Characterization of low-energy excited states in the native state ensemble of non-myristoylated and myristoylated neuronal calcium sensor-1

• Published in: Biochimica et biophysica acta 2011-02, Vol.1814 (2), p.334-344
• Main Authors: Chandra, Kousik, Sharma, Yogendra, Chary, K.V.R.
• Format: Article
• Language: English
• Subjects: Alternate states; Amino Acid Sequence; Animals; Calcium sensor proteins; EF Hand Motifs; In Vitro Techniques; Low-energy excited states; Models, Molecular; Molecular Sequence Data; Myristic Acids - chemistry; Myristic Acids - metabolism; Native state; Neuronal Calcium-Sensor Proteins - chemistry; Neuronal Calcium-Sensor Proteins - genetics; Neuronal Calcium-Sensor Proteins - metabolism; Neuropeptides - chemistry; Neuropeptides - genetics; Neuropeptides - metabolism; Nonlinear Dynamics; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protons; Rats; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Sequence Homology, Amino Acid; Temperature; Thermodynamics
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2010.10.007

Information on the low-energy excited states of a given protein is important as this controls the structural adaptability and various biological functions of proteins such as co-operativity, response towards various external perturbations. In this article, we characterized individual residues in both non-myristoylated (non-myr) and myristoylated (myr) neuronal calcium sensor-1 (NCS-1) that access alternate states by measuring nonlinear temperature dependence of the backbone amide-proton ( 1H N) chemical shifts. We found that ~ 20% of the residues in the protein access alternative conformations in non-myr case, which increases to ~ 28% for myr NCS-1. These residues are spread over the entire polypeptide stretch and include the edges of α-helices and β-strands, flexible loop regions, and the Ca 2+-binding loops. Besides, residues responsible for the absence of Ca 2+–myristoyl switch are also found accessing alternative states. The C-terminal domain is more populated with these residues compared to its N-terminal counterpart. Individual EF-hands in NCS-1 show significantly different number of alternate states. This observation prompts us to conclude that this may lead to differences in their individual conformational flexibility and has implications on the functionality. Theoretical simulations reveal that these low-energy excited states are within an energy band of 2–4 kcal/mol with respect to the native state. ► Twenty percent residues of non-myristoylated neuronal calcium sensor-1 access alternate states. ► Myristoylation increases population of residues accessing alternate states in NCS-1. ► The conformation fluctuations are non-uniformly spread over the entire sequence. ► C-terminal domain has more conformational fluctuations that N-terminal counterpart. ► Alternate states are within an energy band of 2–4 kcal/mol with native state.