scholarly journals Convergent Allostery in Ribonucleotide Reductase

2018 ◽  
Author(s):  
William C. Thomas ◽  
F. Phil Brooks ◽  
Audrey A. Burnim ◽  
John-Paul Bacik ◽  
JoAnne Stubbe ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Ribonucleotide Reductase ◽  
Molecular Basis ◽  
Model Organism ◽  
Activity Regulation ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy ◽  
Ribonucleotide Reductases ◽  
Class Ib

AbstractRibonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a new and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible, active tetramer and two novel, inhibited filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

Uncovering the structures of modular polyketide synthases

2015 ◽  
Vol 32 (3) ◽  
pp. 436-453 ◽  
Author(s):  
Kira J. Weissman
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Structural Characterization ◽  
Small Angle ◽  
Single Particle ◽  
Polyketide Synthases ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.

scholarly journals Morphological observations on liposomes bearing covalently bound protein: Studies with freeze-fracture and cryo electron microscopy and small angle X-ray scattering techniques

1998 ◽  
Vol 1370 (1) ◽  
pp. 151-160 ◽  
Author(s):  
Nataša Škalko ◽  
Joke Bouwstra ◽  
Ferry Spies ◽  
Marc Stuart ◽  
P.M Frederik ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Freeze Fracture ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy ◽  
Covalently Bound ◽  
Ray Scattering

scholarly journals Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Benjamin G Horst ◽  
Adam L Yokom ◽  
Daniel J Rosenberg ◽  
Kyle L Morris ◽  
Michal Hammel ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Coiled Coil ◽  
X Ray ◽  
Nitric Oxide Signaling ◽  
Catalytic Domains ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.

scholarly journals Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy

2017 ◽  
Vol 24 (1) ◽  
pp. 13-30 ◽  
Author(s):  
Jin Seob Kim ◽  
Bijan Afsari ◽  
Gregory S. Chirikjian
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Cross Validation ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy ◽  
Ray Scattering

scholarly journals Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy

2019 ◽  
Author(s):  
Benjamin G. Horst ◽  
Adam L. Yokom ◽  
Daniel J. Rosenberg ◽  
Kyle L. Morris ◽  
Michal Hammel ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Electron Microscopy ◽  
Guanylate Cyclase ◽  
Soluble Guanylate Cyclase ◽  
Coiled Coil ◽  
X Ray ◽  
Nitric Oxide Signaling ◽  
Catalytic Domains ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

AbstractSoluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-lengthManduca sextasGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Time-Resolved Cryo-Electron Microscopy of Oscillating Microtubules

1990 ◽  
Vol 48 (1) ◽  
pp. 502-503
Author(s):  
Eva-Maria Mandelkow ◽  
Ron Milligan
Keyword(s):  
Electron Microscopy ◽  
Dynamic Instability ◽  
Entire Solution ◽  
Reaction Scheme ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
A Chain ◽  
Ray Scattering

Microtubules form part of the cytoskeleton of eukaryotic cells. They are hollow libers of about 25 nm diameter made up of 13 protofilaments, each of which consists of a chain of heterodimers of α-and β-tubulin. Microtubules can be assembled in vitro at 37°C in the presence of GTP which is hydrolyzed during the reaction, and they are disassembled at 4°C. In contrast to most other polymers microtubules show the behavior of “dynamic instability”, i.e. they can switch between phases of growth and phases of shrinkage, even at an overall steady state [1]. In certain conditions an entire solution can be synchronized, leading to autonomous oscillations in the degree of assembly which can be observed by X-ray scattering (Fig. 1), light scattering, or electron microscopy [2-5]. In addition such solutions are capable of generating spontaneous spatial patterns [6].In an earlier study we have analyzed the structure of microtubules and their cold-induced disassembly by cryo-EM [7]. One result was that disassembly takes place by loss of protofilament fragments (tubulin oligomers) which fray apart at the microtubule ends. We also looked at microtubule oscillations by time-resolved X-ray scattering and proposed a reaction scheme [4] which involves a cyclic interconversion of tubulin, microtubules, and oligomers (Fig. 2). The present study was undertaken to answer two questions: (a) What is the nature of the oscillations as seen by time-resolved cryo-EM? (b) Do microtubules disassemble by fraying protofilament fragments during oscillations at 37°C?

scholarly journals Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures

Soft Matter ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. 3096-3104
Author(s):  
Valeria Castelletto ◽  
Jani Seitsonen ◽  
Janne Ruokolainen ◽  
Ian W. Hamley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Small Angle ◽  
Self Assembly ◽  
X Ray ◽  
Cryogenic Transmission Electron Microscopy ◽  
X Ray Scattering ◽  
Transmission Electron ◽  
Ph Dependent ◽  
Ray Scattering

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties.

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