Investigating Electrostatics and Dynamics in Confinement and Constructs Using Two-Dimensional Infrared Spectroscopy and Molecular Simulations.

macromolecular dynamics;ultrafast multidimensional spectroscopy;electrostatics;Chemistry;Science;Chemistry

White, Aaron MichaelGeva, Eitan ;

University of Michigan

关键词: macromolecular dynamics;    ultrafast multidimensional spectroscopy;    electrostatics;    Chemistry;    Science;    Chemistry;   

Others  :  https://deepblue.lib.umich.edu/bitstream/handle/2027.42/120712/amwhi_1.pdf?sequence=1&isAllowed=y

瑞士|英语

来源: The Illinois Digital Environment for Access to Learning and Scholarship

【 摘 要 】

Understanding the ultrafast dynamics of enzymes is required to fully explain what makes them such efficient catalysts. Two-dimensional infrared (2D-IR) spectroscopy along with molecular modeling helps provide a more complete description of the environment of enzyme active sites and other related systems.A carbonyl-labeled copper site in a de novo peptide exhibits vibrationally driven nonequilibrium dynamics when characterized using 2D-IR spectroscopy. The source of the dynamics is found to be the coupling of the CO stretching mode to the CuCO bending mode, enhanced by distortions to the histidine side chains binding the copper. QM/MM calculations show the source of the distortions to be primarily from electrostatic interactions with the peptide.Using similar calculations, but with a refined sampling of starting structures, other de novo peptides are modeled to identify a candidate that will show different nonequilibrium dynamics from the original metalloenzyme. The selected enzyme is more catalytically active, and calculations predict a smaller coupling between the CO stretching and CuCO bending modes. This prediction is confirmed using 2D-IR, where the nonequilibrium dynamics have a smaller amplitude, but occur on the same time scale.Several thiocyanate salts in the Hofmeister series are studied in neat D2O and with alpha-cyclodextrin (a-CD). In neat D2O, 2D-IR shows slightly faster spectral diffusion for kosmotropes and slower spectral diffusion for chaotropes. When a-CD is introduced to the system, an additional slowly decaying component of the FFCF is found. The presence of the slower dynamics indicates the nitrogen in thiocyanate is not solvent exposed, but embedded in the interior of the a-CD.A combination of 2D-IR and molecular modeling was also needed to characterize the structure of a labeled crown either with a nearby sodium thiocyanate contact ion pair. The spectral diffusion of the metal carbonyl label shows dynamics occurring on a slower time scale than the vibrational lifetime of the probe. DFT calculations show that two different conformations of the thiocyanate ion around the crown ether have similar energies, but produce different CO frequencies. The time to sample these states is longer than the vibrational lifetime of the metal carbonyl.