Conformational landscapes

JM Troyer, EE Cohen. Protein conformational landscapes Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23 97-110, 1995. 

Subramanian, G., Ferguson, D.M. Conformational landscape of selectivity m-opioid agonists in gas phase and in aqueous solution The Fentanyl Series, Drug Design and Discovery 2000, 17, 53-... 

Akiyama, S., Takahashi, S., Kimura, T., Ishimori, K., Morishima, I., Nishikawa, Y., and Fujisawa, T. (2002). Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle X-ray scattering. Proc. Natl. Acad. Sci. USA 99, 1329-1334. 

Matrix Isolation VCD Spectroscopy for Probing Conformational Landscapes... 

Conformational Landscapes of Highly Flexible Chiral Molecules and Chiral Molecular Complexes... 

Fig. 4.19. Conformational Landscapes in Horse radish peroxidase from [39]...

From Here to There Conformational Landscapes and Solubility Probes. 174... 

After asserting the nanostructured nature of ionic liquids, the structural analysis of these fluids continued in two different directions. The first was to check how the built-in flexibility of the isolated ions of the model affect (or are affected by) the nanostructured nature of the ionic liquid, and how that can influence properties like viscosity, electrical conductivity, or diffusion coefficients. It must be stressed that the charges in the CLAP model are fixed to the atomic positions, which means that the most obvious way to probe the relation between the structure of the ionic liquid as a whole in terms of the structure of its individual ions is to investigate the flexibility (conformational landscape) of the latter. The second alternative direction was to probe the structure of ionic liquids not by regarding into the structure of the component ions but by instead using an external probe (for example, a neutral molecular species), solubility experiments with selected solute molecules being the most obvious experimental approach. 

The conformational landscapes of two ILs build from [NTf2] and from /V-propyl-and /V-butyI -A -methylpyrroIidinium were investigated from Raman spectroscopy, MD, and ab initio techniques [135], For [NTf2] the three-dimensional PES and the corresponding MD simulations confirmed the existence of two stable isomers (see also [37, 36]). The anion was calculated to be flexible, albeit hindered, but capable of interconversion between conformers in the liquid state, a result also confirmed by the Raman data. In the case of the ALV-dialkylpyrrolidinium cations, the PES showed a much more limited conformational behavior of the pyrrolidinium ring [135],... 

Huang Z, Yu W, Lin Z (2006) Exploration of the full conformational landscapes of gaseous aromatic amino acid phenylalanine An ab initio study. Journal of Molecular Stiucture THEOCHEM 758 195-202... 

Snoek L, Robertson E, Kroemer R, Simons J (2000) Conformational landscapes in amino acids infrared and ultraviolet ion-dip spectroscopy of phenylalanine in the gas phase. Chem. Phys. Lett. 321 49... 

Butler CF, Peet C, Mason AE, Voice MW, Leys D, Munro AW (2013) Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias. J Biol Chem 288 25387-25399... 

Dihedral PCA on the five endocyclic angles of the dihydroxylated p-o-xylosyl derivatives an orientation table to fully explore the conformational landscape... 

Snoek LC, Kroemer RT, Hockridge MR, Simons JP (2001) Conformational landscapes of aromatic amino acids in the gas phase infrared and ultraviolet ion dip spectroscopy of tryptophan. Phys Chem Chem Phys 3 1819... 

Gloaguen E, Brenner V, Alauddin M, Tardivel B, Mons M, Zehnacker-Rentien A, Declerck V, Aitken DJ (2014) Direct spectroscopic evidence of hyperconjugation unveils the conformational landscape of hydrazides. Angew Ch Int Ed. doi 10.1002/anie.201407801... 

The spectroscopic investigation of CBH conformational landscapes in the gas phase was pioneered by the group of John P. Simons in Oxford in the early 2000s. This work began by solving the structural preferences of the most naturally... 

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