulate cell functions and can become of therapeutic potential. To explore such recognition events and to fabricate discovery assays, effective biophysical tools need to be advanced. When carefully designed, new fluorescent nucleosides can serve an unparalleled role in such studies. Our criteria for "ideal" fluorescent nucleoside analogs include: (a) high structural similarity to the native nucleobases to faithfully mimic their size and shape, as well as hybridization and recognition properties; (b) red-shifted absorption bands; (c) red-shifted emission band (preferably in the visible); (d) a reasonable emission quantum efficiency; and, importantly, (e) sensitivity of their photophysical parameters to changes in the microenvironment. Our program, aimed at the development of new emissive isomorphic nucleoside analogs, has yielded several useful nucleobases. Selected analogs were implemented in fluorescence-based assays. This overview presents the motivation for this work by introducing RNA-ligand interactions and discusses the design and synthesis of fluorescent isosteric nucleobase analogs and their utilization for the fabrication of "real-time" fluorescence-based biophysical assays.

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