scholarly journals Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jean Paul Armache ◽  
Nathan Gamarra ◽  
Stephanie L Johnson ◽  
John D Leonard ◽  
Shenping Wu ◽  
...  
Keyword(s):  
The Other ◽  
Structural Basis ◽  
Reaction Intermediates ◽  
Dna Translocation ◽  
Allosteric Control ◽  
Histone Octamer ◽  
Nucleosome Sliding

The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn’t show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.

scholarly journals Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

2019 ◽  
Author(s):  
Jean-Paul Armache ◽  
Nathan Gamarra ◽  
Stephanie L. Johnson ◽  
John D. Leonard ◽  
Shenping Wu ◽  
...  
Keyword(s):  
The Other ◽  
Structural Basis ◽  
Reaction Intermediates ◽  
Dna Translocation ◽  
Chromatin Remodeler ◽  
Conformational States ◽  
Allosteric Control ◽  
Histone Octamer ◽  
Nucleosome Sliding

AbstractThe SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, are disordered. The disordered acidic patch is expected to inhibit the second SNF2h promoter, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn’t show octamer deformation, but surprisingly shows a 2bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.One sentence summaryCryo-EM structures capture different conformational states of chromatin remodeler-nucleosome complexes.

scholarly journals Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate

2010 ◽  
Vol 107 (28) ◽  
pp. 12487-12492 ◽  
Author(s):  
Meng-Xi Zhao ◽  
Yong-Liang Jiang ◽  
Yong-Xing He ◽  
Yi-Fei Chen ◽  
Yan-Bin Teng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Nitrogen Starvation ◽  
Structural Basis ◽  
Allosteric Control

scholarly journals Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase

2020 ◽  
Vol 117 (33) ◽  
pp. 19914-19925 ◽  
Author(s):  
Anahita Daruwalla ◽  
Jianye Zhang ◽  
Ho Jun Lee ◽  
Nimesh Khadka ◽  
Erik R. Farquhar ◽  
...  
Keyword(s):  
Active Site ◽  
Molecular Basis ◽  
Structural Basis ◽  
Reaction Intermediates ◽  
Catalytic Activities ◽  
Selective Stabilization ◽  
Carotenoid Cleavage Dioxygenases ◽  
Active Site Cavity ◽  
Binding Cleft ◽  
Shed Light

Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD–carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD fromCandidatusNitrosotalea devanaterra (NdCCD).NdCCD was active toward β-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14′–C13′ alkene bond to produce β-apo-14′-carotenals. The structure ofNdCCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-formingSynechocystisapocarotenoid oxygenase (SynACO) but similar to the vertebrate retinoid isomerase RPE65. The structure ofNdCCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.

scholarly journals Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome

2021 ◽  
Vol 118 (4) ◽  
pp. e2014498118
Author(s):  
Ilana M. Nodelman ◽  
Zhongtian Shen ◽  
Robert F. Levendosky ◽  
Gregory D. Bowman
Keyword(s):  
Bound States ◽  
Atp Binding ◽  
Dna Binding Domain ◽  
Dna Translocation ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Nucleosome Sliding ◽  
Underlying Mechanisms ◽  
Histone Core ◽  
Block Sliding

Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements—the chromodomains and bridge—reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.

scholarly journals Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

2017 ◽  
Author(s):  
Toru Niina ◽  
Giovanni B. Brandani ◽  
Cheng Tan ◽  
Shoji Takada
Keyword(s):  
Hydrogen Bond ◽  
Dna Sequence ◽  
Base Pair ◽  
Sliding Mode ◽  
Nucleosome Positioning ◽  
Eukaryotic Genome ◽  
Coarse Grained ◽  
Histone Octamer ◽  
Hydrogen Bond Interactions ◽  
Nucleosome Sliding

AbstractWhile nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements.Author summaryNucleosomes are fundamental units of chromatin folding consisting of double-stranded DNA wrapped ∼1.7 times around a histone octamer. By densely populating the eukaryotic genome, nucleosomes enable efficient genome compaction inside the cellular nucleus. However, the portion of DNA occupied by a nucleosome can hardly be accessed by other DNA-binding proteins, obstructing fundamental cellular processes such as DNA replication and transcription. DNA compaction and access by other proteins can simultaneously be achieved via the dynamical repositioning of nucleosomes, which can slide along the DNA sequence. In this study, we developed and used coarse-grained molecular dynamics simulations to reveal the molecular details of nucleosome sliding. We find that the sliding mode is highly dependent on the underlying DNA sequence. Specifically, a sequence with a strong nucleosome positioning signal slides via large jumps by five and ten base pairs, preserving the optimal DNA bending profile. On the other hand, uniform sequences without the positioning signal slide via a screw-like motion of DNA, one base pair at the time. These results show that sequence has a large effect not only on the formation of nucleosomes, but also on the kinetics of repositioning.

