scholarly journals Abstract P-36: Structural Analysis of Conformational Changes of Bacterial and Eukaryotic Tubulins

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S27-S28
Author(s):  
Liubov Makarova ◽  
Alena Korshunova
Keyword(s):  
Structural Analysis ◽  
Conformational Changes ◽  
Structural Changes ◽  
Dynamic Instability ◽  
Amino Acid Sequences ◽  
Anchor Point ◽  
Final State ◽  
Gtp Hydrolysis ◽  
Alpha Tubulin ◽  
Β Tubulin

Background: Eukaryotic α- and β-tubulin proteins stand out among tubulin-like proteins by their ability to form hollow dynamically unstable microtubules (MT) with 13 protofilaments. Microtubules are part of the cell cytoskeleton and play a key role in chromosome division in mitosis. A considerable amount of anticancer drugs works on microtubules level breaking its dynamic. But the mechanism of dynamic instability and works of these drugs remains unknown. Bacteria of the genus Prostecobacter have unique bacterial tubulins (BtubA/B) capable to form hollow dynamically unstable 5 protofilament MTs (miniMT). Instead of great differences, both tubulins have many common features. Eukaryotic tubulin was known to have structural changes through GTP hydrolysis (compactization for approximately 2 Å and a twist for 0,1˚). «Anchor point» structure in alpha-tubulin was noticed to be a fixed point in this movement. Methods: We performed comparative structural analysis of BtubA/B and α- and β-tubulin proteins using USCF Chimera10 and MEGA X software. This data was obtained due to a comparison of 3 structures of microtubules with different nucleotides [pdb6DPU, 6DPV, 6DPW] and two structures for bacterial tubulins (miniMT [pdb5o09] and BtubA/B-dimer [pdb2BTQ]). Results: We noticed that bacterial tubulins form shorter protofilaments in miniMT than eukaryotic ones. It can be explained as compaction in two sites instead of one site in eukaryotic MT. Also, the most motionless point of min MT turned out the same "anchor point." Phylogenetic analysis showed that this structure is very conservative in these orthologs. Moreover, the final state of both tubulins (GDP) repeats each other. Conclusion: Our results suggest that bacterial tubulin can have movements through GTP hydrolysis similar to eukaryotic one. And it means that despite different amino acid sequences, bacterial and eukaryotic tubulins have similar keys structures for dynamic instability.

scholarly journals Dominant-Lethal α-Tubulin Mutants Defective in Microtubule Depolymerization in Yeast

2001 ◽  
Vol 12 (12) ◽  
pp. 3973-3986 ◽  
Author(s):  
Kirk R. Anders ◽  
David Botstein
Keyword(s):  
Dynamic Instability ◽  
Time Lapse ◽  
Inducible Promoter ◽  
Spindle Pole ◽  
Yeast Cells ◽  
Microtubule Depolymerization ◽  
Gtp Hydrolysis ◽  
Mutant Proteins ◽  
Gtpase Activation ◽  
Β Tubulin

The dynamic instability of microtubules has long been understood to depend on the hydrolysis of GTP bound to β-tubulin, an event stimulated by polymerization and necessary for depolymerization. Crystallographic studies of tubulin show that GTP is bound by β-tubulin at the longitudinal dimer-dimer interface and contacts particular α-tubulin residues in the next dimer along the protofilament. This structural arrangement suggests that these contacts could account for assembly-stimulated GTP hydrolysis. As a test of this hypothesis, we examined, in yeast cells, the effect of mutating the α-tubulin residues predicted, on structural grounds, to be involved in GTPase activation. Mutation of these residues to alanine (i.e., D252A and E255A) created poisonous α-tubulins that caused lethality even as minor components of the α-tubulin pool. When the mutant α-tubulins were expressed from the galactose-inducible promoter ofGAL1, cells rapidly acquired aberrant microtubule structures. Cytoplasmic microtubules were largely bundled, spindle assembly was inhibited, preexisting spindles failed to completely elongate, and occasional, stable microtubules were observed unattached to spindle pole bodies. Time-lapse microscopy showed that microtubule dynamics had ceased. Microtubules containing the mutant proteins did not depolymerize, even in the presence of nocodazole. These data support the view that α-tubulin is a GTPase-activating protein that acts, during microtubule polymerization, to stimulate GTP hydrolysis in β-tubulin and thereby account for the dynamic instability of microtubules.

