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Molecular dynamics simulation of poly(spiropyran‐ L ‐glutamate): Influence of chromophore isomerization
Author(s) -
Pachter Ruth,
Cooper Thomas M.,
Natarajan L. V.,
Obermeier Keith A.,
Crane Robert L.,
Adams W. Wade
Publication year - 1992
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360320902
Subject(s) - merocyanine , spiropyran , chromophore , chemistry , isomerization , photochromism , molecular dynamics , photochemistry , hydrogen bond , helix (gastropod) , stereochemistry , molecule , photoisomerization , zwitterion , computational chemistry , organic chemistry , ecology , snail , biology , catalysis
Abstract A study of the influence of the spiropyran to merocyanine ring opening on a model of poly(spiropyran‐ L ‐glutamate) as implied by the experimental data (T. M. Cooper, K. A. Obermeier, L. V. Natarajan, and R. L. Crane (1992) Photochemistry and Photobiology , 55, 1–7) is presented. The individual chromophore is studied by the AM1 semiempirical approach, while molecular mechanics and dynamics calculations are employed in the analysis of the poly(spiropyran‐ L ‐glutamate) model. It is shown that the α‐helical secondary structure is less conserved in the polypeptide substituted with the merocyanine form of the chromophore. In particular, larger side‐chain flexibility, increased backbone hydrogen‐bond lengths, as well as a larger helix bending are calculated. Furthermore, a random conformational minimization calculation finds the intrinsic behavior of the spiropyran molecular system as being more of a helix “maker” than its merocyanine analogue. The interactions of the chromophore substituent with other side chains prove, in part, that an early event in the decay of the α‐helical structure is the formation of hydrogen bonds between the carboxylic acid groups and the merocyanine oxygens. The results lend support to the experimental observation that the merocyanine group destabilizes the α‐helical framework of the polypeptide, thus possibly allowing the entry of solvent molecules into the α‐helical core, while spiropyran in its closed form shields it from the solvent. © 1992 John Wiley & Sons, Inc.