Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations

2021 ◽  
Author(s):  
Kiyoshi Yagi ◽  
Shingo Ito ◽  
Yuji Sugita
Keyword(s):  
Free Energy ◽  
Minimum Energy ◽  
Enzymatic Reactions ◽  
Energy Profiles ◽  
Free Energy Profiles ◽  
Energy Pathways

scholarly journals Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions

2006 ◽  
Vol 110 (6) ◽  
pp. 2934-2941 ◽  
Author(s):  
Edina Rosta ◽  
Marco Klähn ◽  
Arieh Warshel
Keyword(s):  
Free Energy ◽  
Ab Initio ◽  
Enzymatic Reactions ◽  
Energy Profiles ◽  
Free Energy Profiles

scholarly journals Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

2021 ◽  
Author(s):  
Amanuel Wolde-Kidan ◽  
Anna Herrmann ◽  
Albert Prause ◽  
Michael Gradzielski ◽  
Rainer Haag ◽  
...  
Keyword(s):  
Free Energy ◽  
Time Resolved ◽  
Energy Profiles ◽  
Penetration Data ◽  
Free Energy Profiles

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

Chemical free energy profiles for martensitic transformation of CuAlNi at finite temperatures

2021 ◽  
Vol 195 ◽  
pp. 110478
Author(s):  
Zewei Li ◽  
Hengshan Hu ◽  
Yubao Zhen
Keyword(s):  
Free Energy ◽  
Martensitic Transformation ◽  
Energy Profiles ◽  
Chemical Free Energy ◽  
Free Energy Profiles

scholarly journals Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels

1997 ◽  
Vol 73 (4) ◽  
pp. 1699-1716 ◽  
Author(s):  
Y. Hao ◽  
M.R. Pear ◽  
D.D. Busath
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Gramicidin A ◽  
Organic Cations ◽  
Energy Profiles ◽  
Free Energy Profiles

Adsorption-Induced Structural Transition of an Interpenetrated Porous Coordination Polymer: Detailed Exploration of Free Energy Profiles

Langmuir ◽  
2012 ◽  
Vol 28 (11) ◽  
pp. 5093-5100 ◽  
Author(s):  
Hayato Sugiyama ◽  
Satoshi Watanabe ◽  
Hideki Tanaka ◽  
Minoru T. Miyahara
Keyword(s):  
Free Energy ◽  
Coordination Polymer ◽  
Structural Transition ◽  
Energy Profiles ◽  
Porous Coordination Polymer ◽  
Free Energy Profiles

scholarly journals Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

2017 ◽  
Vol 147 (15) ◽  
pp. 152718 ◽  
Author(s):  
Clark Templeton ◽  
Szu-Hua Chen ◽  
Arman Fathizadeh ◽  
Ron Elber
Keyword(s):  
Free Energy ◽  
Minimum Energy ◽  
Minimum Free Energy ◽  
Rock Climbing ◽  
Global Algorithm ◽  
Energy Pathways

A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases

2012 ◽  
Vol 8 (5) ◽  
pp. 1795-1801 ◽  
Author(s):  
Kirill Zinovjev ◽  
Sergi Martí ◽  
Iñaki Tuñón
Keyword(s):  
Free Energy ◽  
Condensed Phases ◽  
Energy Profiles ◽  
Collective Coordinate ◽  
Free Energy Profiles
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