Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

150

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

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.