Abstract:
:Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Troitzsch RZ,Tulip PR,Crain J,Martyna GJdoi
10.1529/biophysj.108.134916subject
Has Abstractpub_date
2008-12-01 00:00:00pages
5014-20issue
11eissn
0006-3495issn
1542-0086pii
S0006-3495(08)78928-8journal_volume
95pub_type
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