scholarly journals Structural basis for the activity and allosteric control of diguanylate cyclase

2005 ◽  
Vol 61 (a1) ◽  
pp. c235-c235
Author(s):  
C. Chan ◽  
R. Paul ◽  
D. Samoray ◽  
N. Amiot ◽  
B. Giese ◽  
...  
Keyword(s):  
Structural Basis ◽  
Diguanylate Cyclase ◽  
Allosteric Control

Colocalization of dihydropyridine and ryanodine receptors in neonate rabbit heart using confocal microscopy

2000 ◽  
Vol 279 (1) ◽  
pp. H202-H209 ◽  
Author(s):  
Franklin Sedarat ◽  
Liqun Xu ◽  
Edwin D. W. Moore ◽  
Glen F. Tibbits
Keyword(s):  
Confocal Microscopy ◽  
Ventricular Myocytes ◽  
Ryanodine Receptors ◽  
Spatial Association ◽  
Age Groups ◽  
Rabbit Heart ◽  
The Other ◽  
Structural Basis ◽  
Double Labeling ◽  
Neonatal Heart

Because of undeveloped T tubules and sparse sarcoplasmic reticulum, Ca2+-induced Ca2+ release (CICR) may not be the major mechanism providing contractile Ca2+ in the neonatal heart. Spatial association of dihydropyridine receptors (DHPRs) and ryanodine receptors (RyRs), a key factor for CICR, was examined in isolated neonatal rabbit ventricular myocytes aged 3–20 days by double-labeling immunofluorescence and confocal microscopy. We found a significant increase ( P < 0.0005) in the degree of colocalization of DHPR and RyR during development. The number of voxels containing DHPR that also contained RyR in the 3-day-old group (62 ± 1.8%) was significantly lower than in the other age groups (76 ± 1.3 in 6-day old, 75 ± 1.2 in 10-day old, and 79 ± 0.9% in 20-day old). The number of voxels containing RyR that also contained DHPR was significantly higher in the 20-day-old group (17 ± 0.5%) compared with the other age groups (10 ± 0.7 in 3-day old, 11 ± 0.6 in 6-day old, and 11 ± 0.5% in 10-day old). During this period, the pattern of colocalization changed from mostly peripheral to mostly internal couplings. Our results provide a structural basis for the diminished prominence of CICR in neonatal heart.

EM studies of the structural basis of tactile learning and memory

1989 ◽  
Vol 47 ◽  
pp. 954-955 ◽  
Author(s):  
J. David Robertson ◽  
Psyche Lee
Keyword(s):  
Learning And Memory ◽  
Negative Stimulus ◽  
Growth Cones ◽  
The Body ◽  
The Other ◽  
Structural Basis ◽  
Octopus Vulgaris ◽  
Electron Microscopic ◽  
Plastic Ball ◽  
Tactile Learning

It has long been speculated that a rearrangement of neurites might occur in learning neuropils to provide a structural basis of learning and memory. However, this has never been proven definitively, even though there is evidence that new synapses are formed in response to cortical activity in mammals and birds [see(l)] We are studying this problem using Octopus vulgaris. The nervous system of octopus is the most advanced of all invertebrates. It can readily learn and remember a training paradigm whereby it is taught to associate food with touching a smooth plastic ball (positive stimulus) and a 10 VAC electric shock with touching a plastic ball roughened by cutting grooves into its surface (negative stimulus). Touch learning occurs primarily in the inferior frontal system. The brain of the animal can be split sagittaly into two halves and one half brain shown to control the ipsilateral half of the body. Four arms can be taught to respond positively to touching a smooth ball and the other four negatively to touching the same ball. If the posterior buccal (PB) lobe on one side is removed surgically that side of the animal cannot learn the paradigm, while the other half does. We postulate that learning involves formation of new synapses forming as in development or in tissue culture, via growth cones. We have tested this proposition in one way (1-2). It is known that the drug cytochalasin B (CB) interferes with the polymerization of actin monomers in growth cones and that this results in the reversible collapse of their filopodia. If our theory is correct, injecting CB into the PB lobe should block learning without having any effect on memory or overall functioning of the PB lobe neuropil. We have found that this is true. However, since CB has other effects, it is necessary to demonstrate directly that filopodia are involved. We report here on preliminary electron microscopic (EM) studies of the PB lobe neuropil directed to this problem.

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