Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

113-POS Board 33 Cyanylated Cysteine as an Infrared Reporter of Calmodulin-Ligand Interactions: Experimental Measurements, Molecular Dynamics Simulations and Multi-level Calculations of IR Lineshape

Rosalind J. Xu , Casey H. Londergan. Haverford College, Haverford, PA, USA.

The structure and dynamic conformational ensembles of calmodulin (CaM), with and without Ca 2+ and a 26-residue synthetic peptide (M13) comprising the binding domain of skeletal muscle myosin light chain kinase, were studied by inserting an artificial SCN probe group at different sites along both the CaM and M13 chains. The IR CN stretching absorption frequency of the probe group displays solvatochromic shifts due to different polarity and hydrogen bonding environments. Comparisons between CN stretching frequencies of each mutant in the different binding states of the CaM/M13 complex showed varying changes in degree of probe solvent exposure upon binding. To gain a more quantitative understanding of IR frequencies and lineshapes at each mutated site, all-atom molecular dynamics (MD) simulations including the artificial probe group were performed using a modified AMBER99SB forcefield, and solvent- accessible surface areas of SCN probe at each mutated site were calculated. Two methods were attempted for IR lineshape simulation: a QM/MM method adapted from Layfield and Hammes- Schiffer and a solvatochromic effective fragment potential (SolEFP) method adapted from Blasiak and Cho. Despite challenges in a mature and direct theory-experiment connection, we have nevertheless determined some new fine-grained details about the structural ensembles of CaM under different conditions and we also have constructed a dual experimental/simulation methodology that could be applied to various protein systems.

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