scholarly journals Does Covera-19 know ‘when to hold ‘em or ‘when to fold ‘em? A translational thought experiment

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gerald Dieter Griffin
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Structural Integrity ◽  
Thought Experiment ◽  
Amino Acid Sequences ◽  
Acid And Base ◽  
Effects Of Ph ◽  
Base Balance ◽  
Environmental Milieu ◽  
And Function

AbstractThe function of proteins depends on their structure. The structural integrity of proteins is dynamic and depends on interacting nearby neighboring moieties that influence their properties and induce folding and structural changes. The conformational changes induced by these nearby neighbors in the micro-environmental milieu at that moment are guided by chemical or electrical bonding attractions.There are few literature references that describe the potential for environmental milieu changes to disfavor SARS-CoV-2 attachment to a receptor for survival outside of a host. There are many studies on the effects of pH (acid and base balance) supporting its importance for protein structure and function, but few focus on pH role in extracellular or intracellular protein or actionable requirements of Covera-19.‘Fold ‘em or Hold ‘em’ is seen by the various functions and effects of furin as it seeks an acidic milieu for action or compatible amino acid sequences which is currently aided by its histidine component and the structural changes of proteins as they enter or exit the host. Questions throughout the text are posed to focus on current thoughts as reviewing applicable COVID-19 translational research science in order to understand the complexities of Covid-19.The pH needs of COVID-19 players and its journey through the human host and environment as well as some efficacious readily available repurposed drugs and out-of-the box and easily available treatments are reviewed.

scholarly journals Structural transitions in the GTP cap visualized by cryo-EM of catalytically inactive microtubules

2021 ◽  
Author(s):  
Benjamin J LaFrance ◽  
Johanna Roostalu ◽  
Gil Henkin ◽  
Basil J Greber ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Conformational Changes ◽  
Binding Proteins ◽  
Dynamic Instability ◽  
Structural Transitions ◽  
Gtp Hydrolysis ◽  
Tirf Microscopy ◽  
Mechanistic Insight ◽  
Catalytically Active

Microtubules (MTs) are polymers of alphabeta-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes, and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here we use cryo-EM and TIRF microscopy of GTP hydrolysis-deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice, but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wildtype GDP-MTs. End binding proteins of the EB family have the ability to compact both mutant GTP-lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wildtype MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these first high-resolution structures of truly GTP-bound MTs add mechanistic insight to our understanding of MT dynamic instability.

scholarly journals Chlamydomonas reinhardtii Tubulin-Gene Disruptants for Efficient Isolation of Strains Bearing Novel Tubulin Mutations

2020 ◽  
Author(s):  
Takako Kato-Minoura ◽  
Yutaro Ogiwara ◽  
Takashi Yamano ◽  
Hideya Fukuzawa ◽  
Ritsu Kamiya
Keyword(s):  
Drug Resistance ◽  
Chlamydomonas Reinhardtii ◽  
Structural Changes ◽  
Human Cancer ◽  
Amino Acid Sequences ◽  
Drug Binding ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Tubulin Mutations ◽  
Β Tubulin

ABSTRACTThe single-cell green alga Chlamydomonas reinhardtii possesses two α-tubulin genes (tua1 and tua2) and two β-tubulin genes (tub1 and tub2), with the two genes in each pair encoding identical amino acid sequences. Here, we used an aphVIII gene cassette insertional library to establish eight disruptants with defective tua2, tub1, or tub2 expression. None of the disruptants exhibited apparent defects in cell growth, flagellar length, or flagellar regeneration after amputation. Because few tubulin mutants of C. reinhardtii have been reported to date, we then used our disruptants, together with a tua1 disruptant obtained from the Chlamydomonas Library Project (CLiP), to isolate novel tubulin-mutants resistant to the anti-tubulin agents propyzamide and oryzalin. As a result of several trials, we obtained 8 strains bearing 7 different α-tubulin mutations and 24 strains bearing 12 different β-tubulin mutations. Some of these mutations are known to confer drug resistance in human cancer cells. Thus, single-tubulin-gene disruptants are an efficient means of isolating novel C. reinhardtii tubulin mutants.IMPORTANCEChlamydomonas reinhardtii is a useful organism for the study of tubulin function; however, only five kinds of tubulin mutations have been reported to date. This scarcity is partly due to C. reinhardtii possessing two tubulin genes each for α- and β-tubulin. Here, we obtained several strains in which one of the α- or β-tubulin genes was disrupted, and then used those disruptants to isolate 32 strains bearing 19 mostly novel tubulin mutations that conferred differing degrees of resistance to two anti-tubulin compounds. The majority of the tubulin mutations were located outside of the drug-binding sites in the three-dimensional tubulin structure, suggesting that structural changes underlie the drug resistance conferred by these mutations. Thus, single-tubulin-gene disruptants are an efficient means of generating tubulin mutants for the study of the structure–function relationship of tubulin and for the development of novel therapies based on anti-tubulin agents.

