scholarly journals Insights into Photosynthetic Energy Transfer Gained from Free-Energy Structure: Coherent Transport, Incoherent Hopping, and Vibrational Assistance Revisited

2021 ◽  
Author(s):  
Akihito Ishizaki ◽  
Graham R. Fleming
Keyword(s):  
Free Energy ◽  
Energy Transfer ◽  
Energy Structure ◽  
Coherent Transport

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

2019 ◽  
Author(s):  
Duy Phuoc Tran ◽  
Akio Kitao
Keyword(s):  
Free Energy ◽  
Transcriptional Activation ◽  
Binding Free Energy ◽  
Energy Structure ◽  
Induced Fit ◽  
Hydrogen Bond Formation ◽  
Conformational Selection ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Dissociation Mechanisms

<p>We investigate association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor repressor protein p53 (TAD-p53) with murine double-minute clone 2 protein (MDM2). Using the combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard MD, and Markov state model, we are successful in obtaining the lowest free energy structure of MDM2/TAD-p53 complex as the structure very close to that in crystal without prior knowledge. This method also reproduces the experimentally measured standard binding free energy, and association and dissociation rate constants solely with the accumulated MD simulation cost of 11.675 μs, in spite of the fact that actual dissociation occurs in the order of a second. Although there exist a few complex intermediates with similar free energies, TAD-p53 first binds MDM2 as the second lowest free energy intermediate dominantly (> 90% in flux), taking a form similar to one of the intermediate structures in its monomeric state. The mechanism of this step has a feature of conformational selection. In the second step, dehydration of the interface, formation of π-π stackings of the side-chains, and main-chain relaxation/hydrogen bond formation to complete α-helix take place, showing features of induced fit. In addition, dehydration (dewetting) is a key process for the final relaxation around the complex interface. These results demonstrate a more fine-grained view of the IDR association/dissociation beyond classical views of protein conformational change upon binding.</p>

TAP free energy structure of SK spin glasses

1985 ◽  
Vol 18 (18) ◽  
pp. L529-L535 ◽  
Author(s):  
K Nemoto ◽  
H Takayama
Keyword(s):  
Free Energy ◽  
Spin Glasses ◽  
Energy Structure

scholarly journals Momentum flux parasitic to free-energy transfer

2017 ◽  
Vol 57 (8) ◽  
pp. 086036 ◽  
Author(s):  
T. Stoltzfus-Dueck ◽  
B. Scott
Keyword(s):  
Free Energy ◽  
Energy Transfer ◽  
Momentum Flux

Photoinduced double [2 + 2] cycloaddition relay of yne–allenones for highly diastereoselective synthesis of hexacyclic 1-naphthols

2020 ◽  
Vol 7 (19) ◽  
pp. 2975-2980 ◽  
Author(s):  
Shan-Shan Zhu ◽  
Jiang-Nan Zhou ◽  
Quan-Long Wu ◽  
Wen-Juan Hao ◽  
Shu-Jiang Tu ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Transfer ◽  
Diastereoselective Synthesis ◽  
First Time

A new photoinduced photocatalyst-free energy-transfer strategy for double [2 + 2] cycloaddition relay of yne–allenones is reported for the first time and used to produce a series of hitherto unreported hexacyclic 1-naphthols.

scholarly journals LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i258-i267 ◽  
Author(s):  
He Zhang ◽  
Liang Zhang ◽  
David H Mathews ◽  
Liang Huang
Keyword(s):  
Free Energy ◽  
Partition Function ◽  
Structure Prediction ◽  
Linear Time ◽  
Minimum Free Energy ◽  
Supplementary Information ◽  
Sequence Length ◽  
Energy Structure ◽  
Base Pairing ◽  
Long Distance

Abstract Motivation RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more severe than cubic-time free energy minimization due to a substantially larger constant factor in runtime. Results Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna RNAfold and CONTRAfold (e.g. 2.5 days versus 1.3 min on a sequence with length 32 753 nt). More interestingly, the resulting base-pairing probabilities are even better correlated with the ground-truth structures. LinearPartition also leads to a small accuracy improvement when used for downstream structure prediction on families with the longest length sequences (16S and 23S rRNAs), as well as a substantial improvement on long-distance base pairs (500+ nt apart). Availability and implementation Code: http://github.com/LinearFold/LinearPartition; Server: http://linearfold.org/partition. Supplementary information Supplementary data are available at Bioinformatics online.

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