AFM images of open and collapsed states of yeast condensin suggest a scrunching model for DNA loop extrusion

SUMMARYStructural Maintenance of Chromosome (SMC) protein complexes are the key organizers of the spatiotemporal structure of chromosomes. The condensin SMC complex, which compacts DNA during mitosis, was recently shown to be a molecular motor that extrudes large loops of DNA. The mechanism of this unique motor, which takes large steps along DNA at low ATP consumption, remains elusive however. Here, we use Atomic Force Microscopy (AFM) to visualize the structure of yeast condensin and condensin-DNA complexes. Condensin is found to exhibit mainly open ‘O’ shapes and collapsed ‘B’ shapes, and it cycles dynamically between these two states over time. Condensin binds double-stranded DNA via a HEAT subunit and, surprisingly, also via the hinge domain. On extruded DNA loops, we observe a single condensin complex at the loop stem, where the neck size of the DNA loop correlates with the width of the condensin complex. Our results suggest that condensin extrudes DNA by a fast cyclic switching of its conformation between O and B shapes, consistent with a scrunching model.

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Study of substrate-directed ordering of long double-stranded DNA molecules on bare highly oriented pyrolytic graphite surface based on atomic force microscopy relocation imaging

Journal of Vacuum Science & Technology B Microelectronics and Nanometer Structures Processing Measurement and Phenomena ◽

10.1116/1.2968698 ◽

2008 ◽

Vol 26 (5) ◽

pp. L41 ◽

Cited By ~ 5

Author(s):

Huabin Wang ◽

Hongjie An ◽

Feng Zhang ◽

Zhixiang Zhang ◽

Ming Ye ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Pyrolytic Graphite ◽

Graphite Surface ◽

Dna Molecules ◽

Highly Oriented Pyrolytic Graphite ◽

Force Microscopy ◽

Double Stranded Dna ◽

Atomic Force

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Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy

Journal of Visualized Experiments ◽

10.3791/3061 ◽

2011 ◽

Cited By ~ 2

Author(s):

Patrick J. M. Murphy ◽

Morgan Shannon ◽

John Goertz

Keyword(s):

Atomic Force Microscopy ◽

Recombinant Dna ◽

Protein Complexes ◽

Force Microscopy ◽

Atomic Force

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Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

10.1101/2021.02.25.432963 ◽

2021 ◽

Author(s):

Hiroki Koide ◽

Noriyuki Kodera ◽

Shveta Bisht ◽

Shoji Takada ◽

Tsuyoshi Terakawa

Keyword(s):

Molecular Dynamics ◽

Atomic Force Microscopy ◽

Molecular Dynamics Simulations ◽

Coarse Grained ◽

Force Microscopy ◽

Atomic Force ◽

Dna Loop ◽

Dynamics Simulations ◽

Dsdna Binding ◽

Hinge Domain

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.

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Visualization and identification of hepatitis c viral particles by atomic force microscopy combined with ms/ms analysis

Biomeditsinskaya Khimiya ◽

10.18097/pbmc20105601026 ◽

2010 ◽

Vol 56 (1) ◽

pp. 26-39 ◽

Cited By ~ 13

Author(s):

A.L. Kaysheva ◽

Yu.D. Ivanov ◽

V.G. Zgoda ◽

P.A. Frantsuzov ◽

T.O. Pleshakova ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Hepatitis C ◽

Protein Complexes ◽

Mass Spectrometric ◽

Force Microscopy ◽

Atomic Force ◽

Spectrometric Identification ◽

Detection And Identification ◽

Viral Particles ◽

Mass Spectrometric Identification

Possibility of detection and identification of hepatitis C viral particles with mass spectrometry (MS) in combination with atomic force microscopy (AFM) had been investigated. AFM/MS approach is based on two technologies: 1. AFM-biospecific fishing that allows to detect, concentrate from solution and to count protein complexes on a surface of AFM-nanochip; 2. mass spectrometric identification of these complexes. AFM-biospecific fishing of HCVcoreAg from solution was carried onto surface of AFM-nanochips with immobilized anti-HCVcoreAg. It was shown that HCVcoreAg/anti-HCVcoreim complexes were formed onto AFM-nanochips in quantity sufficient for mass spectrometric identification. Thus, AFM/MS approach allows to identify fragments of hepatitis C virus fished onto a surface of AFM-nanochip from serum.

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DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Nucleic Acids Research ◽

10.1093/nar/gkz497 ◽

2019 ◽

Vol 47 (13) ◽

pp. 6956-6972 ◽

Cited By ~ 27

Author(s):

John F Marko ◽

Paolo De Los Rios ◽

Alessandro Barducci ◽

Stephan Gruber

Keyword(s):

Protein Complexes ◽

Molecular Motor ◽

Strong Dependence ◽

Extrusion Process ◽

Chromosomal Dna ◽

Step Size ◽

New Class ◽

Pull Out ◽

Structural Maintenance Of Chromosome ◽

Brownian Loop

AbstractCells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a ‘loop extrusion’ process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor ‘track’—in this case DNA—are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with ‘stalling’ occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (Escherichia coli MukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.

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Real-time imaging of DNA loop extrusion by condensin

Science ◽

10.1126/science.aar7831 ◽

2018 ◽

Vol 360 (6384) ◽

pp. 102-105 ◽

Cited By ~ 280

Author(s):

Mahipal Ganji ◽

Indra A. Shaltiel ◽

Shveta Bisht ◽

Eugene Kim ◽

Ana Kalichava ◽

...

Keyword(s):

Real Time ◽

Adenosine Triphosphate ◽

Genome Organization ◽

Protein Complexes ◽

Dna Loops ◽

Base Pairs ◽

Real Time Imaging ◽

Condensin Complex ◽

Dna Loop

It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.

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