scholarly journals Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules

2022 ◽  
Vol 119 (2) ◽  
pp. e2114994119
Author(s):  
Benjamin J. LaFrance ◽  
Johanna Roostalu ◽  
Gil Henkin ◽  
Basil J. Greber ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Conformational Changes ◽  
Total Internal Reflection ◽  
Dynamic Instability ◽  
Wild Type ◽  
Gtp Hydrolysis ◽  
Cryo Electron Microscopy ◽  
Catalytically Active ◽  
The Stability ◽  
Insight Into

Microtubules (MTs) are polymers of αβ-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here, we use cryo-electron microscopy and total internal reflection fluorescence microscopy of GTP hydrolysis–deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wild-type GDP-MTs. End-binding proteins of the EB family have the ability to compact both mutant GTP lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wild-type MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these structures of catalytically inactive MTs add mechanistic insight into the GTP state of MTs, the stability of the GTP- and GDP-bound lattice, and our overall understanding of MT dynamic instability.

scholarly journals Mechanistic Origins of Dynamic Instability in Filaments from the Phage Tubulin, PhuZ

2018 ◽  
Author(s):  
Elena A. Zehr ◽  
Alexis Rohu ◽  
Yanxin Liu ◽  
Kliment A. Verba ◽  
Joe Pogliano ◽  
...  
Keyword(s):  
Structural Changes ◽  
Dynamic Instability ◽  
Microtubule Dynamics ◽  
Gtp Hydrolysis ◽  
Filament Assembly ◽  
Gtp Binding ◽  
C Terminus ◽  
Molecular Description

SUMMARYA bacteriophage-encoded tubulin homologue, PhuZ, harnesses dynamic instability to position genomes of ՓKZ-like bacteriophage at the midline of their Pseudomonas hosts, facilitating phage infectivity. While much has been learned about molecular origins of microtubule dynamics, how GTP binding and hydrolysis control dynamics in the divergent 3-stranded PhuZ filaments is not understood. Here we present cryo-EM reconstructions of the PhuZ filamentin a pre-hydrolysis (3.5Å) and three post-hydrolysis states (4.2 Å, 7.3 Å and 8.1 Å resolutions), likely representing distinct depolymerization stages. Core polymerization-induced structural changes reveal similarities to αβ-tubulin, suggesting broad conservation within the tubulin family. By contrast, GTP hydrolysis is sensed quite differently and is communicated by the divergent PhuZ C-terminus to the lateral interface, leading to PhuZ polymer destabilization. This provides a contrasting molecular description of how nucleotide state can be harnessed by the tubulin fold to regulate filament assembly, metastability and disassembly.

Analysis of the Mechanism of Microtubule Dynamic Instability Using a UV Microbeam to Sever Elongating Microtubules

1988 ◽  
Vol 46 ◽  
pp. 122-123
Author(s):  
R.A Walker ◽  
S. Inoue ◽  
E.D. Salmon
Keyword(s):  
Dynamic Instability ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
Abrupt Transition ◽  
Microtubule Associated Proteins ◽  
Asymmetrical Structure ◽  
Associated Proteins

Microtubules polymerized in vitro from tubulin purified free of microtubule-associated proteins exhibit dynamic instability (1,2,3). Free microtubule ends exist in persistent phases of elongation or rapid shortening with infrequent, but, abrupt transitions between these phases. The abrupt transition from elongation to rapid shortening is termed catastrophe and the abrupt transition from rapid shortening to elongation is termed rescue. A microtubule is an asymmetrical structure. The plus end grows faster than the minus end. The frequency of catastrophe of the plus end is somewhat greater than the minus end, while the frequency of rescue of the plus end in much lower than for the minus end (4).The mechanism of catastrophe is controversial, but for both the plus and minus microtubule ends, catastrophe is thought to be dependent on GTP hydrolysis. Microtubule elongation occurs by the association of tubulin-GTP subunits to the growing end. Sometime after incorporation into an elongating microtubule end, the GTP is hydrolyzed to GDP, yielding a core of tubulin-GDP capped by tubulin-GTP (“GTP-cap”).

