Thermodynamics of Molecular Machines Using Incremental ITC

2019 ◽  
pp. 129-140
Author(s):  
Benoît Meyer ◽  
Cyrielle da Veiga ◽  
Philippe Dumas ◽  
Eric Ennifar
Keyword(s):  
Molecular Machines

Molecular Machines

2018 ◽  
Author(s):  
Giovanni Zocchi
Keyword(s):  
Molecular Machines

Artificial molecular machines driven by light

10.2741/2741 ◽  
2008 ◽  
Vol 13 (13) ◽  
pp. 1036 ◽  
Author(s):  
Monica Semeraro
Keyword(s):  
Molecular Machines

scholarly journals Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1484
Author(s):  
Christopher Reinknecht ◽  
Anthony Riga ◽  
Jasmin Rivera ◽  
David A. Snyder
Keyword(s):  
Protein Flexibility ◽  
Molecular Machines ◽  
Md Simulations ◽  
Peptide Bond ◽  
Structure Calculation ◽  
Atomic Scale ◽  
Heavy Atoms ◽  
Structural Ensembles ◽  
Atomic Coordinates ◽  
Motional Behavior

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.

scholarly journals Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

2020 ◽  
Vol 22 (1) ◽  
pp. 76
Author(s):  
Aaron Morgan ◽  
Sarah LeGresley ◽  
Christopher Fischer
Keyword(s):  
Free Energy ◽  
Dna Replication ◽  
Recent Work ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Genetic Information ◽  
Molecular Machines ◽  
Mechanical Work ◽  
Eukaryotic Genome ◽  
Hydrolysis Of

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.

scholarly journals Molecular machines for catalysis

2018 ◽  
Vol 2 (3) ◽  
Author(s):  
Lucy van Dijk ◽  
Michael J. Tilby ◽  
Robert Szpera ◽  
Owen A. Smith ◽  
Holly A. P. Bunce ◽  
...  
Keyword(s):  
Molecular Machines

scholarly journals Visualizing the Molecular Machines of Bacterial Motility In-situ with Electron Cryotomography

2006 ◽  
Vol 12 (S02) ◽  
pp. 398-399
Author(s):  
GJ Jensen ◽  
GE Murphy ◽  
GP Henderson ◽  
Z Li ◽  
A Komeili ◽  
...  
Keyword(s):  
Molecular Machines ◽  
Bacterial Motility ◽  
Electron Cryotomography

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Molecular Machines

1998 ◽  
Vol 31 (7) ◽  
pp. 405-414 ◽  
Author(s):  
Vincenzo Balzani ◽  
Marcos Gómez-López ◽  
J. Fraser Stoddart
Keyword(s):  
Molecular Machines
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