Polar Versus Non-polar Local Ordering at Mobile Sites in Proteins: Slowly Relaxing Local Structure Analysis of 15N Relaxation in the Third Immunoglobulin-Binding Domain of Streptococcal Protein G

Oren Tchaicheeyan, Eva Meirovitch

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Abstract

We developed recently the slowly relaxing local structure (SRLS) approach for studying restricted motions in proteins by NMR. The spatial restrictions have been described by potentials comprising the traditional L = 2, K = 0, 2 spherical harmonics. However, the latter are associated with non-polar ordering whereas protein-anchored probes experience polar ordering, described by odd-L spherical harmonics. Here we extend the SRLS potential to include the L = 1, K = 0, 1 spherical harmonics and analyze 15N-1H relaxation from the third immunoglobulin-binding domain of streptococcal protein G (GB3) with the polar L = 1 potential (coefficients c01 and c11) or the non-polar L = 2 potential (coefficients c02 and c22). Strong potentials, with ∼c01∼ ∼ 60 for L = 1 and ∼c02∼ ∼ 20 for L = 2 (in units of kBT), are detected. In the α-helix of GB3 the coefficients of the rhombic terms are c11 ∼ c22 ∼ 0; in the preceding (following) chain segment they are ∼c11∼ ∼ 6 for L = 1 and ∼c22∼ ∼ 14 for L = 2 (∼c11∼ ∼ 3 for L = 1 and ∼c22∼ ∼ 7 for L = 2). The local diffusion rate, D2, lies in the 5 × 109-1 × 1011 s-1 range; it is generally larger for L = 1. The main ordering axis deviates moderately from the N-H bond. Corresponding L = 1 and L = 2 potentials and probability density functions are illustrated for residues A26 of the α-helix, Y3 of the β1-strand, and L12 of the β12 loop; they differ considerably. Polar/orientational ordering is shown to be associated with GB3 binding to its cognate Fab fragment. The polarity of the local ordering is clearly an important factor.

Original languageEnglish
Pages (from-to)386-395
Number of pages10
JournalJournal of Physical Chemistry B
Volume120
Issue number3
DOIs
StatePublished - 28 Jan 2016

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© 2016 American Chemical Society.

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