scholarly journals Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements

Structure ◽  
2019 ◽  
Vol 27 (2) ◽  
pp. 359-370.e12 ◽  
Author(s):  
Fabrizio Marinelli ◽  
Giacomo Fiorin
Keyword(s):  
Structural Characterization ◽  
Atomistic Simulations

scholarly journals Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

2020 ◽  
Vol 22 (37) ◽  
pp. 21083-21093 ◽  
Author(s):  
Ilias Patmanidis ◽  
Alex H. de Vries ◽  
Tsjerk A. Wassenaar ◽  
Wenjun Wang ◽  
Giuseppe Portale ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Building Blocks ◽  
Atomistic Simulations ◽  
Self Assembled

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers.

scholarly journals Structural Characterization of Supramolecular Hollow Nanotubes with Atomistic Simulations and SAXS

2020 ◽  
Author(s):  
Ilias Patmanidis ◽  
Alex H. de Vries ◽  
Tsjerk A. Wassenaar ◽  
Wenjun Wang ◽  
Giuseppe Portale ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Structural Characterization ◽  
Building Blocks ◽  
Structural Features ◽  
Cyanine Dye ◽  
Atomistic Simulations ◽  
Dynamics Simulations ◽  
Stable Structures

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into doublewalled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.<br>

scholarly journals Structural Characterization of Supramolecular Hollow Nanotubes with Atomistic Simulations and SAXS

2020 ◽  
Author(s):  
Ilias Patmanidis ◽  
Alex H. de Vries ◽  
Tsjerk A. Wassenaar ◽  
Wenjun Wang ◽  
Giuseppe Portale ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Optical Properties ◽  
Structural Characterization ◽  
Building Blocks ◽  
Structural Features ◽  
Cyanine Dye ◽  
Atomistic Simulations ◽  
Dynamics Simulations ◽  
Stable Structures

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into doublewalled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.<br>

New ultrastructural findings about Borrelia burgdorferi by cryofixation, negative staining, thin sectioning and scanning techniques

1990 ◽  
Vol 48 (3) ◽  
pp. 582-583
Author(s):  
S. F. Hayes ◽  
M. D. Corwin ◽  
T. G. Schwan ◽  
D. W. Dorward ◽  
W. Burgdorfer
Keyword(s):  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Structural Characterization ◽  
Negative Staining ◽  
Low Speed ◽  
Thin Sectioning ◽  
Ultrastructural Findings

Characterization of Borrelia burgdorferi strains by means of negative staining EM has become an integral part of many studies related to the biology of the Lyme disease organism. However, relying solely upon negative staining to compare new isolates with prototype B31 or other borreliae is often unsatisfactory. To obtain more satisfactory results, we have relied upon a correlative approach encompassing a variety EM techniques, i.e., scanning for topographical features and cryotomy, negative staining and thin sectioning to provide a more complete structural characterization of B. burgdorferi.For characterization, isolates of B. burgdorferi were cultured in BSK II media from which they were removed by low speed centrifugation. The sedimented borrelia were carefully resuspended in stabilizing buffer so as to preserve their features for scanning and negative staining. Alternatively, others were prepared for conventional thin sectioning and for cryotomy using modified procedures. For thin sectioning, the fixative described by Ito, et al.

Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90

2011 ◽  
Vol 44 (06) ◽  
Author(s):  
A Bracher ◽  
C Kozany ◽  
AK Thost ◽  
F Hausch
Keyword(s):  
Structural Characterization ◽  
Ppiase Domain

Structural characterization of dendrobine-type sesquiterpene alkaloids from the stems of Dendrobium nobile using LC-MS/MS

Planta Medica ◽  
2014 ◽  
Vol 80 (10) ◽  
Author(s):  
YH Wang ◽  
B Avula ◽  
N Abe ◽  
F Wei ◽  
M Wang ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Dendrobium Nobile

Structural characterization of monacolin compounds from red yeast rice by liquid chromatography and tandem mass

Planta Medica ◽  
2015 ◽  
Vol 81 (11) ◽  
Author(s):  
YH Wang ◽  
B Avula ◽  
Z Zhang ◽  
M Wang ◽  
S Sagi ◽  
...  
Keyword(s):  
Liquid Chromatography ◽  
Structural Characterization ◽  
Red Yeast Rice ◽  
Tandem Mass ◽  
Red Yeast
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