scholarly journals Calculating the Binding Free Energy Difference between Conformational Changes of AT-Rich DNA Sequences

2020 ◽  
Vol 118 (3) ◽  
pp. 218a
Author(s):  
Md Lokman Hossen ◽  
Prem P. Chapagain ◽  
Bernard Gerstman
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Dna Sequences ◽  
Binding Free Energy ◽  
Energy Difference ◽  
Free Energy Difference

scholarly journals Integrin extension enables ultrasensitive regulation by cytoskeletal force

2017 ◽  
Vol 114 (18) ◽  
pp. 4685-4690 ◽  
Author(s):  
Jing Li ◽  
Timothy A. Springer
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Large Scale ◽  
Tensile Force ◽  
Energy Difference ◽  
Length Scale ◽  
Ligand Complex ◽  
Free Energy Difference ◽  
Cytoskeletal Dynamics ◽  
Integrin Ligand

Integrins undergo large-scale conformational changes upon activation. Signaling events driving integrin activation have previously been discussed conceptually, but not quantitatively. Here, recent measurements of the intrinsic ligand-binding affinity and free energy of each integrin conformational state on the cell surface, together with the length scales of conformational change, are used to quantitatively compare models of activation. We examine whether binding of cytoskeletal adaptors to integrin cytoplasmic domains is sufficient for activation or whether exertion of tensile force by the actin cytoskeleton across the integrin–ligand complex is also required. We find that only the combination of adaptor binding and cytoskeletal force provides ultrasensitive regulation. Moreover, switch-like activation by force depends on the large, >130 Å length-scale change in integrin extension, which is well tailored to match the free-energy difference between the inactive (bent-closed) and active (extended-open) conformations. The length scale and energy cost in integrin extension enable activation by force in the low pN range and appear to be the key specializations that enable cell adhesion through integrins to be coordinated with cytoskeletal dynamics.

Conformational analysis of 1,4-disubstituted cyclohexanes. III. trans-1,4-Di(trifluoroacetoxy)cyclohexane

1969 ◽  
Vol 47 (3) ◽  
pp. 429-431 ◽  
Author(s):  
Gordon Wood ◽  
E. P. Woo ◽  
M. H. Miskow
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Low Temperature ◽  
Conformational Analysis ◽  
Integration Method ◽  
Standard Free Energy ◽  
Energy Difference ◽  
Free Energy Difference ◽  
Conformational Free Energy

By the low temperature nuclear magnetic resonance integration method the standard free energy difference between the diequatorial and the diaxial forms of 1-H,4-H-trans-1,4-di(trifluoroacetoxy)-cyclohexane-d8 was found to be 77 ± 5 cal/mole. The conformational free energy (−ΔG0) of the trifluoroacetoxy group in the monosubstituted cyclohexane was 485 ± 4 cal/mole at the same temperature. The non-additivity of the −ΔG0 values is discussed in terms of transannular electrostatic interaction.

A comprehensive computational examination of transannular Diels–Alder reactions of unsubstituted C14 trienes — Barriers, template effects, and the Curtin–Hammett principle

2001 ◽  
Vol 79 (8) ◽  
pp. 1284-1292 ◽  
Author(s):  
Saul Wolfe ◽  
Anthony V Buckley ◽  
Noham Weinberg
Keyword(s):  
Free Energy ◽  
Energy Difference ◽  
Diels Alder ◽  
Molecular Orbital Calculations ◽  
Free Energy Difference ◽  
Molecular Mechanics Calculations ◽  
Geometrical Isomers ◽  
Free Energy Of Activation ◽  
Transition Structures ◽  
Cyclic Compounds

A combination of MM3-level molecular mechanics calculations and PM3-level semiempirical molecular orbital calculations has been employed, in conjunction with an algorithm for the comprehensive conformational analysis of cyclic compounds, to obtain 1202 unique 1,3,9-cyclotetradecatriene conformations, distributed over the six possible geometrical isomers, and 70 unique transannular Diels–Alder transition structures leading to the six possible stereoisomeric tricyclic olefins. A kinetic analysis that takes into account all minima of a given geometrical isomer and all transition structures leading to the same tricyclic product leads to a free energy of activation that is almost the same as the free energy difference between the lowest minimum and the lowest transition structure (the Curtin–Hammett principle). A substantial template effect, mainly entropic in origin, is found when the transannular reactions are compared to the Diels–Alder reactions of the cognate 2,4-hexatrienes with the 2-butenes. Although the cyclization of the trans-cis-trans triene favours the cis-anti-cis over the trans-anti-trans product by more than 20 kcal mol–1, the situation is reversed in the acyclic reaction. A cyclic triene that can cyclize directly to a trans-anti-trans tricycle can therefore be proposed.Key words: molecular models, Deslongchamps, Takahashi, trans-anti-trans tricycle, MM3, PM3, transition states.

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