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

Influence of Ascorbic Acid on the Structure and Function of Alpha-2- macroglobulin: Investigations using Spectroscopic and Thermodynamic Techniques

2020 ◽  
Vol 27 (3) ◽  
pp. 201-209
Author(s):  
Syed Saqib Ali ◽  
Mohammad Khalid Zia ◽  
Tooba Siddiqui ◽  
Haseeb Ahsan ◽  
Fahim Halim Khan
Keyword(s):  
Ascorbic Acid ◽  
Conformational Changes ◽  
Structural Changes ◽  
The Body ◽  
Titration Calorimetry ◽  
Spectroscopic Techniques ◽  
Human Beings ◽  
Plasma Ascorbic Acid ◽  
Dietary Antioxidant ◽  
And Function

Background: Ascorbic acid is a classic dietary antioxidant which plays an important role in the body of human beings. It is commonly found in various foods as well as taken as dietary supplement. Objective: The plasma ascorbic acid concentration may range from low, as in chronic or acute oxidative stress to high if delivered intravenously during cancer treatment. Sheep alpha-2- macroglobulin (α2M), a human α2M homologue is a large tetrameric glycoprotein of 630 kDa with antiproteinase activity, found in sheep’s blood. Methods: In the present study, the interaction of ascorbic acid with alpha-2-macroglobulin was explored in the presence of visible light by utilizing various spectroscopic techniques and isothermal titration calorimetry (ITC). Results: UV-vis and fluorescence spectroscopy suggests the formation of a complex between ascorbic acid and α2M apparent by increased absorbance and decreased fluorescence. Secondary structural changes in the α2M were investigated by CD and FT-IR spectroscopy. Our findings suggest the induction of subtle conformational changes in α2M induced by ascorbic acid. Thermodynamics signatures of ascorbic acid and α2M interaction indicate that the binding is an enthalpy-driven process. Conclusion: It is possible that ascorbic acid binds and compromises antiproteinase activity of α2M by inducing changes in the secondary structure of the protein.

Metastability in Monolayer Films Transferred onto Solid Substrates by the Langmuir-Blodgett Method: IR Evidence for Transfer-Induced Phase Transitions

1994 ◽  
Vol 48 (10) ◽  
pp. 1196-1203 ◽  
Author(s):  
Fazale R. Rana ◽  
Suci Widayati ◽  
Brian W. Gregory ◽  
Richard A. Dluhy
Keyword(s):  
Fatty Acid ◽  
Conformational Changes ◽  
Structural Changes ◽  
High Surface ◽  
Solid Substrate ◽  
Water Interface ◽  
Monolayer Films ◽  
Langmuir Blodgett ◽  
Monomolecular Film ◽  
Air Water Interface

The rate at which a monomolecular film is deposited onto a solid substrate in the Langmuir-Blodgett process of preparing supported monolayer films influences the final structure of the transferred film. Attenuated total reflectance infrared spectroscopic studies of monolayers transferred to germanium substrates show that the speed at which the substrate is drawn through the air/water interface influences the final conformation in the hydrocarbon chains of amphiphilic film molecules. This transfer-induced effect is especially evident when the monolayer is transferred from the expanded region of surface-pressure-molecular-area isotherms at low surface pressures; the effect is minimized when the film molecules are transferred from condensed phases at high surface pressures. This phenomenon has been observed for both a fatty acid and a phospholipid, which suggests that these conformational changes may occur in a variety of hydrocarbon amphiphiles transferred from the air/water interface. This conformational ordering may be due to a kinetically limited phase transition taking place in the meniscus formed between the solid substrate and aqueous subphase. In addition, the results obtained for both the phospholipid and fatty acid suggest that the structure of the amphiphile may help determine the extent and nature of the transfer-speed-induced structural changes taking place in the monomolecular film.

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